Starting phenix.real_space_refine on Sat Oct 12 21:42:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pql_17822/10_2024/8pql_17822.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pql_17822/10_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_17822/10_2024/8pql_17822.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pql_17822/10_2024/8pql_17822.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pql_17822/10_2024/8pql_17822.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pql_17822/10_2024/8pql_17822.cif" } 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. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 8.57, per 1000 atoms: 0.63 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 - 3.00 Amino acid : True - 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: 4.00 Conformation dependent library (CDL) restraints added in 2.2 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... Secondary structure from input PDB file: 78 helices and 25 sheets defined 49.8% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'C' and resid 7 through 21 Processing helix chain 'C' and resid 119 through 133 Processing helix chain 'C' and resid 141 through 154 Processing helix chain 'C' and resid 159 through 179 Processing helix chain 'C' and resid 186 through 191 removed outlier: 6.147A pdb=" N TYR C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N CYS C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 186 through 191' Processing helix chain 'E' and resid 22 through 34 Processing helix chain 'E' and resid 37 through 41 Processing helix chain 'E' and resid 56 through 59 No H-bonds generated for 'chain 'E' and resid 56 through 59' Processing helix chain 'K' and resid 55 through 58 No H-bonds generated for 'chain 'K' and resid 55 through 58' Processing helix chain 'K' and resid 81 through 89 Processing helix chain 'U' and resid 22 through 34 Processing helix chain 'U' and resid 37 through 41 Processing helix chain 'U' and resid 56 through 59 No H-bonds generated for 'chain 'U' and resid 56 through 59' Processing helix chain 'A' and resid 12 through 19 removed outlier: 3.769A pdb=" N THR A 19 " --> pdb=" O ASN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 25 Processing helix chain 'A' and resid 33 through 46 removed outlier: 3.662A pdb=" N ASP A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE A 39 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N SER A 40 " --> pdb=" O ASN A 36 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASP A 41 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE A 42 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N TYR A 43 " --> pdb=" O PHE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 79 Processing helix chain 'A' and resid 86 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 111 Processing helix chain 'A' and resid 139 through 152 Processing helix chain 'A' and resid 156 through 170 removed outlier: 3.739A pdb=" N ASN A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ASP A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) 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 200 through 228 Proline residue: A 210 - end of helix Processing helix chain 'A' and resid 235 through 251 removed outlier: 3.793A pdb=" N ILE A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 274 removed outlier: 4.351A pdb=" N HIS A 274 " --> pdb=" O MET A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'A' and resid 291 through 303 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) removed outlier: 4.180A pdb=" N ALA A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 328 Processing helix chain 'A' and resid 337 through 358 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 387 through 398 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 429 through 444 Processing helix chain 'A' and resid 453 through 465 Processing helix chain 'A' and resid 471 through 496 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 589 Processing helix chain 'A' and resid 596 through 603 removed outlier: 4.198A pdb=" N THR A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 619 Processing helix chain 'H' and resid 6 through 11 removed outlier: 3.727A pdb=" N ALA H 10 " --> pdb=" O ALA H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 20 No H-bonds generated for 'chain 'H' and resid 17 through 20' 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 91 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 137 Processing helix chain 'H' and resid 152 through 159 removed outlier: 3.648A pdb=" N LYS H 159 " --> pdb=" O ILE H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 171 removed outlier: 5.626A pdb=" N GLN H 166 " --> pdb=" O LYS H 162 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR H 167 " --> pdb=" O GLU H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 191 Processing helix chain 'H' and resid 195 through 204 Processing helix chain 'H' and resid 217 through 224 Processing helix chain 'H' and resid 228 through 235 Processing helix chain 'H' and resid 241 through 257 Processing helix chain 'H' and resid 262 through 278 Processing helix chain 'H' and resid 305 through 308 No H-bonds generated for 'chain 'H' and resid 305 through 308' Processing helix chain 'H' and resid 315 through 329 Processing helix chain 'H' and resid 335 through 351 Processing helix chain 'H' and resid 355 through 368 removed outlier: 3.952A pdb=" N ASN H 359 " --> pdb=" O LYS H 355 " (cutoff:3.500A) Processing helix chain 'H' and resid 377 through 393 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 427 Processing helix chain 'H' and resid 435 through 454 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 475 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 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 580 through 583 No H-bonds generated for 'chain 'H' and resid 580 through 583' Processing helix chain 'H' and resid 586 through 597 Processing helix chain 'H' and resid 607 through 616 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 83 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 97 through 109 removed outlier: 5.505A pdb=" N LEU D 101 " --> pdb=" O PRO D 97 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLU D 102 " --> pdb=" O GLU D 98 " (cutoff:3.500A) 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 helix chain 'G' and resid 57 through 60 No H-bonds generated for 'chain 'G' and resid 57 through 60' Processing sheet with id=1, first strand: chain 'G' and resid 42 through 45 No H-bonds generated for sheet with id=1 Processing sheet with id=2, first strand: chain 'G' and resid 73 through 79 No H-bonds generated for sheet with id=2 Processing sheet with id=3, first strand: chain 'G' and resid 2 through 8 No H-bonds generated for sheet with id=3 Processing sheet with id=4, first strand: chain 'G' and resid 12 through 19 No H-bonds generated for sheet with id=4 Processing sheet with id=6, first strand: chain 'D' and resid 18 through 23 No H-bonds generated for sheet with id=6 Processing sheet with id=7, first strand: chain 'D' and resid 59 through 61 No H-bonds generated for sheet with id=7 Processing sheet with id=8, first strand: chain 'C' and resid 28 through 32 No H-bonds generated for sheet with id=8 Processing sheet with id=9, first strand: chain 'C' and resid 40 through 46 No H-bonds generated for sheet with id=9 Processing sheet with id=10, first strand: chain 'C' and resid 57 through 63 No H-bonds generated for sheet with id=10 Processing sheet with id=11, first strand: chain 'C' and resid 74 through 77 No H-bonds generated for sheet with id=11 Processing sheet with id=12, first strand: chain 'E' and resid 12 through 16 No H-bonds generated for sheet with id=12 Processing sheet with id=13, first strand: chain 'E' and resid 2 through 6 No H-bonds generated for sheet with id=13 Processing sheet with id=14, first strand: chain 'E' and resid 66 through 70 No H-bonds generated for sheet with id=14 Processing sheet with id=15, first strand: chain 'E' and resid 42 through 44 No H-bonds generated for sheet with id=15 Processing sheet with id=16, first strand: chain 'U' and resid 12 through 16 No H-bonds generated for sheet with id=16 Processing sheet with id=17, first strand: chain 'U' and resid 2 through 6 No H-bonds generated for sheet with id=17 Processing sheet with id=18, first strand: chain 'U' and resid 66 through 70 No H-bonds generated for sheet with id=18 Processing sheet with id=19, first strand: chain 'U' and resid 42 through 44 No H-bonds generated for sheet with id=19 Processing sheet with id=20, first strand: chain 'A' and resid 507 through 512 No H-bonds generated for sheet with id=20 Processing sheet with id=21, first strand: chain 'K' and resid 27 through 34 No H-bonds generated for sheet with id=21 Processing sheet with id=22, first strand: chain 'A' and resid 552 through 556 No H-bonds generated for sheet with id=22 Processing sheet with id=A, first strand: chain 'A' and resid 561 through 566 Processing sheet with id=B, first strand: chain 'A' and resid 593 through 594 Processing sheet with id=23, first strand: chain 'K' and resid 70 through 72 No H-bonds generated for sheet with id=23 Processing sheet with id=24, first strand: chain 'K' and resid 78 through 80 No H-bonds generated for sheet with id=24 549 hydrogen bonds defined for protein. 1644 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: 3.51 Time building geometry restraints manager: 4.17 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: 0.00 - 1.77: 18329 1.77 - 3.54: 384 3.54 - 5.31: 92 5.31 - 7.08: 26 7.08 - 8.85: 16 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: 92 2.57 - 3.15: 10776 3.15 - 3.73: 20595 3.73 - 4.32: 25206 4.32 - 4.90: 42433 Nonbonded interactions: 99102 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 3.040 nonbonded pdb=" O TYR C 57 " pdb=" OG1 THR C 172 " model vdw 2.232 3.040 nonbonded pdb=" O GLN E 49 " pdb=" OH TYR E 59 " model vdw 2.263 3.040 nonbonded pdb=" OE2 GLU A 208 " pdb=" OG SER A 258 " model vdw 2.267 3.040 ... (remaining 99097 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 34.540 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.920 ------------------------------------------------------------------------------- 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= 0.230 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 : 1.498 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: 0.2907 time to fit residues: 142.3251 Evaluate side-chains 341 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 337 time to evaluate : 1.546 ------------------------------------------------------------------------------- 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: 6.9990 chunk 134 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7251 moved from start: 0.0667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13828 Z= 0.239 Angle : 0.584 8.268 18847 Z= 0.304 Chirality : 0.041 0.161 2223 Planarity : 0.005 0.074 2418 Dihedral : 6.243 103.978 1959 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 5.82 % Allowed : 29.04 % Favored : 65.13 % 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: -0.61 (0.20), residues: 1807 helix: 1.04 (0.18), residues: 922 sheet: -1.63 (0.59), residues: 85 loop : -2.07 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 33 HIS 0.005 0.001 HIS H 616 PHE 0.015 0.001 PHE H 612 TYR 0.020 0.001 TYR D 79 ARG 0.008 0.000 ARG A 251 *********************** 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 423 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 347 time to evaluate : 1.600 Fit side-chains REVERT: H 178 LYS cc_start: 0.8285 (mmtp) cc_final: 0.8045 (mmtm) REVERT: H 244 ARG cc_start: 0.7126 (mtm-85) cc_final: 0.6824 (mtm-85) REVERT: H 319 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7553 (mtt-85) REVERT: H 428 GLN cc_start: 0.6568 (tm-30) cc_final: 0.6280 (tm-30) REVERT: U 27 LYS cc_start: 0.8729 (mtpt) cc_final: 0.8370 (tttt) REVERT: A 37 ASP cc_start: 0.7439 (t0) cc_final: 0.7141 (t0) REVERT: A 297 MET cc_start: 0.7942 (ttm) cc_final: 0.7666 (ttm) REVERT: A 393 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7702 (mptt) REVERT: A 396 ASP cc_start: 0.7410 (p0) cc_final: 0.7185 (p0) REVERT: A 441 LYS cc_start: 0.8384 (ttmt) cc_final: 0.8045 (ttmm) REVERT: D 82 ARG cc_start: 0.6983 (tpt90) cc_final: 0.6750 (tpt90) outliers start: 76 outliers final: 41 residues processed: 391 average time/residue: 0.2705 time to fit residues: 151.6965 Evaluate side-chains 381 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 338 time to evaluate : 1.572 ------------------------------------------------------------------------------- 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 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 E residue 9 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 407 THR Chi-restraints excluded: chain H residue 516 GLU 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 56 LEU 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 215 THR Chi-restraints excluded: chain A residue 265 GLU 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 416 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain G residue 31 VAL 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: 6.9990 chunk 50 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 144 optimal weight: 0.4980 chunk 160 optimal weight: 9.9990 chunk 55 optimal weight: 0.0170 chunk 129 optimal weight: 1.9990 overall best weight: 1.0422 ------------------------------------------------------------------------------- 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: 0.7280 moved from start: 0.0949 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= 0.280 Angle : 0.603 8.914 18847 Z= 0.315 Chirality : 0.043 0.197 2223 Planarity : 0.006 0.073 2418 Dihedral : 5.230 72.451 1954 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 6.44 % Allowed : 28.05 % Favored : 65.52 % 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: -0.70 (0.20), residues: 1807 helix: 0.99 (0.17), residues: 919 sheet: -1.87 (0.57), residues: 92 loop : -2.12 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 33 HIS 0.005 0.001 HIS D 68 PHE 0.016 0.001 PHE H 612 TYR 0.024 0.001 TYR D 79 ARG 0.010 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 431 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 347 time to evaluate : 1.564 Fit side-chains revert: symmetry clash REVERT: C 18 LYS cc_start: 0.8569 (mtmm) cc_final: 0.8365 (mtmm) REVERT: C 119 ASN cc_start: 0.7640 (p0) cc_final: 0.7396 (p0) REVERT: H 178 LYS cc_start: 0.8312 (mmtp) cc_final: 0.8022 (mmtm) REVERT: H 319 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7732 (mtt-85) REVERT: K 24 VAL cc_start: 0.7839 (p) cc_final: 0.7627 (m) REVERT: A 37 ASP cc_start: 0.7524 (t0) cc_final: 0.7183 (t0) REVERT: A 251 ARG cc_start: 0.7912 (ttm-80) cc_final: 0.7365 (ttm-80) REVERT: A 297 MET cc_start: 0.7990 (ttm) cc_final: 0.7714 (ttm) REVERT: A 390 LEU cc_start: 0.8243 (mt) cc_final: 0.7990 (mp) REVERT: A 393 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7782 (mptt) REVERT: A 441 LYS cc_start: 0.8425 (ttmt) cc_final: 0.8134 (ttmm) REVERT: A 457 MET cc_start: 0.7592 (tpp) cc_final: 0.7335 (tpp) REVERT: A 517 TRP cc_start: 0.8352 (m100) cc_final: 0.8081 (m100) REVERT: A 598 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7437 (pm20) outliers start: 84 outliers final: 61 residues processed: 395 average time/residue: 0.2671 time to fit residues: 151.0110 Evaluate side-chains 406 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 342 time to evaluate : 1.542 ------------------------------------------------------------------------------- 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 52 LEU 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 141 ASN Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain E residue 9 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 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 291 THR Chi-restraints excluded: chain H residue 319 ARG Chi-restraints excluded: chain H residue 334 HIS 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 516 GLU Chi-restraints excluded: chain H residue 555 ASP 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 17 VAL Chi-restraints excluded: chain U residue 43 LEU Chi-restraints excluded: chain U residue 56 LEU 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 248 ILE 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 357 VAL Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 395 CYS 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 577 VAL 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 78 THR Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 74 THR 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: 0.4980 chunk 121 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 17 optimal weight: 0.0970 chunk 77 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 162 optimal weight: 0.8980 chunk 172 optimal weight: 0.8980 chunk 154 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 143 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: A 362 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13828 Z= 0.200 Angle : 0.578 8.796 18847 Z= 0.298 Chirality : 0.041 0.303 2223 Planarity : 0.005 0.071 2418 Dihedral : 5.004 64.092 1954 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 5.90 % Allowed : 30.04 % Favored : 64.06 % 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: -0.57 (0.20), residues: 1807 helix: 1.10 (0.18), residues: 920 sheet: -1.87 (0.57), residues: 92 loop : -2.05 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 33 HIS 0.004 0.001 HIS H 616 PHE 0.012 0.001 PHE H 612 TYR 0.017 0.001 TYR C 57 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 425 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 348 time to evaluate : 1.537 Fit side-chains REVERT: C 18 LYS cc_start: 0.8501 (mtmm) cc_final: 0.8291 (mtmm) REVERT: C 119 ASN cc_start: 0.7564 (p0) cc_final: 0.7331 (p0) REVERT: H 100 GLN cc_start: 0.8055 (pm20) cc_final: 0.7779 (pm20) REVERT: H 319 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7687 (mtt-85) REVERT: K 23 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6702 (pm20) REVERT: K 24 VAL cc_start: 0.7827 (p) cc_final: 0.7625 (m) REVERT: A 37 ASP cc_start: 0.7512 (t0) cc_final: 0.7122 (t0) REVERT: A 247 GLU cc_start: 0.7293 (tm-30) cc_final: 0.6979 (tm-30) REVERT: A 251 ARG cc_start: 0.7994 (ttm-80) cc_final: 0.7499 (ttm-80) REVERT: A 393 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7805 (mptt) REVERT: A 396 ASP cc_start: 0.7475 (p0) cc_final: 0.7179 (p0) REVERT: A 438 MET cc_start: 0.7316 (mtm) cc_final: 0.6949 (mtm) REVERT: A 441 LYS cc_start: 0.8374 (ttmt) cc_final: 0.8073 (ttmm) REVERT: A 454 GLU cc_start: 0.7756 (mp0) cc_final: 0.7534 (mp0) REVERT: A 455 GLU cc_start: 0.7381 (tp30) cc_final: 0.6824 (mm-30) outliers start: 77 outliers final: 54 residues processed: 393 average time/residue: 0.2557 time to fit residues: 145.7406 Evaluate side-chains 402 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 345 time to evaluate : 1.556 ------------------------------------------------------------------------------- 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 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 141 ASN Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain E residue 9 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 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 334 HIS 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 565 SER Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain K residue 79 PHE Chi-restraints excluded: chain K residue 80 HIS Chi-restraints excluded: chain K residue 97 ASP Chi-restraints excluded: chain U residue 4 PHE Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 248 ILE 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 335 MET Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 542 LEU 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 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: 0.9990 chunk 2 optimal weight: 1.9990 chunk 128 optimal weight: 0.4980 chunk 70 optimal weight: 0.3980 chunk 146 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 154 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN A 320 HIS A 362 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13828 Z= 0.224 Angle : 0.578 8.985 18847 Z= 0.299 Chirality : 0.041 0.236 2223 Planarity : 0.005 0.069 2418 Dihedral : 4.983 59.919 1954 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 7.28 % Allowed : 28.58 % Favored : 64.14 % 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: -0.57 (0.20), residues: 1807 helix: 1.11 (0.18), residues: 919 sheet: -1.85 (0.57), residues: 92 loop : -2.07 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 517 HIS 0.012 0.001 HIS A 320 PHE 0.014 0.001 PHE H 612 TYR 0.019 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 431 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 336 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 119 ASN cc_start: 0.7608 (p0) cc_final: 0.7362 (p0) REVERT: H 244 ARG cc_start: 0.7353 (mtm110) cc_final: 0.7021 (mtm-85) REVERT: H 319 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7710 (mtt-85) REVERT: U 27 LYS cc_start: 0.8742 (mtpt) cc_final: 0.8406 (tttt) REVERT: A 37 ASP cc_start: 0.7544 (t0) cc_final: 0.7118 (t0) REVERT: A 251 ARG cc_start: 0.8006 (ttm-80) cc_final: 0.7801 (ttm-80) REVERT: A 393 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7803 (mptt) REVERT: A 415 LEU cc_start: 0.8564 (mm) cc_final: 0.8331 (mp) REVERT: A 441 LYS cc_start: 0.8404 (ttmt) cc_final: 0.8074 (ttmm) outliers start: 95 outliers final: 71 residues processed: 396 average time/residue: 0.2918 time to fit residues: 168.3766 Evaluate side-chains 407 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 334 time to evaluate : 1.454 ------------------------------------------------------------------------------- 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 124 LEU 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 E residue 9 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 184 THR Chi-restraints excluded: chain H residue 205 CYS 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 334 HIS 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 565 SER Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain K residue 79 PHE Chi-restraints excluded: chain K residue 80 HIS Chi-restraints excluded: chain K residue 84 ILE 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 43 LEU Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 60 ASN 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 59 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 137 MET 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 282 CYS 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 357 VAL Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 439 LEU 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 622 MET Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 645 SER 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 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: 3.9990 chunk 34 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 172 optimal weight: 0.0070 chunk 142 optimal weight: 0.0980 chunk 79 optimal weight: 0.0010 chunk 14 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 166 optimal weight: 0.6980 overall best weight: 0.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 41 GLN A 320 HIS A 362 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.1040 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= 0.175 Angle : 0.571 10.193 18847 Z= 0.290 Chirality : 0.040 0.269 2223 Planarity : 0.005 0.067 2418 Dihedral : 4.784 59.864 1954 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 6.44 % Allowed : 29.35 % Favored : 64.21 % 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: -0.40 (0.21), residues: 1807 helix: 1.25 (0.18), residues: 914 sheet: -1.78 (0.57), residues: 92 loop : -1.95 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 517 HIS 0.007 0.001 HIS A 320 PHE 0.012 0.001 PHE C 148 TYR 0.021 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 429 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 345 time to evaluate : 1.738 Fit side-chains REVERT: C 119 ASN cc_start: 0.7468 (p0) cc_final: 0.7198 (p0) REVERT: H 244 ARG cc_start: 0.7244 (mtm110) cc_final: 0.6851 (mtm-85) REVERT: H 319 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7688 (mtt-85) REVERT: H 588 CYS cc_start: 0.7114 (m) cc_final: 0.6838 (m) REVERT: H 592 ARG cc_start: 0.7647 (mtm110) cc_final: 0.7223 (mtm180) REVERT: K 97 ASP cc_start: 0.6143 (OUTLIER) cc_final: 0.5873 (m-30) REVERT: U 27 LYS cc_start: 0.8703 (mtpt) cc_final: 0.8488 (tttt) REVERT: A 37 ASP cc_start: 0.7537 (t0) cc_final: 0.7073 (t0) REVERT: A 219 TYR cc_start: 0.8001 (m-10) cc_final: 0.7745 (m-10) REVERT: A 247 GLU cc_start: 0.7351 (tm-30) cc_final: 0.7000 (tm-30) REVERT: A 251 ARG cc_start: 0.8044 (ttm-80) cc_final: 0.7531 (ttm-80) REVERT: A 396 ASP cc_start: 0.7274 (p0) cc_final: 0.6971 (p0) REVERT: A 438 MET cc_start: 0.7085 (mtm) cc_final: 0.6814 (mtm) REVERT: A 454 GLU cc_start: 0.7722 (mp0) cc_final: 0.7398 (mp0) REVERT: A 517 TRP cc_start: 0.8273 (m100) cc_final: 0.8039 (m100) REVERT: A 519 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7674 (pt) outliers start: 84 outliers final: 60 residues processed: 391 average time/residue: 0.2739 time to fit residues: 153.6430 Evaluate side-chains 404 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 341 time to evaluate : 1.686 ------------------------------------------------------------------------------- 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 166 ARG Chi-restraints excluded: chain E residue 9 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 129 LEU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 205 CYS 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 319 ARG Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 334 HIS 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 53 CYS Chi-restraints excluded: chain K residue 79 PHE Chi-restraints excluded: chain K residue 80 HIS Chi-restraints excluded: chain K residue 84 ILE 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 56 LEU 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 84 LEU Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 269 ARG 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 357 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 453 SER 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 577 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 102 GLU 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: 0.0030 chunk 98 optimal weight: 6.9990 chunk 125 optimal weight: 0.0170 chunk 97 optimal weight: 0.6980 chunk 144 optimal weight: 0.1980 chunk 96 optimal weight: 0.4980 chunk 171 optimal weight: 0.4980 chunk 107 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 overall best weight: 0.2428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 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: 0.7197 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13828 Z= 0.168 Angle : 0.581 10.828 18847 Z= 0.292 Chirality : 0.040 0.290 2223 Planarity : 0.005 0.064 2418 Dihedral : 4.619 59.270 1954 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 5.52 % Allowed : 29.50 % Favored : 64.98 % 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: -0.32 (0.21), residues: 1807 helix: 1.35 (0.18), residues: 908 sheet: -1.71 (0.57), residues: 92 loop : -1.95 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 27 HIS 0.003 0.001 HIS A 73 PHE 0.011 0.001 PHE C 148 TYR 0.012 0.001 TYR H 470 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 409 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 337 time to evaluate : 1.526 Fit side-chains REVERT: C 119 ASN cc_start: 0.7449 (p0) cc_final: 0.7166 (p0) REVERT: H 244 ARG cc_start: 0.7202 (mtm110) cc_final: 0.6773 (mtm-85) REVERT: H 319 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7682 (mtt-85) REVERT: H 588 CYS cc_start: 0.7300 (m) cc_final: 0.7072 (m) REVERT: H 592 ARG cc_start: 0.7639 (mtm110) cc_final: 0.7208 (mtm180) REVERT: K 97 ASP cc_start: 0.6275 (OUTLIER) cc_final: 0.5930 (m-30) REVERT: A 37 ASP cc_start: 0.7525 (t0) cc_final: 0.7076 (t0) REVERT: A 219 TYR cc_start: 0.8018 (m-10) cc_final: 0.7738 (m-10) REVERT: A 251 ARG cc_start: 0.8005 (ttm-80) cc_final: 0.7645 (ttm-80) REVERT: A 396 ASP cc_start: 0.7251 (p0) cc_final: 0.6783 (p0) REVERT: A 441 LYS cc_start: 0.8344 (ttmt) cc_final: 0.8051 (ttmm) REVERT: A 519 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7762 (pt) outliers start: 72 outliers final: 51 residues processed: 382 average time/residue: 0.2708 time to fit residues: 149.3952 Evaluate side-chains 384 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 330 time to evaluate : 1.643 ------------------------------------------------------------------------------- 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 166 ARG Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 319 ARG Chi-restraints excluded: chain H residue 334 HIS 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 565 SER Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain K residue 79 PHE Chi-restraints excluded: chain K residue 84 ILE 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 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 84 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 269 ARG 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 439 LEU Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 95 ILE 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: 0.7980 chunk 102 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 33 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 116 optimal weight: 0.0050 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 156 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 41 GLN A 362 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13828 Z= 0.213 Angle : 0.608 10.859 18847 Z= 0.307 Chirality : 0.042 0.313 2223 Planarity : 0.005 0.067 2418 Dihedral : 4.964 68.326 1954 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 5.98 % Allowed : 29.89 % Favored : 64.14 % 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: -0.34 (0.21), residues: 1807 helix: 1.31 (0.18), residues: 909 sheet: -1.72 (0.57), residues: 92 loop : -1.94 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 517 HIS 0.005 0.001 HIS K 80 PHE 0.018 0.001 PHE A 350 TYR 0.018 0.001 TYR A 558 ARG 0.005 0.000 ARG K 91 *********************** 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 414 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 336 time to evaluate : 1.765 Fit side-chains revert: symmetry clash REVERT: C 119 ASN cc_start: 0.7493 (p0) cc_final: 0.7232 (p0) REVERT: H 244 ARG cc_start: 0.7268 (mtm110) cc_final: 0.7047 (mtt-85) REVERT: H 319 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7713 (mtt-85) REVERT: H 588 CYS cc_start: 0.7200 (m) cc_final: 0.6922 (m) REVERT: A 37 ASP cc_start: 0.7549 (t0) cc_final: 0.7119 (t0) REVERT: A 219 TYR cc_start: 0.8008 (m-10) cc_final: 0.7707 (m-10) REVERT: A 251 ARG cc_start: 0.8000 (ttm-80) cc_final: 0.7652 (ttm-80) REVERT: A 276 GLN cc_start: 0.7985 (pp30) cc_final: 0.7380 (mt0) REVERT: A 441 LYS cc_start: 0.8381 (ttmt) cc_final: 0.8113 (ttmm) REVERT: A 451 MET cc_start: 0.7208 (tmm) cc_final: 0.6941 (tmm) REVERT: A 519 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7727 (pt) REVERT: A 642 MET cc_start: 0.6710 (mmp) cc_final: 0.6508 (mmp) outliers start: 78 outliers final: 66 residues processed: 386 average time/residue: 0.2673 time to fit residues: 148.5694 Evaluate side-chains 402 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 334 time to evaluate : 1.493 ------------------------------------------------------------------------------- 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 166 ARG Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 184 THR 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 334 HIS 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 565 SER Chi-restraints excluded: chain K residue 53 CYS 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 17 VAL Chi-restraints excluded: chain U residue 43 LEU 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 84 LEU Chi-restraints excluded: chain A residue 137 MET 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 248 ILE Chi-restraints excluded: chain A residue 265 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 353 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 560 CYS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 645 SER 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 75 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 0.1980 chunk 159 optimal weight: 0.0000 chunk 164 optimal weight: 0.0970 chunk 96 optimal weight: 0.9980 chunk 69 optimal weight: 0.0970 chunk 125 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 104 optimal weight: 0.0980 chunk 169 optimal weight: 2.9990 overall best weight: 0.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13828 Z= 0.170 Angle : 0.602 11.598 18847 Z= 0.300 Chirality : 0.041 0.311 2223 Planarity : 0.005 0.066 2418 Dihedral : 4.702 60.949 1954 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 4.60 % Allowed : 31.57 % Favored : 63.83 % 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: -0.26 (0.21), residues: 1807 helix: 1.40 (0.18), residues: 902 sheet: -1.61 (0.57), residues: 92 loop : -1.90 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 87 HIS 0.005 0.001 HIS K 80 PHE 0.018 0.001 PHE A 350 TYR 0.013 0.001 TYR A 259 ARG 0.005 0.000 ARG A 325 *********************** 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 394 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 334 time to evaluate : 1.606 Fit side-chains revert: symmetry clash REVERT: C 88 GLU cc_start: 0.7712 (tp30) cc_final: 0.7502 (tp30) REVERT: C 119 ASN cc_start: 0.7405 (p0) cc_final: 0.7115 (p0) REVERT: H 244 ARG cc_start: 0.7204 (mtm110) cc_final: 0.6958 (mtt-85) REVERT: H 319 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7558 (mtt-85) REVERT: H 588 CYS cc_start: 0.7290 (m) cc_final: 0.7073 (m) REVERT: H 592 ARG cc_start: 0.7617 (mtm110) cc_final: 0.7192 (mtm180) REVERT: A 37 ASP cc_start: 0.7536 (t0) cc_final: 0.7035 (t0) REVERT: A 149 LYS cc_start: 0.5071 (tmmt) cc_final: 0.4737 (ttpt) REVERT: A 251 ARG cc_start: 0.8017 (ttm-80) cc_final: 0.7701 (ttm-80) REVERT: A 276 GLN cc_start: 0.7939 (pp30) cc_final: 0.7346 (mt0) REVERT: A 297 MET cc_start: 0.7887 (tpp) cc_final: 0.7549 (ttm) REVERT: A 453 SER cc_start: 0.7867 (OUTLIER) cc_final: 0.7564 (p) REVERT: A 455 GLU cc_start: 0.7259 (tp30) cc_final: 0.6875 (mm-30) REVERT: A 519 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7792 (pt) outliers start: 60 outliers final: 48 residues processed: 372 average time/residue: 0.2720 time to fit residues: 146.0363 Evaluate side-chains 377 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 326 time to evaluate : 1.512 ------------------------------------------------------------------------------- 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 E residue 55 THR Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 184 THR 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 319 ARG Chi-restraints excluded: chain H residue 334 HIS 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 565 SER Chi-restraints excluded: chain K residue 53 CYS 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 17 VAL Chi-restraints excluded: chain U residue 43 LEU Chi-restraints excluded: chain U residue 65 SER Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 269 ARG 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 353 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain G residue 75 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 0.8980 chunk 80 optimal weight: 0.1980 chunk 117 optimal weight: 0.4980 chunk 177 optimal weight: 6.9990 chunk 163 optimal weight: 0.8980 chunk 141 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 597 HIS A 362 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13828 Z= 0.210 Angle : 0.632 11.783 18847 Z= 0.314 Chirality : 0.042 0.329 2223 Planarity : 0.005 0.067 2418 Dihedral : 4.751 59.602 1954 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 4.83 % Allowed : 30.57 % 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: -0.32 (0.21), residues: 1807 helix: 1.35 (0.18), residues: 907 sheet: -1.67 (0.57), residues: 92 loop : -1.95 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 517 HIS 0.006 0.001 HIS K 80 PHE 0.018 0.001 PHE A 350 TYR 0.015 0.001 TYR D 79 ARG 0.004 0.000 ARG K 91 ********************** 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 397 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 334 time to evaluate : 1.579 Fit side-chains revert: symmetry clash REVERT: C 88 GLU cc_start: 0.7737 (tp30) cc_final: 0.7531 (tp30) REVERT: C 119 ASN cc_start: 0.7458 (p0) cc_final: 0.7191 (p0) REVERT: H 244 ARG cc_start: 0.7269 (mtm110) cc_final: 0.7052 (mtt-85) REVERT: H 319 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7653 (mtt-85) REVERT: H 592 ARG cc_start: 0.7693 (mtm110) cc_final: 0.7263 (mtm180) REVERT: A 37 ASP cc_start: 0.7554 (t0) cc_final: 0.7093 (t0) REVERT: A 92 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7233 (mm-30) REVERT: A 149 LYS cc_start: 0.5056 (tmmt) cc_final: 0.4735 (ttpt) REVERT: A 219 TYR cc_start: 0.8004 (m-10) cc_final: 0.7675 (m-10) REVERT: A 251 ARG cc_start: 0.7993 (ttm-80) cc_final: 0.7662 (ttm-80) REVERT: A 276 GLN cc_start: 0.7976 (pp30) cc_final: 0.7392 (mt0) REVERT: A 297 MET cc_start: 0.7918 (tpp) cc_final: 0.7539 (ttm) REVERT: A 302 ARG cc_start: 0.7799 (ttm-80) cc_final: 0.7577 (ttm-80) REVERT: A 396 ASP cc_start: 0.7248 (p0) cc_final: 0.6853 (p0) REVERT: A 441 LYS cc_start: 0.8347 (ttmt) cc_final: 0.8074 (ttmm) REVERT: A 453 SER cc_start: 0.7892 (OUTLIER) cc_final: 0.7490 (p) REVERT: A 519 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7719 (pt) outliers start: 63 outliers final: 54 residues processed: 376 average time/residue: 0.2585 time to fit residues: 140.2843 Evaluate side-chains 389 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 332 time to evaluate : 1.479 ------------------------------------------------------------------------------- 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 137 PHE Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 184 THR 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 334 HIS Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 383 LEU Chi-restraints excluded: chain H residue 393 MET Chi-restraints excluded: chain H residue 394 LEU Chi-restraints excluded: chain H residue 565 SER Chi-restraints excluded: chain K residue 53 CYS 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 17 VAL Chi-restraints excluded: chain U residue 43 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 84 LEU Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 190 HIS 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 353 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 625 HIS Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain G residue 75 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 1.9990 chunk 130 optimal weight: 0.2980 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 145 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 8 optimal weight: 0.0070 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN H 597 HIS A 362 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.139125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.119182 restraints weight = 25885.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.120739 restraints weight = 13662.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.122050 restraints weight = 10258.197| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13828 Z= 0.190 Angle : 0.626 11.283 18847 Z= 0.309 Chirality : 0.041 0.300 2223 Planarity : 0.005 0.066 2418 Dihedral : 4.742 58.079 1954 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 4.67 % Allowed : 30.88 % Favored : 64.44 % 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: -0.32 (0.21), residues: 1807 helix: 1.37 (0.18), residues: 905 sheet: -1.63 (0.58), residues: 92 loop : -1.97 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 517 HIS 0.005 0.001 HIS K 80 PHE 0.019 0.001 PHE A 350 TYR 0.013 0.001 TYR A 259 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: 3467.83 seconds wall clock time: 64 minutes 7.66 seconds (3847.66 seconds total)