Starting phenix.real_space_refine on Sun Feb 18 10:49:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgs_22330/02_2024/7jgs_22330_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgs_22330/02_2024/7jgs_22330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgs_22330/02_2024/7jgs_22330.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgs_22330/02_2024/7jgs_22330.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgs_22330/02_2024/7jgs_22330_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgs_22330/02_2024/7jgs_22330_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 82 5.49 5 Mg 4 5.21 5 S 111 5.16 5 C 13591 2.51 5 N 3810 2.21 5 O 4145 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 334": "OE1" <-> "OE2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 413": "OE1" <-> "OE2" Residue "B GLU 427": "OE1" <-> "OE2" Residue "B GLU 613": "OE1" <-> "OE2" Residue "B GLU 616": "OE1" <-> "OE2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C GLU 51": "OE1" <-> "OE2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C ARG 125": "NH1" <-> "NH2" Residue "C GLU 153": "OE1" <-> "OE2" Residue "C GLU 157": "OE1" <-> "OE2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 351": "OE1" <-> "OE2" Residue "C GLU 354": "OE1" <-> "OE2" Residue "C GLU 443": "OE1" <-> "OE2" Residue "C ARG 469": "NH1" <-> "NH2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C GLU 482": "OE1" <-> "OE2" Residue "C GLU 485": "OE1" <-> "OE2" Residue "C GLU 504": "OE1" <-> "OE2" Residue "C GLU 573": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "D GLU 3": "OE1" <-> "OE2" Residue "D GLU 7": "OE1" <-> "OE2" Residue "D ARG 27": "NH1" <-> "NH2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D GLU 188": "OE1" <-> "OE2" Residue "D GLU 191": "OE1" <-> "OE2" Residue "D GLU 236": "OE1" <-> "OE2" Residue "D GLU 298": "OE1" <-> "OE2" Residue "D ARG 313": "NH1" <-> "NH2" Residue "D PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 369": "OE1" <-> "OE2" Residue "D GLU 423": "OE1" <-> "OE2" Residue "D ARG 442": "NH1" <-> "NH2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E GLU 129": "OE1" <-> "OE2" Residue "E ARG 144": "NH1" <-> "NH2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "E GLU 223": "OE1" <-> "OE2" Residue "E ARG 252": "NH1" <-> "NH2" Residue "E GLU 260": "OE1" <-> "OE2" Residue "E ARG 293": "NH1" <-> "NH2" Residue "E GLU 320": "OE1" <-> "OE2" Residue "E ARG 345": "NH1" <-> "NH2" Residue "E GLU 394": "OE1" <-> "OE2" Residue "E GLU 395": "OE1" <-> "OE2" Residue "E GLU 439": "OE1" <-> "OE2" Residue "F GLU 223": "OE1" <-> "OE2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A GLU 576": "OE1" <-> "OE2" Residue "A GLU 623": "OE1" <-> "OE2" Residue "A ARG 676": "NH1" <-> "NH2" Residue "A ARG 692": "NH1" <-> "NH2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A ARG 725": "NH1" <-> "NH2" Residue "A GLU 762": "OE1" <-> "OE2" Residue "A ARG 785": "NH1" <-> "NH2" Residue "A ARG 827": "NH1" <-> "NH2" Residue "A GLU 850": "OE1" <-> "OE2" Residue "A GLU 862": "OE1" <-> "OE2" Residue "A ARG 880": "NH1" <-> "NH2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "G ARG 385": "NH1" <-> "NH2" Residue "G GLU 387": "OE1" <-> "OE2" Residue "G GLU 494": "OE1" <-> "OE2" Residue "G ARG 498": "NH1" <-> "NH2" Residue "G GLU 604": "OE1" <-> "OE2" Residue "G GLU 638": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21743 Number of models: 1 Model: "" Number of chains: 13 Chain: "B" Number of atoms: 2290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2290 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 4 Chain: "C" Number of atoms: 4934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4934 Classifications: {'peptide': 614} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 590} Chain breaks: 6 Chain: "D" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3549 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 11, 'TRANS': 429} Chain breaks: 2 Chain: "E" Number of atoms: 3161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3161 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 143 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "A" Number of atoms: 3129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3129 Classifications: {'peptide': 401} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 383} Chain: "G" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2974 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 13, 'TRANS': 358} Chain breaks: 2 Chain: "H" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 700 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "I" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 735 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.81, per 1000 atoms: 0.50 Number of scatterers: 21743 At special positions: 0 Unit cell: (123.981, 162.129, 119.646, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 111 16.00 P 82 15.00 Mg 4 11.99 O 4145 8.00 N 3810 7.00 C 13591 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.14 Conformation dependent library (CDL) restraints added in 4.2 seconds 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4840 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 131 helices and 12 sheets defined 56.0% alpha, 6.5% beta 35 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 8.83 Creating SS restraints... Processing helix chain 'B' and resid 280 through 284 removed outlier: 3.622A pdb=" N PHE B 284 " --> pdb=" O ASP B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 349 removed outlier: 3.957A pdb=" N TYR B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE B 340 " --> pdb=" O TYR B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.610A pdb=" N GLU B 349 " --> pdb=" O CYS B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 371 Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 411 through 422 Processing helix chain 'B' and resid 445 through 455 Processing helix chain 'B' and resid 471 through 473 No H-bonds generated for 'chain 'B' and resid 471 through 473' Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'B' and resid 516 through 523 Processing helix chain 'B' and resid 528 through 544 Processing helix chain 'B' and resid 555 through 564 Processing helix chain 'B' and resid 571 through 583 Processing helix chain 'B' and resid 605 through 614 Processing helix chain 'C' and resid 42 through 45 No H-bonds generated for 'chain 'C' and resid 42 through 45' Processing helix chain 'C' and resid 48 through 88 removed outlier: 5.049A pdb=" N ARG C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N THR C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 109 No H-bonds generated for 'chain 'C' and resid 107 through 109' Processing helix chain 'C' and resid 111 through 123 Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' Processing helix chain 'C' and resid 140 through 158 Processing helix chain 'C' and resid 180 through 182 No H-bonds generated for 'chain 'C' and resid 180 through 182' Processing helix chain 'C' and resid 185 through 195 Processing helix chain 'C' and resid 217 through 229 Processing helix chain 'C' and resid 246 through 252 Processing helix chain 'C' and resid 255 through 260 removed outlier: 3.608A pdb=" N SER C 259 " --> pdb=" O TYR C 255 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS C 260 " --> pdb=" O HIS C 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 255 through 260' Processing helix chain 'C' and resid 271 through 281 Processing helix chain 'C' and resid 294 through 306 Processing helix chain 'C' and resid 311 through 328 removed outlier: 4.462A pdb=" N GLY C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 334 Processing helix chain 'C' and resid 338 through 347 Processing helix chain 'C' and resid 350 through 357 Processing helix chain 'C' and resid 360 through 367 Proline residue: C 364 - end of helix Processing helix chain 'C' and resid 372 through 379 removed outlier: 3.501A pdb=" N ILE C 376 " --> pdb=" O CYS C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 414 Proline residue: C 390 - end of helix Processing helix chain 'C' and resid 426 through 435 Processing helix chain 'C' and resid 442 through 452 Processing helix chain 'C' and resid 456 through 476 Processing helix chain 'C' and resid 485 through 507 Proline residue: C 493 - end of helix Processing helix chain 'C' and resid 563 through 580 removed outlier: 3.664A pdb=" N LYS C 567 " --> pdb=" O ARG C 563 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N GLN C 578 " --> pdb=" O THR C 574 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASP C 579 " --> pdb=" O GLN C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 606 Processing helix chain 'C' and resid 610 through 619 Processing helix chain 'C' and resid 621 through 625 removed outlier: 3.749A pdb=" N MET C 625 " --> pdb=" O HIS C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 653 removed outlier: 3.970A pdb=" N VAL C 648 " --> pdb=" O ASP C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 671 Processing helix chain 'C' and resid 689 through 702 Processing helix chain 'D' and resid 4 through 20 removed outlier: 3.936A pdb=" N LEU D 8 " --> pdb=" O ALA D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 46 removed outlier: 3.525A pdb=" N SER D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 76 Proline residue: D 75 - end of helix Processing helix chain 'D' and resid 96 through 106 Processing helix chain 'D' and resid 121 through 134 Processing helix chain 'D' and resid 149 through 152 No H-bonds generated for 'chain 'D' and resid 149 through 152' Processing helix chain 'D' and resid 156 through 168 removed outlier: 3.755A pdb=" N THR D 159 " --> pdb=" O HIS D 156 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU D 160 " --> pdb=" O ASN D 157 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR D 162 " --> pdb=" O THR D 159 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 164 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE D 165 " --> pdb=" O TYR D 162 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP D 166 " --> pdb=" O ASN D 163 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL D 167 " --> pdb=" O LEU D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 212 through 221 Processing helix chain 'D' and resid 228 through 243 Processing helix chain 'D' and resid 251 through 253 No H-bonds generated for 'chain 'D' and resid 251 through 253' Processing helix chain 'D' and resid 265 through 279 Processing helix chain 'D' and resid 282 through 294 Processing helix chain 'D' and resid 298 through 311 removed outlier: 4.133A pdb=" N HIS D 311 " --> pdb=" O ARG D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 332 Processing helix chain 'D' and resid 336 through 342 removed outlier: 3.639A pdb=" N GLY D 342 " --> pdb=" O GLU D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 360 Processing helix chain 'D' and resid 368 through 379 removed outlier: 3.787A pdb=" N PHE D 378 " --> pdb=" O ARG D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 402 Processing helix chain 'D' and resid 433 through 442 Processing helix chain 'D' and resid 448 through 455 removed outlier: 3.830A pdb=" N GLN D 455 " --> pdb=" O ALA D 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 11 Proline residue: E 10 - end of helix Processing helix chain 'E' and resid 16 through 26 Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 77 through 88 Processing helix chain 'E' and resid 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'E' and resid 101 through 111 removed outlier: 3.743A pdb=" N ARG E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN E 111 " --> pdb=" O GLN E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 133 removed outlier: 3.918A pdb=" N ARG E 132 " --> pdb=" O GLU E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 149 removed outlier: 3.959A pdb=" N ARG E 144 " --> pdb=" O PRO E 140 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N GLN E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLU E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 165 No H-bonds generated for 'chain 'E' and resid 163 through 165' Processing helix chain 'E' and resid 185 through 193 Processing helix chain 'E' and resid 196 through 205 removed outlier: 3.590A pdb=" N GLU E 205 " --> pdb=" O ASN E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 219 removed outlier: 3.807A pdb=" N GLU E 219 " --> pdb=" O GLU E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 237 removed outlier: 3.977A pdb=" N VAL E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 258 removed outlier: 4.000A pdb=" N LYS E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 264 Processing helix chain 'E' and resid 276 through 287 Proline residue: E 282 - end of helix Processing helix chain 'E' and resid 323 through 337 Processing helix chain 'E' and resid 342 through 347 removed outlier: 3.701A pdb=" N LEU E 346 " --> pdb=" O ASP E 343 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE E 347 " --> pdb=" O LYS E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 393 Processing helix chain 'E' and resid 401 through 412 Processing helix chain 'E' and resid 438 through 448 Processing helix chain 'F' and resid 225 through 237 Processing helix chain 'A' and resid 520 through 528 Processing helix chain 'A' and resid 546 through 548 No H-bonds generated for 'chain 'A' and resid 546 through 548' Processing helix chain 'A' and resid 551 through 558 Processing helix chain 'A' and resid 572 through 588 Processing helix chain 'A' and resid 604 through 620 Processing helix chain 'A' and resid 634 through 636 No H-bonds generated for 'chain 'A' and resid 634 through 636' Processing helix chain 'A' and resid 640 through 652 removed outlier: 3.807A pdb=" N ILE A 647 " --> pdb=" O TYR A 644 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR A 648 " --> pdb=" O VAL A 645 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS A 649 " --> pdb=" O GLN A 646 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR A 652 " --> pdb=" O LYS A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 669 Processing helix chain 'A' and resid 686 through 689 No H-bonds generated for 'chain 'A' and resid 686 through 689' Processing helix chain 'A' and resid 696 through 705 Proline residue: A 704 - end of helix Processing helix chain 'A' and resid 722 through 725 No H-bonds generated for 'chain 'A' and resid 722 through 725' Processing helix chain 'A' and resid 729 through 735 Processing helix chain 'A' and resid 747 through 758 removed outlier: 3.781A pdb=" N VAL A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 776 removed outlier: 3.513A pdb=" N GLN A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 799 removed outlier: 3.729A pdb=" N ARG A 791 " --> pdb=" O LEU A 787 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 799 " --> pdb=" O GLU A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 817 Processing helix chain 'A' and resid 823 through 827 Processing helix chain 'A' and resid 831 through 847 removed outlier: 3.531A pdb=" N ALA A 841 " --> pdb=" O LEU A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 868 Processing helix chain 'A' and resid 875 through 887 Processing helix chain 'A' and resid 910 through 917 Processing helix chain 'G' and resid 251 through 259 Processing helix chain 'G' and resid 272 through 286 Processing helix chain 'G' and resid 303 through 312 removed outlier: 3.615A pdb=" N LEU G 311 " --> pdb=" O LEU G 307 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG G 312 " --> pdb=" O SER G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 319 Processing helix chain 'G' and resid 333 through 344 removed outlier: 3.608A pdb=" N VAL G 336 " --> pdb=" O VAL G 333 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR G 337 " --> pdb=" O GLY G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 365 Processing helix chain 'G' and resid 378 through 381 Processing helix chain 'G' and resid 387 through 392 Processing helix chain 'G' and resid 395 through 397 No H-bonds generated for 'chain 'G' and resid 395 through 397' Processing helix chain 'G' and resid 414 through 417 No H-bonds generated for 'chain 'G' and resid 414 through 417' Processing helix chain 'G' and resid 420 through 424 Processing helix chain 'G' and resid 440 through 452 Processing helix chain 'G' and resid 457 through 459 No H-bonds generated for 'chain 'G' and resid 457 through 459' Processing helix chain 'G' and resid 462 through 475 removed outlier: 3.595A pdb=" N ALA G 470 " --> pdb=" O GLN G 466 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA G 474 " --> pdb=" O ALA G 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 479 through 497 removed outlier: 3.709A pdb=" N VAL G 490 " --> pdb=" O GLY G 486 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN G 495 " --> pdb=" O GLU G 491 " (cutoff:3.500A) Processing helix chain 'G' and resid 531 through 541 Processing helix chain 'G' and resid 558 through 573 Processing helix chain 'G' and resid 581 through 594 removed outlier: 3.613A pdb=" N VAL G 587 " --> pdb=" O ARG G 583 " (cutoff:3.500A) Processing helix chain 'G' and resid 602 through 615 removed outlier: 3.817A pdb=" N GLY G 607 " --> pdb=" O ALA G 603 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR G 614 " --> pdb=" O ASP G 610 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG G 615 " --> pdb=" O LEU G 611 " (cutoff:3.500A) Processing helix chain 'G' and resid 626 through 628 No H-bonds generated for 'chain 'G' and resid 626 through 628' Processing helix chain 'G' and resid 637 through 644 Processing helix chain 'G' and resid 647 through 654 removed outlier: 3.728A pdb=" N SER G 652 " --> pdb=" O GLN G 648 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 485 through 488 removed outlier: 6.196A pdb=" N ASN B 352 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TRP B 488 " --> pdb=" O ASN B 352 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU B 354 " --> pdb=" O TRP B 488 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU B 430 " --> pdb=" O HIS B 461 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU B 463 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU B 432 " --> pdb=" O LEU B 463 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N SER B 465 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL B 434 " --> pdb=" O SER B 465 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR B 377 " --> pdb=" O PHE B 431 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE B 433 " --> pdb=" O THR B 377 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU B 379 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N HIS B 435 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 381 " --> pdb=" O HIS B 435 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 588 through 590 Processing sheet with id= C, first strand: chain 'C' and resid 97 through 99 Processing sheet with id= D, first strand: chain 'C' and resid 127 through 131 removed outlier: 6.392A pdb=" N GLN C 204 " --> pdb=" O MET C 128 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N CYS C 130 " --> pdb=" O GLN C 204 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL C 206 " --> pdb=" O CYS C 130 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 706 through 709 removed outlier: 3.616A pdb=" N HIS C 715 " --> pdb=" O SER C 709 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 202 through 204 removed outlier: 8.074A pdb=" N VAL D 203 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU D 53 " --> pdb=" O VAL D 203 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 406 through 408 Processing sheet with id= H, first strand: chain 'E' and resid 176 through 180 removed outlier: 7.977A pdb=" N ILE E 37 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL E 155 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU E 39 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LEU E 157 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLY E 41 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER E 159 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE E 121 " --> pdb=" O CYS E 154 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ILE E 156 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE E 123 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU E 158 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL E 125 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 416 through 420 removed outlier: 7.032A pdb=" N ARG E 431 " --> pdb=" O VAL E 419 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 739 through 742 removed outlier: 8.818A pdb=" N LEU A 740 " --> pdb=" O CYS A 593 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TYR A 595 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N PHE A 742 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER A 597 " --> pdb=" O PHE A 742 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY A 598 " --> pdb=" O ALA A 717 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR A 679 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL A 714 " --> pdb=" O THR A 679 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU A 681 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE A 716 " --> pdb=" O LEU A 681 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL A 683 " --> pdb=" O ILE A 716 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 431 through 435 removed outlier: 8.272A pdb=" N LEU G 293 " --> pdb=" O ILE G 403 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU G 405 " --> pdb=" O LEU G 293 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL G 295 " --> pdb=" O LEU G 405 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLY G 407 " --> pdb=" O VAL G 295 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N GLY G 297 " --> pdb=" O GLY G 407 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA G 409 " --> pdb=" O GLY G 297 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU G 371 " --> pdb=" O LEU G 404 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL G 406 " --> pdb=" O LEU G 371 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU G 373 " --> pdb=" O VAL G 406 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ILE G 408 " --> pdb=" O LEU G 373 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU G 375 " --> pdb=" O ILE G 408 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 618 through 621 902 hydrogen bonds defined for protein. 2607 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 68 stacking parallelities Total time for adding SS restraints: 7.82 Time building geometry restraints manager: 9.88 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: 5797 1.33 - 1.46: 4953 1.46 - 1.58: 11194 1.58 - 1.70: 157 1.70 - 1.83: 163 Bond restraints: 22264 Sorted by residual: bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.34e+01 bond pdb=" C4 ATP E 901 " pdb=" C5 ATP E 901 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.07e+01 bond pdb=" C4 ATP A1001 " pdb=" C5 ATP A1001 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.02e+01 bond pdb=" C4 ATP G 901 " pdb=" C5 ATP G 901 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.93e+01 bond pdb=" C5 ATP E 901 " pdb=" C6 ATP E 901 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.39e+01 ... (remaining 22259 not shown) Histogram of bond angle deviations from ideal: 97.47 - 105.16: 635 105.16 - 112.85: 12036 112.85 - 120.54: 10004 120.54 - 128.23: 7521 128.23 - 135.91: 204 Bond angle restraints: 30400 Sorted by residual: angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 120.57 19.30 1.00e+00 1.00e+00 3.72e+02 angle pdb=" PB ATP G 901 " pdb=" O3B ATP G 901 " pdb=" PG ATP G 901 " ideal model delta sigma weight residual 139.87 121.67 18.20 1.00e+00 1.00e+00 3.31e+02 angle pdb=" PA ATP A1001 " pdb=" O3A ATP A1001 " pdb=" PB ATP A1001 " ideal model delta sigma weight residual 136.83 119.26 17.57 1.00e+00 1.00e+00 3.09e+02 angle pdb=" PB ATP E 901 " pdb=" O3B ATP E 901 " pdb=" PG ATP E 901 " ideal model delta sigma weight residual 139.87 124.37 15.50 1.00e+00 1.00e+00 2.40e+02 angle pdb=" PA ATP E 901 " pdb=" O3A ATP E 901 " pdb=" PB ATP E 901 " ideal model delta sigma weight residual 136.83 121.59 15.24 1.00e+00 1.00e+00 2.32e+02 ... (remaining 30395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 11482 17.97 - 35.94: 1379 35.94 - 53.91: 527 53.91 - 71.89: 102 71.89 - 89.86: 36 Dihedral angle restraints: 13526 sinusoidal: 6113 harmonic: 7413 Sorted by residual: dihedral pdb=" CA LEU G 259 " pdb=" C LEU G 259 " pdb=" N ASN G 260 " pdb=" CA ASN G 260 " ideal model delta harmonic sigma weight residual 180.00 149.83 30.17 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" CA MET E 134 " pdb=" C MET E 134 " pdb=" N ASP E 135 " pdb=" CA ASP E 135 " ideal model delta harmonic sigma weight residual -180.00 -150.35 -29.65 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA MET C 128 " pdb=" C MET C 128 " pdb=" N VAL C 129 " pdb=" CA VAL C 129 " ideal model delta harmonic sigma weight residual -180.00 -156.62 -23.38 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 13523 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2320 0.042 - 0.084: 876 0.084 - 0.127: 233 0.127 - 0.169: 63 0.169 - 0.211: 16 Chirality restraints: 3508 Sorted by residual: chirality pdb=" CB ILE C 590 " pdb=" CA ILE C 590 " pdb=" CG1 ILE C 590 " pdb=" CG2 ILE C 590 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL E 221 " pdb=" CA VAL E 221 " pdb=" CG1 VAL E 221 " pdb=" CG2 VAL E 221 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB ILE C 5 " pdb=" CA ILE C 5 " pdb=" CG1 ILE C 5 " pdb=" CG2 ILE C 5 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 3505 not shown) Planarity restraints: 3607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 872 " 0.059 5.00e-02 4.00e+02 8.90e-02 1.27e+01 pdb=" N PRO A 873 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 873 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 873 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 587 " -0.057 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO C 588 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 588 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 588 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 9 " -0.050 5.00e-02 4.00e+02 7.48e-02 8.96e+00 pdb=" N PRO E 10 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO E 10 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 10 " -0.042 5.00e-02 4.00e+02 ... (remaining 3604 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.09: 7 2.09 - 2.80: 5307 2.80 - 3.50: 27760 3.50 - 4.20: 52569 4.20 - 4.90: 91221 Nonbonded interactions: 176864 Sorted by model distance: nonbonded pdb=" NH1 ARG C 711 " pdb=" C4' DA I 44 " model vdw 1.392 3.550 nonbonded pdb=" NH1 ARG C 711 " pdb=" O3' DA I 44 " model vdw 1.479 2.520 nonbonded pdb=" NH1 ARG C 711 " pdb=" C3' DA I 44 " model vdw 1.628 3.550 nonbonded pdb=" OG SER C 709 " pdb=" O HIS C 715 " model vdw 2.031 2.440 nonbonded pdb=" OG1 THR E 48 " pdb="MG MG E 902 " model vdw 2.068 2.170 ... (remaining 176859 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 6.940 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 62.290 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 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 : 0.006 0.080 22264 Z= 0.345 Angle : 0.938 19.298 30400 Z= 0.583 Chirality : 0.049 0.211 3508 Planarity : 0.007 0.089 3607 Dihedral : 18.330 89.857 8686 Min Nonbonded Distance : 1.392 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.18 % Allowed : 6.18 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.49 (0.13), residues: 2478 helix: -2.42 (0.09), residues: 1450 sheet: -2.18 (0.28), residues: 228 loop : -1.65 (0.18), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 664 HIS 0.009 0.001 HIS C 652 PHE 0.019 0.002 PHE G 447 TYR 0.021 0.002 TYR E 323 ARG 0.010 0.001 ARG G 322 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 306 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 540 TYR cc_start: 0.7672 (t80) cc_final: 0.7307 (t80) REVERT: B 562 CYS cc_start: 0.8065 (m) cc_final: 0.7777 (m) REVERT: B 583 ASP cc_start: 0.8326 (t70) cc_final: 0.7846 (m-30) REVERT: B 584 HIS cc_start: 0.8122 (m90) cc_final: 0.7880 (m170) REVERT: C 398 LEU cc_start: 0.8588 (tp) cc_final: 0.8335 (tt) REVERT: C 435 ASN cc_start: 0.9079 (m-40) cc_final: 0.8838 (t0) REVERT: C 443 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7903 (mm-30) REVERT: C 450 MET cc_start: 0.8680 (mtp) cc_final: 0.7823 (mtp) REVERT: C 451 LEU cc_start: 0.9276 (mt) cc_final: 0.8723 (pp) REVERT: C 457 ASP cc_start: 0.8536 (p0) cc_final: 0.8297 (p0) REVERT: C 699 GLU cc_start: 0.8014 (tt0) cc_final: 0.7453 (mt-10) REVERT: D 185 ASP cc_start: 0.8212 (p0) cc_final: 0.8007 (p0) REVERT: D 347 GLU cc_start: 0.9057 (mp0) cc_final: 0.8577 (mp0) REVERT: D 389 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8001 (mt-10) REVERT: D 426 MET cc_start: 0.8648 (mmm) cc_final: 0.8291 (mmm) REVERT: E 414 ASN cc_start: 0.8993 (t0) cc_final: 0.8636 (p0) REVERT: E 417 SER cc_start: 0.9075 (t) cc_final: 0.8689 (p) REVERT: F 224 ASP cc_start: 0.8881 (t70) cc_final: 0.8235 (p0) REVERT: F 226 GLU cc_start: 0.9235 (mm-30) cc_final: 0.8876 (mp0) REVERT: F 231 ARG cc_start: 0.9049 (ttp80) cc_final: 0.8734 (ttp80) REVERT: F 232 MET cc_start: 0.9345 (tpt) cc_final: 0.9068 (tpp) REVERT: A 618 MET cc_start: 0.8498 (mtp) cc_final: 0.8135 (mtt) REVERT: G 345 GLN cc_start: 0.8993 (mp10) cc_final: 0.8744 (mp10) REVERT: G 570 MET cc_start: 0.7777 (mtp) cc_final: 0.7518 (mtp) outliers start: 4 outliers final: 1 residues processed: 310 average time/residue: 0.4275 time to fit residues: 190.8154 Evaluate side-chains 171 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 170 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.9980 chunk 149 optimal weight: 0.7980 chunk 232 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 325 HIS B 366 GLN B 429 HIS B 544 ASN B 609 GLN C 46 GLN C 133 GLN C 194 ASN C 370 ASN C 449 GLN ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 GLN C 666 GLN D 202 GLN ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 HIS ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 GLN G 356 HIS G 410 ASN G 585 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22264 Z= 0.158 Angle : 0.526 9.508 30400 Z= 0.284 Chirality : 0.037 0.169 3508 Planarity : 0.004 0.061 3607 Dihedral : 17.467 84.627 3716 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.17 % Allowed : 10.10 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.15), residues: 2478 helix: -0.32 (0.12), residues: 1454 sheet: -1.84 (0.29), residues: 254 loop : -0.86 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 664 HIS 0.004 0.001 HIS D 138 PHE 0.022 0.001 PHE C 459 TYR 0.018 0.001 TYR C 255 ARG 0.007 0.000 ARG C 70 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 187 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 391 LYS cc_start: 0.8921 (tptt) cc_final: 0.8205 (tptt) REVERT: B 395 ASP cc_start: 0.8264 (m-30) cc_final: 0.6987 (m-30) REVERT: B 519 MET cc_start: 0.8375 (tmm) cc_final: 0.8127 (tmm) REVERT: B 540 TYR cc_start: 0.7656 (t80) cc_final: 0.7331 (t80) REVERT: B 583 ASP cc_start: 0.8330 (t70) cc_final: 0.7904 (m-30) REVERT: B 584 HIS cc_start: 0.8179 (m90) cc_final: 0.7906 (m170) REVERT: C 185 MET cc_start: 0.8726 (mmm) cc_final: 0.8126 (mmm) REVERT: C 323 MET cc_start: 0.8851 (ttp) cc_final: 0.8632 (ttp) REVERT: C 398 LEU cc_start: 0.8480 (tp) cc_final: 0.8155 (tt) REVERT: C 435 ASN cc_start: 0.9097 (m-40) cc_final: 0.8840 (t0) REVERT: C 699 GLU cc_start: 0.7825 (tt0) cc_final: 0.7086 (mt-10) REVERT: D 347 GLU cc_start: 0.9090 (mp0) cc_final: 0.8602 (mp0) REVERT: D 389 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7996 (mt-10) REVERT: D 426 MET cc_start: 0.8728 (mmm) cc_final: 0.8339 (mmm) REVERT: E 417 SER cc_start: 0.8778 (t) cc_final: 0.8239 (p) REVERT: A 775 LYS cc_start: 0.9109 (mttt) cc_final: 0.8858 (mptt) outliers start: 26 outliers final: 14 residues processed: 205 average time/residue: 0.3450 time to fit residues: 110.1556 Evaluate side-chains 178 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 164 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain E residue 75 TYR Chi-restraints excluded: chain E residue 412 HIS Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain G residue 413 ASP Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain G residue 571 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 193 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 232 optimal weight: 6.9990 chunk 251 optimal weight: 8.9990 chunk 207 optimal weight: 0.9980 chunk 230 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 186 optimal weight: 7.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 615 GLN C 230 HIS ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN A 622 ASN G 530 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22264 Z= 0.274 Angle : 0.557 7.964 30400 Z= 0.293 Chirality : 0.039 0.161 3508 Planarity : 0.004 0.054 3607 Dihedral : 17.657 85.088 3716 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.67 % Allowed : 11.68 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: 0.22 (0.17), residues: 2478 helix: 0.86 (0.14), residues: 1454 sheet: -1.41 (0.31), residues: 248 loop : -0.46 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 276 HIS 0.010 0.001 HIS E 278 PHE 0.015 0.001 PHE C 459 TYR 0.019 0.001 TYR C 255 ARG 0.006 0.000 ARG C 419 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 162 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 391 LYS cc_start: 0.8916 (tptt) cc_final: 0.8115 (tptt) REVERT: B 395 ASP cc_start: 0.8299 (m-30) cc_final: 0.6951 (m-30) REVERT: B 540 TYR cc_start: 0.7767 (t80) cc_final: 0.7495 (t80) REVERT: B 583 ASP cc_start: 0.8403 (t70) cc_final: 0.7969 (m-30) REVERT: B 584 HIS cc_start: 0.8243 (m90) cc_final: 0.7931 (m170) REVERT: C 446 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8266 (tp30) REVERT: D 347 GLU cc_start: 0.9102 (mp0) cc_final: 0.8654 (mp0) REVERT: D 426 MET cc_start: 0.8658 (mmm) cc_final: 0.8197 (mmm) REVERT: D 440 MET cc_start: 0.8688 (mmm) cc_final: 0.8412 (mmm) REVERT: E 254 CYS cc_start: 0.8399 (m) cc_final: 0.7793 (t) REVERT: E 417 SER cc_start: 0.8836 (t) cc_final: 0.8260 (p) REVERT: A 622 ASN cc_start: 0.9213 (OUTLIER) cc_final: 0.8786 (t0) REVERT: G 385 ARG cc_start: 0.8368 (mtp85) cc_final: 0.7812 (mmp80) outliers start: 37 outliers final: 22 residues processed: 188 average time/residue: 0.3633 time to fit residues: 107.5195 Evaluate side-chains 171 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 2.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 75 TYR Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain G residue 413 ASP Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain G residue 571 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 156 optimal weight: 0.8980 chunk 233 optimal weight: 5.9990 chunk 247 optimal weight: 7.9990 chunk 122 optimal weight: 0.0010 chunk 221 optimal weight: 0.0980 chunk 66 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 113 GLN ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 ASN E 278 HIS ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22264 Z= 0.183 Angle : 0.505 12.083 30400 Z= 0.266 Chirality : 0.037 0.157 3508 Planarity : 0.003 0.051 3607 Dihedral : 17.458 87.590 3716 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.58 % Allowed : 12.80 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: 0.86 (0.17), residues: 2478 helix: 1.41 (0.14), residues: 1452 sheet: -1.18 (0.32), residues: 248 loop : -0.29 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 276 HIS 0.006 0.001 HIS E 278 PHE 0.014 0.001 PHE C 459 TYR 0.016 0.001 TYR C 384 ARG 0.005 0.000 ARG F 231 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 158 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9229 (tpp) cc_final: 0.8961 (mmm) REVERT: B 391 LYS cc_start: 0.8928 (tptt) cc_final: 0.8293 (tptt) REVERT: B 395 ASP cc_start: 0.8317 (m-30) cc_final: 0.7748 (m-30) REVERT: B 540 TYR cc_start: 0.7718 (t80) cc_final: 0.7494 (t80) REVERT: B 584 HIS cc_start: 0.8137 (m90) cc_final: 0.7424 (m170) REVERT: C 72 TYR cc_start: 0.8319 (t80) cc_final: 0.8114 (t80) REVERT: C 443 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8241 (tp30) REVERT: C 446 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8313 (tp30) REVERT: D 347 GLU cc_start: 0.9093 (mp0) cc_final: 0.8608 (mp0) REVERT: D 426 MET cc_start: 0.8684 (mmm) cc_final: 0.8203 (mmm) REVERT: E 1 MET cc_start: 0.8138 (tmm) cc_final: 0.7810 (tmm) REVERT: E 254 CYS cc_start: 0.8330 (m) cc_final: 0.7781 (t) REVERT: E 417 SER cc_start: 0.8778 (t) cc_final: 0.8232 (p) outliers start: 35 outliers final: 26 residues processed: 186 average time/residue: 0.3263 time to fit residues: 97.2718 Evaluate side-chains 172 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 625 MET Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain E residue 75 TYR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 413 ASP Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 464 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 211 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 0.3980 chunk 222 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22264 Z= 0.204 Angle : 0.512 12.008 30400 Z= 0.268 Chirality : 0.037 0.158 3508 Planarity : 0.003 0.049 3607 Dihedral : 17.292 87.613 3716 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.67 % Allowed : 13.53 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.18), residues: 2478 helix: 1.75 (0.14), residues: 1455 sheet: -0.98 (0.32), residues: 249 loop : -0.14 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 276 HIS 0.004 0.001 HIS G 284 PHE 0.012 0.001 PHE C 459 TYR 0.023 0.001 TYR C 255 ARG 0.005 0.000 ARG F 231 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 157 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9232 (tpp) cc_final: 0.8963 (mmm) REVERT: B 391 LYS cc_start: 0.8917 (tptt) cc_final: 0.8263 (tptt) REVERT: B 395 ASP cc_start: 0.8294 (m-30) cc_final: 0.7671 (m-30) REVERT: B 540 TYR cc_start: 0.7678 (t80) cc_final: 0.7314 (t80) REVERT: B 584 HIS cc_start: 0.8101 (m90) cc_final: 0.7614 (m-70) REVERT: C 443 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8298 (tp30) REVERT: C 446 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8298 (tp30) REVERT: D 253 ARG cc_start: 0.8215 (tpt90) cc_final: 0.7959 (tpt90) REVERT: D 347 GLU cc_start: 0.9097 (mp0) cc_final: 0.8606 (mp0) REVERT: D 426 MET cc_start: 0.8703 (mmm) cc_final: 0.8237 (mmm) REVERT: E 1 MET cc_start: 0.8194 (tmm) cc_final: 0.7926 (tmm) REVERT: E 254 CYS cc_start: 0.8335 (m) cc_final: 0.7860 (t) REVERT: E 417 SER cc_start: 0.8750 (t) cc_final: 0.8201 (p) REVERT: G 385 ARG cc_start: 0.8378 (mtp85) cc_final: 0.7792 (mmp80) REVERT: G 621 MET cc_start: 0.7845 (mtt) cc_final: 0.7470 (mtt) outliers start: 37 outliers final: 29 residues processed: 186 average time/residue: 0.3340 time to fit residues: 99.6229 Evaluate side-chains 173 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 144 time to evaluate : 2.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 625 MET Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain E residue 75 TYR Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain G residue 413 ASP Chi-restraints excluded: chain G residue 464 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 0.0970 chunk 222 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 247 optimal weight: 5.9990 chunk 205 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 20 optimal weight: 0.0050 chunk 81 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 overall best weight: 2.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22264 Z= 0.228 Angle : 0.518 13.158 30400 Z= 0.271 Chirality : 0.038 0.166 3508 Planarity : 0.003 0.047 3607 Dihedral : 17.149 83.135 3716 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.80 % Allowed : 14.25 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.18), residues: 2478 helix: 1.86 (0.14), residues: 1460 sheet: -0.77 (0.34), residues: 236 loop : -0.08 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 276 HIS 0.005 0.001 HIS E 278 PHE 0.032 0.001 PHE B 611 TYR 0.027 0.001 TYR B 496 ARG 0.005 0.000 ARG F 231 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 150 time to evaluate : 2.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9229 (tpp) cc_final: 0.8960 (mmm) REVERT: B 391 LYS cc_start: 0.8914 (tptt) cc_final: 0.8226 (tptt) REVERT: B 395 ASP cc_start: 0.8289 (m-30) cc_final: 0.7644 (m-30) REVERT: B 417 MET cc_start: 0.8662 (tmm) cc_final: 0.8289 (tmm) REVERT: B 519 MET cc_start: 0.8634 (tmm) cc_final: 0.8397 (tmm) REVERT: B 540 TYR cc_start: 0.7665 (t80) cc_final: 0.7310 (t80) REVERT: B 584 HIS cc_start: 0.8195 (m90) cc_final: 0.7720 (m-70) REVERT: C 185 MET cc_start: 0.8666 (mmm) cc_final: 0.8413 (mmm) REVERT: C 443 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8370 (tp30) REVERT: C 446 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8303 (tp30) REVERT: D 253 ARG cc_start: 0.8326 (tpt90) cc_final: 0.8056 (tpt90) REVERT: D 347 GLU cc_start: 0.9092 (mp0) cc_final: 0.8590 (mp0) REVERT: D 426 MET cc_start: 0.8701 (mmm) cc_final: 0.8197 (mmm) REVERT: E 1 MET cc_start: 0.8203 (tmm) cc_final: 0.7967 (tmm) REVERT: E 254 CYS cc_start: 0.8347 (m) cc_final: 0.7876 (t) REVERT: E 417 SER cc_start: 0.8798 (t) cc_final: 0.8251 (p) REVERT: G 621 MET cc_start: 0.7886 (mtt) cc_final: 0.7611 (mtt) outliers start: 40 outliers final: 32 residues processed: 180 average time/residue: 0.3398 time to fit residues: 96.9970 Evaluate side-chains 171 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 139 time to evaluate : 3.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 625 MET Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain E residue 75 TYR Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain G residue 413 ASP Chi-restraints excluded: chain G residue 464 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 246 optimal weight: 9.9990 chunk 154 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 HIS ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 399 HIS ** E 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 22264 Z= 0.474 Angle : 0.662 12.666 30400 Z= 0.338 Chirality : 0.042 0.157 3508 Planarity : 0.004 0.051 3607 Dihedral : 17.329 80.223 3716 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.12 % Allowed : 14.34 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.18), residues: 2478 helix: 1.60 (0.14), residues: 1487 sheet: -0.83 (0.34), residues: 235 loop : -0.17 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 664 HIS 0.006 0.001 HIS E 278 PHE 0.022 0.002 PHE B 611 TYR 0.015 0.002 TYR C 384 ARG 0.005 0.000 ARG D 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 136 time to evaluate : 2.406 Fit side-chains REVERT: B 391 LYS cc_start: 0.8909 (tptt) cc_final: 0.8214 (tptt) REVERT: B 395 ASP cc_start: 0.8218 (m-30) cc_final: 0.7480 (m-30) REVERT: B 519 MET cc_start: 0.8645 (tmm) cc_final: 0.8371 (tmm) REVERT: B 540 TYR cc_start: 0.7733 (t80) cc_final: 0.7277 (t80) REVERT: B 584 HIS cc_start: 0.8391 (m90) cc_final: 0.7931 (m170) REVERT: C 443 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8383 (tp30) REVERT: C 446 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8326 (tp30) REVERT: D 253 ARG cc_start: 0.8500 (tpt90) cc_final: 0.8271 (tpt90) REVERT: D 347 GLU cc_start: 0.9091 (mp0) cc_final: 0.8600 (mp0) REVERT: D 426 MET cc_start: 0.8661 (mmm) cc_final: 0.8093 (mmm) REVERT: E 417 SER cc_start: 0.8858 (t) cc_final: 0.8252 (p) REVERT: A 622 ASN cc_start: 0.9221 (t0) cc_final: 0.8704 (t0) REVERT: G 385 ARG cc_start: 0.8311 (mtp85) cc_final: 0.7902 (mtp85) outliers start: 47 outliers final: 33 residues processed: 171 average time/residue: 0.3464 time to fit residues: 94.4470 Evaluate side-chains 162 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 129 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 503 ASP Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 625 MET Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain G residue 413 ASP Chi-restraints excluded: chain G residue 464 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 0.0060 chunk 98 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 193 optimal weight: 0.9990 overall best weight: 1.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 GLN ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22264 Z= 0.154 Angle : 0.524 13.469 30400 Z= 0.270 Chirality : 0.037 0.155 3508 Planarity : 0.003 0.048 3607 Dihedral : 17.146 79.811 3716 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.04 % Allowed : 16.23 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.18), residues: 2478 helix: 1.93 (0.14), residues: 1462 sheet: -0.64 (0.34), residues: 232 loop : 0.00 (0.24), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 276 HIS 0.005 0.000 HIS G 284 PHE 0.032 0.001 PHE B 611 TYR 0.019 0.001 TYR C 384 ARG 0.006 0.000 ARG F 231 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 152 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9262 (tpp) cc_final: 0.9005 (mmm) REVERT: B 391 LYS cc_start: 0.8940 (tptt) cc_final: 0.8171 (tptt) REVERT: B 395 ASP cc_start: 0.8262 (m-30) cc_final: 0.7282 (m-30) REVERT: B 417 MET cc_start: 0.8641 (tmm) cc_final: 0.8305 (tmm) REVERT: B 519 MET cc_start: 0.8628 (tmm) cc_final: 0.8354 (tmm) REVERT: B 540 TYR cc_start: 0.7746 (t80) cc_final: 0.7335 (t80) REVERT: B 584 HIS cc_start: 0.8344 (m90) cc_final: 0.7833 (m170) REVERT: C 145 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8041 (mp0) REVERT: C 374 ARG cc_start: 0.8269 (ttm170) cc_final: 0.7768 (mmp80) REVERT: C 443 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8300 (tp30) REVERT: C 446 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8272 (tp30) REVERT: D 253 ARG cc_start: 0.8425 (tpt90) cc_final: 0.8175 (tpt90) REVERT: D 347 GLU cc_start: 0.9051 (mp0) cc_final: 0.8576 (mp0) REVERT: D 426 MET cc_start: 0.8701 (mmm) cc_final: 0.8200 (mmm) REVERT: E 1 MET cc_start: 0.8223 (tmm) cc_final: 0.7967 (tmm) REVERT: E 254 CYS cc_start: 0.8339 (m) cc_final: 0.7871 (t) REVERT: E 417 SER cc_start: 0.8770 (t) cc_final: 0.8306 (m) REVERT: A 685 GLU cc_start: 0.8415 (mp0) cc_final: 0.7099 (mp0) REVERT: G 621 MET cc_start: 0.7816 (mtt) cc_final: 0.7428 (mtt) outliers start: 23 outliers final: 19 residues processed: 169 average time/residue: 0.3409 time to fit residues: 90.7855 Evaluate side-chains 162 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain G residue 413 ASP Chi-restraints excluded: chain G residue 464 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 3.9990 chunk 236 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 180 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22264 Z= 0.195 Angle : 0.534 13.650 30400 Z= 0.274 Chirality : 0.037 0.163 3508 Planarity : 0.003 0.047 3607 Dihedral : 17.054 80.678 3716 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.26 % Allowed : 15.92 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.18), residues: 2478 helix: 1.95 (0.14), residues: 1466 sheet: -0.56 (0.34), residues: 231 loop : 0.02 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 276 HIS 0.008 0.001 HIS E 278 PHE 0.026 0.001 PHE B 611 TYR 0.017 0.001 TYR C 384 ARG 0.005 0.000 ARG F 231 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 150 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9271 (tpp) cc_final: 0.9009 (mmm) REVERT: B 391 LYS cc_start: 0.8912 (tptt) cc_final: 0.8175 (tptt) REVERT: B 395 ASP cc_start: 0.8237 (m-30) cc_final: 0.7345 (m-30) REVERT: B 417 MET cc_start: 0.8635 (tmm) cc_final: 0.8278 (tmm) REVERT: B 519 MET cc_start: 0.8650 (tmm) cc_final: 0.8363 (tmm) REVERT: B 540 TYR cc_start: 0.7773 (t80) cc_final: 0.7417 (t80) REVERT: B 584 HIS cc_start: 0.8347 (m90) cc_final: 0.7814 (m170) REVERT: C 145 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8053 (mp0) REVERT: C 374 ARG cc_start: 0.8286 (ttm170) cc_final: 0.7798 (mmp80) REVERT: C 443 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8330 (tp30) REVERT: C 446 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8297 (tp30) REVERT: C 699 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7378 (tp30) REVERT: D 253 ARG cc_start: 0.8466 (tpt90) cc_final: 0.8222 (tpt90) REVERT: D 347 GLU cc_start: 0.9058 (mp0) cc_final: 0.8601 (mp0) REVERT: D 426 MET cc_start: 0.8715 (mmm) cc_final: 0.8212 (mmm) REVERT: E 254 CYS cc_start: 0.8244 (m) cc_final: 0.7823 (t) REVERT: G 621 MET cc_start: 0.7876 (mtt) cc_final: 0.7497 (mtt) outliers start: 28 outliers final: 25 residues processed: 170 average time/residue: 0.3371 time to fit residues: 90.0650 Evaluate side-chains 169 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 144 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 625 MET Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 413 ASP Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain G residue 600 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 6.9990 chunk 148 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 169 optimal weight: 0.0570 chunk 255 optimal weight: 8.9990 chunk 234 optimal weight: 0.2980 chunk 203 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22264 Z= 0.149 Angle : 0.517 13.884 30400 Z= 0.266 Chirality : 0.037 0.154 3508 Planarity : 0.003 0.048 3607 Dihedral : 16.931 81.006 3716 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.22 % Allowed : 16.05 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.18), residues: 2478 helix: 2.01 (0.14), residues: 1468 sheet: -0.46 (0.34), residues: 231 loop : 0.07 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 276 HIS 0.006 0.000 HIS E 278 PHE 0.026 0.001 PHE B 611 TYR 0.018 0.001 TYR B 496 ARG 0.008 0.000 ARG A 675 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 148 time to evaluate : 2.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9270 (tpp) cc_final: 0.9004 (mmm) REVERT: B 391 LYS cc_start: 0.8895 (tptt) cc_final: 0.8206 (tptt) REVERT: B 395 ASP cc_start: 0.8197 (m-30) cc_final: 0.7418 (m-30) REVERT: B 417 MET cc_start: 0.8626 (tmm) cc_final: 0.8252 (tmm) REVERT: B 519 MET cc_start: 0.8649 (tmm) cc_final: 0.8359 (tmm) REVERT: B 540 TYR cc_start: 0.7760 (t80) cc_final: 0.7441 (t80) REVERT: B 584 HIS cc_start: 0.8311 (m90) cc_final: 0.7755 (m170) REVERT: C 145 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8054 (mp0) REVERT: C 374 ARG cc_start: 0.8297 (ttm170) cc_final: 0.7795 (mmp80) REVERT: C 443 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8323 (tp30) REVERT: C 446 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8332 (tp30) REVERT: D 253 ARG cc_start: 0.8416 (tpt90) cc_final: 0.8201 (tpt90) REVERT: D 347 GLU cc_start: 0.9049 (mp0) cc_final: 0.8583 (mp0) REVERT: D 426 MET cc_start: 0.8745 (mmm) cc_final: 0.8211 (mmm) REVERT: E 1 MET cc_start: 0.8139 (tmm) cc_final: 0.7723 (tmm) REVERT: E 254 CYS cc_start: 0.8194 (m) cc_final: 0.7836 (t) REVERT: G 621 MET cc_start: 0.7866 (mtt) cc_final: 0.7503 (mtt) outliers start: 27 outliers final: 25 residues processed: 170 average time/residue: 0.3484 time to fit residues: 93.5428 Evaluate side-chains 163 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 138 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 625 MET Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 413 ASP Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 464 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 203 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 208 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 178 optimal weight: 0.2980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.086591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.061834 restraints weight = 57428.206| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.19 r_work: 0.2933 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22264 Z= 0.161 Angle : 0.521 14.016 30400 Z= 0.267 Chirality : 0.037 0.175 3508 Planarity : 0.003 0.049 3607 Dihedral : 16.873 81.329 3716 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.26 % Allowed : 16.14 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.18), residues: 2478 helix: 2.02 (0.14), residues: 1469 sheet: -0.33 (0.35), residues: 227 loop : 0.09 (0.24), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 276 HIS 0.005 0.000 HIS E 278 PHE 0.024 0.001 PHE B 611 TYR 0.017 0.001 TYR C 384 ARG 0.009 0.000 ARG A 675 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4057.76 seconds wall clock time: 75 minutes 8.91 seconds (4508.91 seconds total)