Starting phenix.real_space_refine on Fri Feb 16 18:22:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpo_22417/02_2024/7jpo_22417_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpo_22417/02_2024/7jpo_22417.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/7jpo_22417/02_2024/7jpo_22417.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpo_22417/02_2024/7jpo_22417.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpo_22417/02_2024/7jpo_22417_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpo_22417/02_2024/7jpo_22417_neut_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= 0.001 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: 7 Type Number sf(0) Gaussians K 1 8.98 5 P 9 5.49 5 Mg 3 5.21 5 S 82 5.16 5 C 10306 2.51 5 N 2724 2.21 5 O 2962 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 502": "OE1" <-> "OE2" Residue "A TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 567": "OE1" <-> "OE2" Residue "A ASP 623": "OD1" <-> "OD2" Residue "A ARG 646": "NH1" <-> "NH2" Residue "A ARG 721": "NH1" <-> "NH2" Residue "A ASP 724": "OD1" <-> "OD2" Residue "A PHE 735": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 852": "OD1" <-> "OD2" Residue "B PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 295": "OE1" <-> "OE2" Residue "B ASP 321": "OD1" <-> "OD2" Residue "B GLU 358": "OE1" <-> "OE2" Residue "B GLU 456": "OE1" <-> "OE2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "C PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 45": "OE1" <-> "OE2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C ASP 115": "OD1" <-> "OD2" Residue "C PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 123": "OE1" <-> "OE2" Residue "C ASP 182": "OD1" <-> "OD2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 377": "OE1" <-> "OE2" Residue "C TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 449": "OD1" <-> "OD2" Residue "C GLU 452": "OE1" <-> "OE2" Residue "C GLU 549": "OE1" <-> "OE2" Residue "C GLU 553": "OE1" <-> "OE2" Residue "C GLU 565": "OE1" <-> "OE2" Residue "C PHE 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 660": "OE1" <-> "OE2" Residue "C GLU 674": "OE1" <-> "OE2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D GLU 86": "OE1" <-> "OE2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D GLU 121": "OE1" <-> "OE2" Residue "D PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 203": "OE1" <-> "OE2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "D PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "D GLU 264": "OE1" <-> "OE2" Residue "D GLU 304": "OE1" <-> "OE2" Residue "D GLU 325": "OE1" <-> "OE2" Residue "D GLU 341": "OE1" <-> "OE2" Residue "D GLU 383": "OE1" <-> "OE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E GLU 93": "OE1" <-> "OE2" Residue "E ASP 132": "OD1" <-> "OD2" Residue "E PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "E ARG 248": "NH1" <-> "NH2" Residue "E ARG 251": "NH1" <-> "NH2" Residue "E ARG 271": "NH1" <-> "NH2" Residue "E ASP 284": "OD1" <-> "OD2" Residue "E TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 414": "OD1" <-> "OD2" Residue "E PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16087 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2795 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 12, 'TRANS': 339} Chain breaks: 3 Chain: "B" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1726 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 4, 'TRANS': 204} Chain breaks: 1 Chain: "C" Number of atoms: 4863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4863 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 24, 'TRANS': 569} Chain breaks: 7 Chain: "D" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3305 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 13, 'TRANS': 392} Chain breaks: 1 Chain: "E" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3301 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 19, 'TRANS': 385} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 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: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} 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} Time building chain proxies: 9.09, per 1000 atoms: 0.57 Number of scatterers: 16087 At special positions: 0 Unit cell: (90.95, 133.75, 160.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 1 19.00 S 82 16.00 P 9 15.00 Mg 3 11.99 O 2962 8.00 N 2724 7.00 C 10306 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: 6.40 Conformation dependent library (CDL) restraints added in 2.8 seconds 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3822 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 98 helices and 8 sheets defined 53.8% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 508 through 522 removed outlier: 3.860A pdb=" N LYS A 521 " --> pdb=" O PHE A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 556 Processing helix chain 'A' and resid 576 through 587 removed outlier: 3.664A pdb=" N VAL A 579 " --> pdb=" O PRO A 576 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL A 581 " --> pdb=" O GLN A 578 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE A 583 " --> pdb=" O TYR A 580 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU A 584 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 604 Processing helix chain 'A' and resid 622 through 625 Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 658 through 660 No H-bonds generated for 'chain 'A' and resid 658 through 660' Processing helix chain 'A' and resid 683 through 693 Processing helix chain 'A' and resid 702 through 715 Processing helix chain 'A' and resid 719 through 735 Processing helix chain 'A' and resid 748 through 759 removed outlier: 3.565A pdb=" N ASP A 756 " --> pdb=" O MET A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 768 Processing helix chain 'A' and resid 772 through 788 Processing helix chain 'A' and resid 795 through 809 removed outlier: 3.952A pdb=" N ALA A 804 " --> pdb=" O SER A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 828 removed outlier: 3.934A pdb=" N ALA A 821 " --> pdb=" O SER A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 858 Processing helix chain 'B' and resid 240 through 247 Processing helix chain 'B' and resid 271 through 275 removed outlier: 4.023A pdb=" N LEU B 275 " --> pdb=" O THR B 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 271 through 275' Processing helix chain 'B' and resid 284 through 288 Processing helix chain 'B' and resid 296 through 306 removed outlier: 4.010A pdb=" N HIS B 299 " --> pdb=" O LYS B 296 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU B 305 " --> pdb=" O MET B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 329 Processing helix chain 'B' and resid 348 through 358 Processing helix chain 'B' and resid 369 through 382 Processing helix chain 'B' and resid 403 through 413 Processing helix chain 'B' and resid 429 through 432 Processing helix chain 'C' and resid 39 through 65 Processing helix chain 'C' and resid 67 through 86 removed outlier: 4.237A pdb=" N GLY C 83 " --> pdb=" O LYS C 79 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE C 84 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 128 removed outlier: 4.479A pdb=" N ASP C 115 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LEU C 116 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA C 124 " --> pdb=" O SER C 120 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 140 No H-bonds generated for 'chain 'C' and resid 138 through 140' Processing helix chain 'C' and resid 144 through 157 removed outlier: 3.579A pdb=" N SER C 153 " --> pdb=" O GLN C 149 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN C 154 " --> pdb=" O LYS C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 192 Processing helix chain 'C' and resid 227 through 239 removed outlier: 3.860A pdb=" N GLN C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 262 removed outlier: 3.640A pdb=" N LEU C 262 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 270 removed outlier: 5.115A pdb=" N LEU C 270 " --> pdb=" O ALA C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 292 Processing helix chain 'C' and resid 304 through 315 Processing helix chain 'C' and resid 321 through 338 Processing helix chain 'C' and resid 342 through 344 No H-bonds generated for 'chain 'C' and resid 342 through 344' Processing helix chain 'C' and resid 348 through 356 Processing helix chain 'C' and resid 360 through 367 removed outlier: 3.671A pdb=" N GLU C 364 " --> pdb=" O ASN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 377 Processing helix chain 'C' and resid 381 through 389 removed outlier: 3.887A pdb=" N VAL C 385 " --> pdb=" O SER C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 425 removed outlier: 3.704A pdb=" N GLU C 403 " --> pdb=" O GLN C 399 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS C 421 " --> pdb=" O ARG C 417 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE C 422 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 452 through 460 removed outlier: 3.518A pdb=" N VAL C 456 " --> pdb=" O GLU C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 481 Processing helix chain 'C' and resid 488 through 500 removed outlier: 3.814A pdb=" N LYS C 492 " --> pdb=" O GLY C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 565 Processing helix chain 'C' and resid 570 through 572 No H-bonds generated for 'chain 'C' and resid 570 through 572' Processing helix chain 'C' and resid 576 through 578 No H-bonds generated for 'chain 'C' and resid 576 through 578' Processing helix chain 'C' and resid 584 through 591 Processing helix chain 'C' and resid 595 through 604 Processing helix chain 'C' and resid 628 through 636 removed outlier: 3.711A pdb=" N LYS C 634 " --> pdb=" O CYS C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 659 Processing helix chain 'C' and resid 676 through 689 removed outlier: 3.854A pdb=" N LEU C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 28 Processing helix chain 'D' and resid 41 through 56 Processing helix chain 'D' and resid 73 through 86 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 107 through 117 Processing helix chain 'D' and resid 121 through 124 No H-bonds generated for 'chain 'D' and resid 121 through 124' Processing helix chain 'D' and resid 132 through 140 Processing helix chain 'D' and resid 161 through 164 No H-bonds generated for 'chain 'D' and resid 161 through 164' Processing helix chain 'D' and resid 171 through 182 removed outlier: 3.717A pdb=" N ILE D 179 " --> pdb=" O ASN D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 201 No H-bonds generated for 'chain 'D' and resid 198 through 201' Processing helix chain 'D' and resid 204 through 209 Processing helix chain 'D' and resid 223 through 233 Processing helix chain 'D' and resid 243 through 258 removed outlier: 3.809A pdb=" N GLU D 258 " --> pdb=" O GLN D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 272 removed outlier: 3.784A pdb=" N VAL D 265 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 289 removed outlier: 4.322A pdb=" N ARG D 289 " --> pdb=" O LEU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 309 Processing helix chain 'D' and resid 313 through 320 removed outlier: 3.684A pdb=" N GLY D 320 " --> pdb=" O ASN D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 338 Processing helix chain 'D' and resid 346 through 359 removed outlier: 3.831A pdb=" N ARG D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 381 Processing helix chain 'D' and resid 408 through 416 Processing helix chain 'D' and resid 423 through 430 Processing helix chain 'E' and resid 13 through 22 Processing helix chain 'E' and resid 43 through 53 removed outlier: 3.575A pdb=" N THR E 47 " --> pdb=" O LYS E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 84 Processing helix chain 'E' and resid 99 through 110 Processing helix chain 'E' and resid 127 through 129 No H-bonds generated for 'chain 'E' and resid 127 through 129' Processing helix chain 'E' and resid 135 through 142 Proline residue: E 139 - end of helix Processing helix chain 'E' and resid 144 through 148 Processing helix chain 'E' and resid 162 through 164 No H-bonds generated for 'chain 'E' and resid 162 through 164' Processing helix chain 'E' and resid 184 through 191 Processing helix chain 'E' and resid 201 through 215 Processing helix chain 'E' and resid 222 through 236 removed outlier: 3.594A pdb=" N PHE E 233 " --> pdb=" O ALA E 229 " (cutoff:3.500A) Proline residue: E 234 - end of helix Processing helix chain 'E' and resid 238 through 242 Processing helix chain 'E' and resid 250 through 267 Proline residue: E 259 - end of helix removed outlier: 3.500A pdb=" N MET E 265 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLN E 266 " --> pdb=" O LYS E 262 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR E 267 " --> pdb=" O LYS E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 283 Processing helix chain 'E' and resid 304 through 317 Processing helix chain 'E' and resid 321 through 327 removed outlier: 4.517A pdb=" N LYS E 325 " --> pdb=" O ARG E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 369 Processing helix chain 'E' and resid 378 through 389 removed outlier: 3.791A pdb=" N VAL E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR E 389 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 422 Processing helix chain 'E' and resid 428 through 431 No H-bonds generated for 'chain 'E' and resid 428 through 431' Processing sheet with id= A, first strand: chain 'A' and resid 674 through 678 Processing sheet with id= B, first strand: chain 'A' and resid 792 through 794 Processing sheet with id= C, first strand: chain 'B' and resid 443 through 447 removed outlier: 6.701A pdb=" N ASN B 310 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N TYR B 446 " --> pdb=" O ASN B 310 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL B 312 " --> pdb=" O TYR B 446 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 311 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU B 388 " --> pdb=" O TYR B 419 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N ILE B 421 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU B 390 " --> pdb=" O ILE B 421 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N SER B 423 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ILE B 392 " --> pdb=" O SER B 423 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE B 335 " --> pdb=" O PHE B 389 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N LEU B 391 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL B 337 " --> pdb=" O LEU B 391 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 271 through 277 removed outlier: 6.507A pdb=" N ILE C 100 " --> pdb=" O CYS C 272 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N GLU C 274 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR C 102 " --> pdb=" O GLU C 274 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N PHE C 276 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA C 104 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL C 215 " --> pdb=" O ILE C 247 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE C 249 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL C 217 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N GLY C 251 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU C 219 " --> pdb=" O GLY C 251 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 214 through 216 removed outlier: 8.030A pdb=" N ILE D 215 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU D 64 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL D 154 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ILE D 190 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N PHE D 156 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N LEU D 192 " --> pdb=" O PHE D 156 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU D 158 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 385 through 387 Processing sheet with id= G, first strand: chain 'E' and resid 175 through 178 removed outlier: 8.159A pdb=" N ILE E 33 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL E 154 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ILE E 35 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N PHE E 156 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL E 120 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LEU E 155 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE E 122 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LEU E 157 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU E 124 " --> pdb=" O LEU E 157 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 393 through 395 680 hydrogen bonds defined for protein. 1974 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.86 Time building geometry restraints manager: 6.87 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: 4137 1.33 - 1.46: 3174 1.46 - 1.58: 8968 1.58 - 1.70: 15 1.70 - 1.82: 125 Bond restraints: 16419 Sorted by residual: bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.23e+01 bond pdb=" C4 ATP A 901 " pdb=" C5 ATP A 901 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.97e+01 bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.89e+01 bond pdb=" C5 ATP A 901 " pdb=" C6 ATP A 901 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.52e+01 bond pdb=" C5 ATP E 501 " pdb=" C6 ATP E 501 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.48e+01 ... (remaining 16414 not shown) Histogram of bond angle deviations from ideal: 98.07 - 105.65: 298 105.65 - 113.23: 8930 113.23 - 120.81: 7969 120.81 - 128.40: 4896 128.40 - 135.98: 137 Bond angle restraints: 22230 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 139.87 119.33 20.54 1.00e+00 1.00e+00 4.22e+02 angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 121.72 18.15 1.00e+00 1.00e+00 3.29e+02 angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 123.09 16.78 1.00e+00 1.00e+00 2.81e+02 angle pdb=" PA ATP E 501 " pdb=" O3A ATP E 501 " pdb=" PB ATP E 501 " ideal model delta sigma weight residual 136.83 122.38 14.45 1.00e+00 1.00e+00 2.09e+02 angle pdb=" PA ATP D 901 " pdb=" O3A ATP D 901 " pdb=" PB ATP D 901 " ideal model delta sigma weight residual 136.83 123.11 13.72 1.00e+00 1.00e+00 1.88e+02 ... (remaining 22225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8831 17.98 - 35.96: 920 35.96 - 53.94: 173 53.94 - 71.92: 48 71.92 - 89.90: 29 Dihedral angle restraints: 10001 sinusoidal: 4163 harmonic: 5838 Sorted by residual: dihedral pdb=" CA GLN D 31 " pdb=" C GLN D 31 " pdb=" N SER D 32 " pdb=" CA SER D 32 " ideal model delta harmonic sigma weight residual -180.00 -156.71 -23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA ARG D 359 " pdb=" C ARG D 359 " pdb=" N LYS D 360 " pdb=" CA LYS D 360 " ideal model delta harmonic sigma weight residual -180.00 -157.35 -22.65 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA VAL D 364 " pdb=" C VAL D 364 " pdb=" N TYR D 365 " pdb=" CA TYR D 365 " ideal model delta harmonic sigma weight residual -180.00 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 9998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2109 0.073 - 0.146: 369 0.146 - 0.219: 47 0.219 - 0.292: 9 0.292 - 0.365: 4 Chirality restraints: 2538 Sorted by residual: chirality pdb=" CB THR B 449 " pdb=" CA THR B 449 " pdb=" OG1 THR B 449 " pdb=" CG2 THR B 449 " both_signs ideal model delta sigma weight residual False 2.55 2.19 0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CB ILE C 435 " pdb=" CA ILE C 435 " pdb=" CG1 ILE C 435 " pdb=" CG2 ILE C 435 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CB ILE C 643 " pdb=" CA ILE C 643 " pdb=" CG1 ILE C 643 " pdb=" CG2 ILE C 643 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.48e+00 ... (remaining 2535 not shown) Planarity restraints: 2798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 639 " -0.046 2.00e-02 2.50e+03 4.75e-02 5.65e+01 pdb=" CG TRP A 639 " 0.127 2.00e-02 2.50e+03 pdb=" CD1 TRP A 639 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TRP A 639 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A 639 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 639 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 639 " -0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 639 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 639 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 639 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 238 " 0.053 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO E 239 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO E 239 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 239 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 448 " 0.015 2.00e-02 2.50e+03 1.82e-02 8.28e+00 pdb=" CG TRP C 448 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP C 448 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP C 448 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 448 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP C 448 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 448 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 448 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 448 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP C 448 " -0.000 2.00e-02 2.50e+03 ... (remaining 2795 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.69: 195 2.69 - 3.30: 17228 3.30 - 3.91: 30011 3.91 - 4.53: 40705 4.53 - 5.14: 63771 Nonbonded interactions: 151910 Sorted by model distance: nonbonded pdb=" OG1 THR E 44 " pdb="MG MG E 502 " model vdw 2.073 2.170 nonbonded pdb=" O3G ATP E 501 " pdb="MG MG E 502 " model vdw 2.090 2.170 nonbonded pdb=" O1B ATP A 901 " pdb="MG MG A 902 " model vdw 2.091 2.170 nonbonded pdb=" OG1 THR A 541 " pdb="MG MG A 902 " model vdw 2.123 2.170 nonbonded pdb=" O3B ATP D 901 " pdb="MG MG D 902 " model vdw 2.124 2.170 ... (remaining 151905 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.820 Check model and map are aligned: 0.320 Set scattering table: 0.170 Process input model: 46.070 Find NCS groups from input model: 0.540 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 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 : 0.007 0.081 16419 Z= 0.423 Angle : 1.085 20.536 22230 Z= 0.643 Chirality : 0.059 0.365 2538 Planarity : 0.007 0.079 2798 Dihedral : 15.981 89.895 6179 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.16), residues: 1928 helix: -1.10 (0.13), residues: 1105 sheet: -0.33 (0.35), residues: 187 loop : -1.74 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.127 0.005 TRP A 639 HIS 0.019 0.002 HIS C 81 PHE 0.046 0.004 PHE D 132 TYR 0.039 0.003 TYR C 609 ARG 0.028 0.002 ARG C 353 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 1.970 Fit side-chains revert: symmetry clash REVERT: A 786 ARG cc_start: 0.7124 (mtt180) cc_final: 0.6896 (mpt-90) REVERT: B 418 ILE cc_start: 0.7203 (tt) cc_final: 0.6987 (mt) REVERT: C 705 ARG cc_start: 0.5936 (mmp80) cc_final: 0.5280 (mmp-170) REVERT: D 247 GLU cc_start: 0.6905 (tm-30) cc_final: 0.6568 (tm-30) REVERT: E 133 MET cc_start: 0.8204 (mtp) cc_final: 0.7691 (mtt) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.3125 time to fit residues: 112.5094 Evaluate side-chains 180 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 1.9990 chunk 147 optimal weight: 0.0040 chunk 81 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 58 optimal weight: 0.2980 chunk 92 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 688 GLN A 825 HIS C 458 GLN C 624 ASN D 46 HIS D 362 HIS E 100 ASN E 195 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16419 Z= 0.171 Angle : 0.523 6.133 22230 Z= 0.273 Chirality : 0.039 0.162 2538 Planarity : 0.004 0.052 2798 Dihedral : 8.733 81.473 2208 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.72 % Allowed : 6.16 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.18), residues: 1928 helix: 0.16 (0.15), residues: 1121 sheet: -0.10 (0.36), residues: 187 loop : -1.35 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 639 HIS 0.005 0.001 HIS C 81 PHE 0.021 0.001 PHE D 230 TYR 0.016 0.001 TYR A 683 ARG 0.006 0.001 ARG C 353 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 187 time to evaluate : 1.947 Fit side-chains REVERT: A 571 MET cc_start: 0.8451 (tpp) cc_final: 0.8226 (mmt) REVERT: A 808 MET cc_start: 0.7419 (mpp) cc_final: 0.7063 (mpp) REVERT: B 418 ILE cc_start: 0.7364 (tt) cc_final: 0.7053 (mt) REVERT: C 705 ARG cc_start: 0.5892 (mmp80) cc_final: 0.5266 (mmp-170) REVERT: D 247 GLU cc_start: 0.7005 (tm-30) cc_final: 0.6687 (tm-30) REVERT: D 284 MET cc_start: 0.7798 (tpt) cc_final: 0.7056 (tpt) REVERT: E 133 MET cc_start: 0.8213 (mtp) cc_final: 0.7842 (mtt) outliers start: 13 outliers final: 10 residues processed: 194 average time/residue: 0.2917 time to fit residues: 83.1047 Evaluate side-chains 175 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 165 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 6 ASN Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 360 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 146 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 190 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 175 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 654 ASN C 335 HIS ** C 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 GLN E 27 HIS E 195 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16419 Z= 0.203 Angle : 0.511 6.811 22230 Z= 0.263 Chirality : 0.039 0.167 2538 Planarity : 0.004 0.041 2798 Dihedral : 8.619 88.122 2208 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.00 % Allowed : 9.21 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.19), residues: 1928 helix: 0.64 (0.16), residues: 1124 sheet: 0.02 (0.36), residues: 187 loop : -1.23 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 639 HIS 0.007 0.001 HIS B 336 PHE 0.021 0.002 PHE B 441 TYR 0.021 0.001 TYR B 454 ARG 0.006 0.001 ARG E 255 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 180 time to evaluate : 1.930 Fit side-chains revert: symmetry clash REVERT: A 571 MET cc_start: 0.8482 (tpp) cc_final: 0.8206 (mmt) REVERT: A 808 MET cc_start: 0.7433 (mpp) cc_final: 0.7170 (mpp) REVERT: B 418 ILE cc_start: 0.7400 (tt) cc_final: 0.7121 (mt) REVERT: C 705 ARG cc_start: 0.5815 (mmp80) cc_final: 0.5167 (mmp-170) REVERT: D 247 GLU cc_start: 0.7051 (tm-30) cc_final: 0.6779 (tm-30) REVERT: D 284 MET cc_start: 0.8085 (tpt) cc_final: 0.7421 (tpt) outliers start: 18 outliers final: 13 residues processed: 191 average time/residue: 0.2995 time to fit residues: 83.9781 Evaluate side-chains 176 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 163 time to evaluate : 1.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 6 ASN Chi-restraints excluded: chain E residue 360 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 174 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 84 optimal weight: 0.1980 chunk 118 optimal weight: 0.8980 chunk 177 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 462 ASN C 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16419 Z= 0.195 Angle : 0.496 6.781 22230 Z= 0.255 Chirality : 0.039 0.160 2538 Planarity : 0.003 0.035 2798 Dihedral : 8.420 86.676 2208 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.00 % Allowed : 10.87 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.19), residues: 1928 helix: 0.87 (0.16), residues: 1133 sheet: 0.07 (0.36), residues: 188 loop : -1.21 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 639 HIS 0.006 0.001 HIS B 336 PHE 0.019 0.001 PHE B 441 TYR 0.014 0.001 TYR B 454 ARG 0.004 0.000 ARG E 255 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 178 time to evaluate : 1.792 Fit side-chains revert: symmetry clash REVERT: B 418 ILE cc_start: 0.7416 (tt) cc_final: 0.7185 (mt) REVERT: C 705 ARG cc_start: 0.5805 (mmp80) cc_final: 0.5136 (mmp-170) REVERT: D 247 GLU cc_start: 0.7020 (tm-30) cc_final: 0.6759 (tm-30) outliers start: 18 outliers final: 15 residues processed: 192 average time/residue: 0.2920 time to fit residues: 83.0143 Evaluate side-chains 180 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 165 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 6 ASN Chi-restraints excluded: chain E residue 360 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 156 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 160 optimal weight: 0.0980 chunk 129 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 354 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16419 Z= 0.151 Angle : 0.471 9.187 22230 Z= 0.241 Chirality : 0.038 0.151 2538 Planarity : 0.003 0.032 2798 Dihedral : 8.054 84.677 2208 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.11 % Allowed : 12.20 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.19), residues: 1928 helix: 1.14 (0.16), residues: 1122 sheet: 0.14 (0.37), residues: 188 loop : -1.06 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 639 HIS 0.004 0.001 HIS C 81 PHE 0.021 0.001 PHE E 328 TYR 0.012 0.001 TYR A 565 ARG 0.005 0.000 ARG E 255 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 178 time to evaluate : 2.008 Fit side-chains revert: symmetry clash REVERT: A 571 MET cc_start: 0.8462 (tpp) cc_final: 0.8229 (mmt) REVERT: B 418 ILE cc_start: 0.7386 (tt) cc_final: 0.7168 (mt) REVERT: C 705 ARG cc_start: 0.5830 (mmp80) cc_final: 0.5202 (mmp-170) REVERT: D 247 GLU cc_start: 0.7002 (tm-30) cc_final: 0.6753 (tm-30) outliers start: 20 outliers final: 13 residues processed: 192 average time/residue: 0.3068 time to fit residues: 86.4956 Evaluate side-chains 186 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 173 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 644 ASN Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 60 PHE Chi-restraints excluded: chain E residue 360 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 63 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 46 optimal weight: 0.0770 chunk 187 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 overall best weight: 1.1940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16419 Z= 0.224 Angle : 0.515 9.960 22230 Z= 0.261 Chirality : 0.039 0.157 2538 Planarity : 0.003 0.034 2798 Dihedral : 8.174 89.561 2208 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.83 % Allowed : 12.48 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.19), residues: 1928 helix: 1.07 (0.16), residues: 1126 sheet: 0.12 (0.37), residues: 188 loop : -1.10 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 639 HIS 0.007 0.001 HIS B 336 PHE 0.022 0.002 PHE E 328 TYR 0.013 0.001 TYR B 454 ARG 0.006 0.000 ARG E 255 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 180 time to evaluate : 1.937 Fit side-chains revert: symmetry clash REVERT: A 571 MET cc_start: 0.8493 (tpp) cc_final: 0.8225 (mmt) REVERT: B 418 ILE cc_start: 0.7436 (tt) cc_final: 0.7209 (mt) REVERT: C 705 ARG cc_start: 0.5817 (mmp80) cc_final: 0.5541 (mmp80) outliers start: 33 outliers final: 29 residues processed: 203 average time/residue: 0.3041 time to fit residues: 90.6527 Evaluate side-chains 195 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 166 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 553 GLN Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 644 ASN Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 6 ASN Chi-restraints excluded: chain E residue 60 PHE Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 422 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 180 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16419 Z= 0.302 Angle : 0.575 11.272 22230 Z= 0.291 Chirality : 0.041 0.167 2538 Planarity : 0.004 0.037 2798 Dihedral : 8.427 89.939 2208 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.11 % Allowed : 13.53 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.19), residues: 1928 helix: 0.89 (0.16), residues: 1123 sheet: 0.03 (0.37), residues: 187 loop : -1.21 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 639 HIS 0.009 0.001 HIS B 336 PHE 0.026 0.002 PHE E 328 TYR 0.019 0.002 TYR A 683 ARG 0.006 0.001 ARG E 255 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 178 time to evaluate : 1.908 Fit side-chains revert: symmetry clash REVERT: A 571 MET cc_start: 0.8518 (tpp) cc_final: 0.8247 (mmt) REVERT: B 418 ILE cc_start: 0.7381 (tt) cc_final: 0.7139 (mt) outliers start: 38 outliers final: 33 residues processed: 206 average time/residue: 0.2994 time to fit residues: 90.6351 Evaluate side-chains 194 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 161 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 553 GLN Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain A residue 733 CYS Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 483 CYS Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 644 ASN Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 6 ASN Chi-restraints excluded: chain E residue 60 PHE Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain E residue 427 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 118 optimal weight: 0.3980 chunk 127 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 17 optimal weight: 0.0670 chunk 146 optimal weight: 0.7980 chunk 170 optimal weight: 0.8980 chunk 179 optimal weight: 0.9980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 381 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16419 Z= 0.148 Angle : 0.490 11.012 22230 Z= 0.250 Chirality : 0.038 0.159 2538 Planarity : 0.003 0.033 2798 Dihedral : 7.944 89.388 2208 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.33 % Allowed : 14.31 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.20), residues: 1928 helix: 1.14 (0.16), residues: 1126 sheet: 0.22 (0.37), residues: 188 loop : -1.09 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 639 HIS 0.004 0.001 HIS D 362 PHE 0.027 0.001 PHE E 328 TYR 0.020 0.001 TYR B 454 ARG 0.004 0.000 ARG E 255 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 176 time to evaluate : 1.960 Fit side-chains REVERT: A 571 MET cc_start: 0.8427 (tpp) cc_final: 0.8219 (mmt) REVERT: B 418 ILE cc_start: 0.7283 (tt) cc_final: 0.7043 (mt) outliers start: 24 outliers final: 19 residues processed: 197 average time/residue: 0.2866 time to fit residues: 84.2454 Evaluate side-chains 181 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 162 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 644 ASN Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 60 PHE Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 427 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.5980 chunk 174 optimal weight: 0.6980 chunk 179 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 173 optimal weight: 0.7980 chunk 114 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN D 96 GLN D 381 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 16419 Z= 0.157 Angle : 0.489 11.096 22230 Z= 0.249 Chirality : 0.038 0.161 2538 Planarity : 0.003 0.032 2798 Dihedral : 7.715 88.789 2208 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.39 % Allowed : 14.70 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.20), residues: 1928 helix: 1.23 (0.16), residues: 1127 sheet: 0.31 (0.38), residues: 188 loop : -1.04 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 639 HIS 0.004 0.001 HIS D 362 PHE 0.046 0.001 PHE E 328 TYR 0.023 0.001 TYR B 454 ARG 0.002 0.000 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 176 time to evaluate : 1.963 Fit side-chains REVERT: A 571 MET cc_start: 0.8453 (tpp) cc_final: 0.8243 (mmt) REVERT: B 273 ARG cc_start: 0.7648 (mpt-90) cc_final: 0.7258 (mpt-90) REVERT: B 418 ILE cc_start: 0.7263 (tt) cc_final: 0.7034 (mt) REVERT: C 705 ARG cc_start: 0.5757 (mmp80) cc_final: 0.5117 (mmp-170) outliers start: 25 outliers final: 23 residues processed: 198 average time/residue: 0.2928 time to fit residues: 85.9145 Evaluate side-chains 192 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 169 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 483 CYS Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 644 ASN Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 60 PHE Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 427 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 184 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 193 optimal weight: 0.8980 chunk 177 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 291 ASN B 394 ASN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN D 46 HIS D 96 GLN D 381 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 16419 Z= 0.180 Angle : 0.501 10.486 22230 Z= 0.254 Chirality : 0.038 0.161 2538 Planarity : 0.003 0.030 2798 Dihedral : 7.734 89.946 2208 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.39 % Allowed : 14.70 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.20), residues: 1928 helix: 1.23 (0.16), residues: 1126 sheet: 0.32 (0.38), residues: 188 loop : -1.06 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 639 HIS 0.005 0.001 HIS B 336 PHE 0.041 0.001 PHE E 328 TYR 0.020 0.001 TYR B 454 ARG 0.002 0.000 ARG D 260 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 167 time to evaluate : 1.949 Fit side-chains REVERT: A 571 MET cc_start: 0.8460 (tpp) cc_final: 0.8248 (mmt) REVERT: B 273 ARG cc_start: 0.7648 (mpt-90) cc_final: 0.7241 (mpt-90) REVERT: B 418 ILE cc_start: 0.7272 (tt) cc_final: 0.7054 (mt) REVERT: C 705 ARG cc_start: 0.5761 (mmp80) cc_final: 0.5123 (mmp-170) outliers start: 25 outliers final: 25 residues processed: 189 average time/residue: 0.2869 time to fit residues: 80.8760 Evaluate side-chains 189 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 483 CYS Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 644 ASN Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 60 PHE Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 427 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 154 optimal weight: 0.0000 chunk 64 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 135 optimal weight: 0.3980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.115304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.093901 restraints weight = 26707.534| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.88 r_work: 0.3233 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 16419 Z= 0.141 Angle : 0.487 10.293 22230 Z= 0.246 Chirality : 0.038 0.173 2538 Planarity : 0.003 0.028 2798 Dihedral : 7.521 88.119 2208 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.44 % Allowed : 14.59 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.20), residues: 1928 helix: 1.32 (0.16), residues: 1128 sheet: 0.33 (0.38), residues: 187 loop : -1.01 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 639 HIS 0.017 0.001 HIS B 393 PHE 0.033 0.001 PHE E 328 TYR 0.018 0.001 TYR A 565 ARG 0.005 0.000 ARG E 255 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3335.45 seconds wall clock time: 61 minutes 30.47 seconds (3690.47 seconds total)