Starting phenix.real_space_refine on Sun Feb 18 09:45:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk2_22359/02_2024/7jk2_22359_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk2_22359/02_2024/7jk2_22359.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/7jk2_22359/02_2024/7jk2_22359.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk2_22359/02_2024/7jk2_22359.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk2_22359/02_2024/7jk2_22359_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk2_22359/02_2024/7jk2_22359_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 78 5.49 5 Mg 4 5.21 5 S 110 5.16 5 C 13528 2.51 5 N 3786 2.21 5 O 4113 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 279": "OE1" <-> "OE2" Residue "B GLU 326": "OE1" <-> "OE2" Residue "B GLU 334": "OE1" <-> "OE2" Residue "B PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 419": "OE1" <-> "OE2" Residue "B GLU 421": "OE1" <-> "OE2" Residue "B GLU 564": "OE1" <-> "OE2" Residue "B ASP 604": "OD1" <-> "OD2" Residue "B GLU 614": "OE1" <-> "OE2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C GLU 88": "OE1" <-> "OE2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 153": "OE1" <-> "OE2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 412": "OE1" <-> "OE2" Residue "C GLU 443": "OE1" <-> "OE2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C GLU 482": "OE1" <-> "OE2" Residue "C GLU 485": "OE1" <-> "OE2" Residue "C GLU 573": "OE1" <-> "OE2" Residue "C GLU 592": "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 81": "OE1" <-> "OE2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 298": "OE1" <-> "OE2" Residue "D GLU 369": "OE1" <-> "OE2" Residue "D GLU 423": "OE1" <-> "OE2" Residue "D GLU 425": "OE1" <-> "OE2" Residue "D ARG 442": "NH1" <-> "NH2" Residue "E GLU 20": "OE1" <-> "OE2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 144": "NH1" <-> "NH2" Residue "E GLU 147": "OE1" <-> "OE2" Residue "E GLU 164": "OE1" <-> "OE2" Residue "E GLU 215": "OE1" <-> "OE2" Residue "E GLU 219": "OE1" <-> "OE2" Residue "E GLU 223": "OE1" <-> "OE2" Residue "E ARG 293": "NH1" <-> "NH2" Residue "E TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 345": "NH1" <-> "NH2" Residue "E GLU 427": "OE1" <-> "OE2" Residue "A GLU 557": "OE1" <-> "OE2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "A GLU 639": "OE1" <-> "OE2" Residue "A GLU 666": "OE1" <-> "OE2" Residue "A ARG 676": "NH1" <-> "NH2" Residue "A ARG 692": "NH1" <-> "NH2" Residue "A GLU 752": "OE1" <-> "OE2" Residue "A GLU 762": "OE1" <-> "OE2" Residue "A GLU 767": "OE1" <-> "OE2" Residue "A ARG 774": "NH1" <-> "NH2" Residue "A ARG 785": "NH1" <-> "NH2" Residue "A ARG 880": "NH1" <-> "NH2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "G GLU 279": "OE1" <-> "OE2" Residue "G GLU 286": "OE1" <-> "OE2" Residue "G GLU 343": "OE1" <-> "OE2" Residue "G GLU 353": "OE1" <-> "OE2" Residue "G ARG 385": "NH1" <-> "NH2" Residue "G GLU 387": "OE1" <-> "OE2" Residue "G GLU 445": "OE1" <-> "OE2" Residue "G ARG 481": "NH1" <-> "NH2" Residue "G GLU 491": "OE1" <-> "OE2" Residue "G ARG 498": "NH1" <-> "NH2" Residue "G GLU 637": "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: 21619 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: 4892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 4892 Classifications: {'peptide': 609} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 585} Chain breaks: 7 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: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 660 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "I" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 693 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} 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: 11.36, per 1000 atoms: 0.53 Number of scatterers: 21619 At special positions: 0 Unit cell: (127.449, 156.06, 121.38, 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 110 16.00 P 78 15.00 Mg 4 11.99 O 4113 8.00 N 3786 7.00 C 13528 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.78 Conformation dependent library (CDL) restraints added in 3.5 seconds 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4830 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 123 helices and 11 sheets defined 54.3% alpha, 6.5% beta 33 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 9.49 Creating SS restraints... Processing helix chain 'B' and resid 280 through 284 Processing helix chain 'B' and resid 324 through 348 removed outlier: 3.901A pdb=" N TYR B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE B 340 " --> pdb=" O TYR B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix 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 525 removed outlier: 3.973A pdb=" N SER B 525 " --> pdb=" O SER B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 543 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 87 removed outlier: 5.217A pdb=" N ARG C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N THR C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 121 removed outlier: 4.542A pdb=" N LEU C 111 " --> pdb=" O PRO C 108 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER C 112 " --> pdb=" O ASP C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 158 Processing helix chain 'C' and resid 185 through 196 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: 4.310A pdb=" N LYS C 260 " --> pdb=" O HIS C 256 " (cutoff:3.500A) 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: 4.459A pdb=" N GLY C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 334 removed outlier: 3.603A pdb=" N LEU C 334 " --> pdb=" O ALA C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 346 Processing helix chain 'C' and resid 350 through 356 Processing helix chain 'C' and resid 360 through 367 Proline residue: C 364 - end of helix Processing helix chain 'C' and resid 384 through 415 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 576 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: 4.048A pdb=" N MET C 625 " --> pdb=" O HIS C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 653 Processing helix chain 'C' and resid 661 through 671 Processing helix chain 'C' and resid 688 through 702 Processing helix chain 'D' and resid 4 through 20 removed outlier: 3.885A pdb=" N LEU D 8 " --> pdb=" O ALA D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 44 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 153 Processing helix chain 'D' and resid 156 through 164 removed outlier: 5.972A pdb=" N LEU D 160 " --> pdb=" O ASN D 157 " (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 223 removed outlier: 3.599A pdb=" N LEU D 223 " --> pdb=" O CYS D 219 " (cutoff:3.500A) 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 283 through 294 Processing helix chain 'D' and resid 298 through 311 removed outlier: 3.928A 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: 3.936A pdb=" N GLY D 342 " --> pdb=" O GLU D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 361 Processing helix chain 'D' and resid 368 through 379 removed outlier: 3.784A 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 removed outlier: 3.572A pdb=" N GLN D 441 " --> pdb=" O HIS D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 453 Processing helix chain 'E' and resid 2 through 8 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: 3.712A pdb=" N GLN E 111 " --> pdb=" O GLN E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 133 removed outlier: 3.622A pdb=" N ARG E 132 " --> pdb=" O GLU E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 149 removed outlier: 3.655A pdb=" N ARG E 144 " --> pdb=" O PRO E 140 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLN E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 6.451A 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 Processing helix chain 'E' and resid 212 through 217 Processing helix chain 'E' and resid 223 through 237 removed outlier: 4.052A pdb=" N VAL E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 258 removed outlier: 4.080A 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 286 Proline residue: E 282 - end of helix Processing helix chain 'E' and resid 323 through 337 Processing helix chain 'E' and resid 340 through 346 removed outlier: 3.737A pdb=" N LYS E 344 " --> pdb=" O LYS E 341 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU E 346 " --> pdb=" O ASP E 343 " (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 551 through 558 Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'A' and resid 604 through 620 Processing helix chain 'A' and resid 641 through 651 removed outlier: 3.842A pdb=" N ILE A 647 " --> pdb=" O TYR A 644 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR A 648 " --> pdb=" O VAL A 645 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 651 " --> pdb=" O TYR A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 670 Processing helix chain 'A' and resid 686 through 688 No H-bonds generated for 'chain 'A' and resid 686 through 688' 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 Processing helix chain 'A' and resid 766 through 777 removed outlier: 3.905A pdb=" N GLN A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 799 removed outlier: 3.614A 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: 3.524A 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 removed outlier: 3.740A pdb=" N ARG A 880 " --> pdb=" O GLY A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 916 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: 3.709A pdb=" N ARG G 312 " --> pdb=" O SER G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 316 No H-bonds generated for 'chain 'G' and resid 314 through 316' Processing helix chain 'G' and resid 336 through 344 Processing helix chain 'G' and resid 353 through 365 removed outlier: 3.644A pdb=" N LYS G 365 " --> pdb=" O GLN G 361 " (cutoff:3.500A) Processing helix chain 'G' and resid 378 through 381 Processing helix chain 'G' and resid 387 through 397 removed outlier: 3.755A pdb=" N TRP G 395 " --> pdb=" O THR G 391 " (cutoff:3.500A) Proline residue: G 396 - end of helix 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 421 through 424 Processing helix chain 'G' and resid 440 through 453 Processing helix chain 'G' and resid 462 through 475 Processing helix chain 'G' and resid 479 through 497 removed outlier: 3.781A pdb=" N VAL G 490 " --> pdb=" O GLY G 486 " (cutoff:3.500A) removed outlier: 3.900A 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 572 Processing helix chain 'G' and resid 581 through 594 removed outlier: 3.541A pdb=" N VAL G 587 " --> pdb=" O ARG G 583 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG G 590 " --> pdb=" O GLU G 586 " (cutoff:3.500A) Processing helix chain 'G' and resid 602 through 615 removed outlier: 3.838A pdb=" N GLY G 607 " --> pdb=" O ALA G 603 " (cutoff:3.500A) removed outlier: 4.085A 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: 3.989A 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: 6.284A pdb=" N ASN B 352 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N TRP B 488 " --> pdb=" O ASN B 352 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU B 354 " --> pdb=" O TRP B 488 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR B 377 " --> pdb=" O PHE B 431 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE B 433 " --> pdb=" O THR B 377 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU B 379 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N HIS B 435 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 6.807A 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 100 removed outlier: 5.969A pdb=" N LEU C 205 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL C 239 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL C 207 " --> pdb=" O VAL C 239 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 706 through 708 Processing sheet with id= E, first strand: chain 'D' and resid 202 through 204 removed outlier: 8.208A pdb=" N VAL D 203 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU D 53 " --> pdb=" O VAL D 203 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 406 through 408 Processing sheet with id= G, first strand: chain 'E' and resid 176 through 180 removed outlier: 7.936A pdb=" N ILE E 37 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL E 155 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU E 39 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU E 157 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N GLY E 41 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N SER E 159 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE E 121 " --> pdb=" O CYS E 154 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ILE E 156 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE E 123 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LEU E 158 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL E 125 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 416 through 420 removed outlier: 6.827A pdb=" N ARG E 431 " --> pdb=" O VAL E 419 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 739 through 741 removed outlier: 8.924A pdb=" N LEU A 740 " --> pdb=" O CYS A 593 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TYR A 595 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR A 679 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N VAL A 714 " --> pdb=" O THR A 679 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU A 681 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE A 716 " --> pdb=" O LEU A 681 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL A 683 " --> pdb=" O ILE A 716 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 431 through 435 removed outlier: 3.884A pdb=" N GLY G 291 " --> pdb=" O ILE G 403 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU G 371 " --> pdb=" O LEU G 404 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N VAL G 406 " --> pdb=" O LEU G 371 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU G 373 " --> pdb=" O VAL G 406 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ILE G 408 " --> pdb=" O LEU G 373 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU G 375 " --> pdb=" O ILE G 408 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 618 through 621 915 hydrogen bonds defined for protein. 2631 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 8.00 Time building geometry restraints manager: 9.43 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: 5140 1.33 - 1.45: 4406 1.45 - 1.57: 12271 1.57 - 1.69: 150 1.69 - 1.81: 162 Bond restraints: 22129 Sorted by residual: bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 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 E 901 " pdb=" C5 ATP E 901 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.92e+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 5.87e+01 bond pdb=" C4 ATP A1001 " pdb=" C5 ATP A1001 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.69e+01 bond pdb=" C5 ATP E 901 " pdb=" C6 ATP E 901 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.62e+01 ... (remaining 22124 not shown) Histogram of bond angle deviations from ideal: 99.14 - 106.61: 977 106.61 - 114.08: 12709 114.08 - 121.54: 11519 121.54 - 129.01: 4840 129.01 - 136.47: 155 Bond angle restraints: 30200 Sorted by residual: angle pdb=" PB ATP G 901 " pdb=" O3B ATP G 901 " pdb=" PG ATP G 901 " ideal model delta sigma weight residual 139.87 121.25 18.62 1.00e+00 1.00e+00 3.47e+02 angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 121.27 18.60 1.00e+00 1.00e+00 3.46e+02 angle pdb=" PB ATP E 901 " pdb=" O3B ATP E 901 " pdb=" PG ATP E 901 " ideal model delta sigma weight residual 139.87 121.96 17.91 1.00e+00 1.00e+00 3.21e+02 angle pdb=" PA ATP G 901 " pdb=" O3A ATP G 901 " pdb=" PB ATP G 901 " ideal model delta sigma weight residual 136.83 120.10 16.73 1.00e+00 1.00e+00 2.80e+02 angle pdb=" PB ATP A1001 " pdb=" O3B ATP A1001 " pdb=" PG ATP A1001 " ideal model delta sigma weight residual 139.87 123.68 16.19 1.00e+00 1.00e+00 2.62e+02 ... (remaining 30195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 11488 17.90 - 35.80: 1351 35.80 - 53.71: 478 53.71 - 71.61: 106 71.61 - 89.51: 25 Dihedral angle restraints: 13448 sinusoidal: 6051 harmonic: 7397 Sorted by residual: dihedral pdb=" CA LYS C 712 " pdb=" C LYS C 712 " pdb=" N THR C 713 " pdb=" CA THR C 713 " ideal model delta harmonic sigma weight residual -180.00 -152.09 -27.91 0 5.00e+00 4.00e-02 3.12e+01 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 180.00 153.34 26.66 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA ASN E 338 " pdb=" C ASN E 338 " pdb=" N ALA E 339 " pdb=" CA ALA E 339 " ideal model delta harmonic sigma weight residual 180.00 153.76 26.24 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 13445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3041 0.070 - 0.140: 409 0.140 - 0.210: 33 0.210 - 0.280: 2 0.280 - 0.350: 2 Chirality restraints: 3487 Sorted by residual: chirality pdb=" CG LEU A 750 " pdb=" CB LEU A 750 " pdb=" CD1 LEU A 750 " pdb=" CD2 LEU A 750 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.07e+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 2.36 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA THR B 471 " pdb=" N THR B 471 " pdb=" C THR B 471 " pdb=" CB THR B 471 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 3484 not shown) Planarity restraints: 3594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 664 " -0.030 2.00e-02 2.50e+03 2.13e-02 1.13e+01 pdb=" CG TRP C 664 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP C 664 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP C 664 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 664 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 664 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 664 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 664 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 664 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 664 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 9 " -0.054 5.00e-02 4.00e+02 8.04e-02 1.04e+01 pdb=" N PRO E 10 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO E 10 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 10 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 872 " 0.053 5.00e-02 4.00e+02 7.96e-02 1.01e+01 pdb=" N PRO A 873 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 873 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 873 " 0.043 5.00e-02 4.00e+02 ... (remaining 3591 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 266 2.65 - 3.22: 18141 3.22 - 3.78: 34068 3.78 - 4.34: 47350 4.34 - 4.90: 75879 Nonbonded interactions: 175704 Sorted by model distance: nonbonded pdb=" OG1 THR D 63 " pdb="MG MG D 902 " model vdw 2.092 2.170 nonbonded pdb=" O2B ATP E 901 " pdb="MG MG E 902 " model vdw 2.112 2.170 nonbonded pdb=" OG1 THR A 605 " pdb="MG MG A1002 " model vdw 2.113 2.170 nonbonded pdb=" O2B ATP D 901 " pdb="MG MG D 902 " model vdw 2.121 2.170 nonbonded pdb=" OG1 THR E 48 " pdb="MG MG E 902 " model vdw 2.121 2.170 ... (remaining 175699 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: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.970 Check model and map are aligned: 0.290 Set scattering table: 0.190 Process input model: 64.750 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 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 0.078 22129 Z= 0.352 Angle : 0.916 18.617 30200 Z= 0.568 Chirality : 0.048 0.350 3487 Planarity : 0.007 0.080 3594 Dihedral : 17.904 89.509 8618 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.23 % Allowed : 8.00 % Favored : 91.78 % 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: -3.50 (0.13), residues: 2471 helix: -2.34 (0.10), residues: 1449 sheet: -1.53 (0.31), residues: 225 loop : -2.07 (0.18), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP C 664 HIS 0.006 0.001 HIS B 468 PHE 0.021 0.002 PHE D 304 TYR 0.018 0.002 TYR G 588 ARG 0.006 0.001 ARG A 785 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 290 time to evaluate : 2.434 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: symmetry clash REVERT: B 333 MET cc_start: 0.9140 (tpp) cc_final: 0.8713 (mmm) REVERT: B 555 PHE cc_start: 0.7807 (t80) cc_final: 0.7510 (t80) REVERT: C 145 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8067 (mt-10) REVERT: C 326 PHE cc_start: 0.8955 (m-10) cc_final: 0.8542 (m-10) REVERT: C 417 LEU cc_start: 0.8562 (tp) cc_final: 0.8287 (tp) REVERT: C 573 GLU cc_start: 0.8444 (tt0) cc_final: 0.8206 (tm-30) REVERT: C 658 MET cc_start: 0.7999 (tpt) cc_final: 0.7477 (mmm) REVERT: D 347 GLU cc_start: 0.8750 (mp0) cc_final: 0.8383 (mp0) REVERT: E 82 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8239 (mt-10) REVERT: E 394 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7501 (pp20) REVERT: A 618 MET cc_start: 0.8689 (mtp) cc_final: 0.8477 (mtt) REVERT: A 666 GLU cc_start: 0.8629 (tp30) cc_final: 0.8351 (tp30) outliers start: 5 outliers final: 4 residues processed: 294 average time/residue: 0.4118 time to fit residues: 175.5668 Evaluate side-chains 189 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 185 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 750 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 215 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 121 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 231 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 366 GLN B 544 ASN ** C 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 GLN C 464 ASN C 626 GLN D 82 ASN D 157 ASN D 202 GLN E 218 GLN ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 GLN E 454 GLN A 749 GLN A 838 GLN G 254 ASN G 356 HIS G 533 GLN ** G 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22129 Z= 0.204 Angle : 0.546 9.370 30200 Z= 0.290 Chirality : 0.038 0.174 3487 Planarity : 0.004 0.060 3594 Dihedral : 16.977 68.058 3666 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.22 % Allowed : 11.61 % Favored : 87.17 % 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: -1.32 (0.16), residues: 2471 helix: -0.41 (0.13), residues: 1459 sheet: -1.15 (0.32), residues: 235 loop : -1.39 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 664 HIS 0.004 0.001 HIS C 580 PHE 0.017 0.001 PHE C 459 TYR 0.012 0.001 TYR C 430 ARG 0.009 0.000 ARG A 641 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 193 time to evaluate : 2.621 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: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9162 (tpp) cc_final: 0.8811 (mmm) REVERT: B 419 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8084 (mt-10) REVERT: C 145 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8086 (mt-10) REVERT: C 384 TYR cc_start: 0.8404 (t80) cc_final: 0.7962 (t80) REVERT: C 504 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7970 (mp0) REVERT: C 586 ASP cc_start: 0.7581 (m-30) cc_final: 0.6976 (p0) REVERT: C 658 MET cc_start: 0.8066 (tpt) cc_final: 0.7588 (mmm) REVERT: D 347 GLU cc_start: 0.8825 (mp0) cc_final: 0.8478 (mp0) REVERT: E 82 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8334 (mt-10) REVERT: A 666 GLU cc_start: 0.8625 (tp30) cc_final: 0.8250 (tp30) REVERT: A 807 MET cc_start: 0.8077 (ttm) cc_final: 0.7836 (tpp) REVERT: A 915 TYR cc_start: 0.9316 (t80) cc_final: 0.9112 (t80) outliers start: 27 outliers final: 14 residues processed: 212 average time/residue: 0.3525 time to fit residues: 115.8337 Evaluate side-chains 177 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 162 time to evaluate : 2.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 456 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 128 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 192 optimal weight: 6.9990 chunk 157 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 231 optimal weight: 5.9990 chunk 250 optimal weight: 6.9990 chunk 206 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 186 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 325 HIS ** C 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN C 291 HIS C 325 HIS ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 345 GLN G 596 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22129 Z= 0.173 Angle : 0.499 9.109 30200 Z= 0.265 Chirality : 0.037 0.163 3487 Planarity : 0.004 0.051 3594 Dihedral : 17.053 71.410 3663 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.72 % Allowed : 12.25 % Favored : 86.04 % 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: -0.02 (0.17), residues: 2471 helix: 0.73 (0.14), residues: 1451 sheet: -0.92 (0.32), residues: 243 loop : -0.96 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 664 HIS 0.003 0.001 HIS C 615 PHE 0.017 0.001 PHE C 459 TYR 0.016 0.001 TYR C 72 ARG 0.006 0.000 ARG B 370 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 181 time to evaluate : 2.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9164 (tpp) cc_final: 0.8831 (mmm) REVERT: B 395 ASP cc_start: 0.8367 (p0) cc_final: 0.8142 (p0) REVERT: C 128 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7744 (mtp) REVERT: C 145 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8170 (mt-10) REVERT: C 384 TYR cc_start: 0.8243 (t80) cc_final: 0.8010 (t80) REVERT: C 400 PHE cc_start: 0.9031 (m-80) cc_final: 0.8829 (m-80) REVERT: C 449 GLN cc_start: 0.8873 (mm-40) cc_final: 0.8559 (mt0) REVERT: C 586 ASP cc_start: 0.7670 (m-30) cc_final: 0.7106 (p0) REVERT: C 658 MET cc_start: 0.8079 (tpt) cc_final: 0.7576 (mmm) REVERT: D 45 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7597 (mp0) REVERT: D 347 GLU cc_start: 0.8853 (mp0) cc_final: 0.8517 (mp0) REVERT: E 82 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8307 (mt-10) REVERT: E 254 CYS cc_start: 0.8305 (m) cc_final: 0.8077 (t) REVERT: E 446 LYS cc_start: 0.9153 (tmmt) cc_final: 0.8779 (ptpp) REVERT: A 666 GLU cc_start: 0.8565 (tp30) cc_final: 0.8194 (tp30) REVERT: A 788 ASP cc_start: 0.8834 (m-30) cc_final: 0.8385 (t0) outliers start: 38 outliers final: 22 residues processed: 207 average time/residue: 0.3323 time to fit residues: 108.9970 Evaluate side-chains 190 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain G residue 295 VAL Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 426 CYS Chi-restraints excluded: chain G residue 456 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 229 optimal weight: 9.9990 chunk 174 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 110 optimal weight: 0.0020 chunk 155 optimal weight: 3.9990 chunk 232 optimal weight: 10.0000 chunk 246 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 220 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 overall best weight: 2.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 470 ASN ** C 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22129 Z= 0.258 Angle : 0.528 10.315 30200 Z= 0.276 Chirality : 0.038 0.165 3487 Planarity : 0.003 0.046 3594 Dihedral : 17.010 71.305 3663 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.90 % Allowed : 13.56 % Favored : 84.55 % 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: 0.61 (0.17), residues: 2471 helix: 1.23 (0.14), residues: 1461 sheet: -0.76 (0.33), residues: 249 loop : -0.68 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 276 HIS 0.003 0.001 HIS G 284 PHE 0.017 0.001 PHE C 459 TYR 0.025 0.001 TYR C 72 ARG 0.006 0.000 ARG A 617 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 170 time to evaluate : 2.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9154 (tpp) cc_final: 0.8837 (mmm) REVERT: C 128 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7794 (mtp) REVERT: C 145 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8249 (mt-10) REVERT: C 323 MET cc_start: 0.9097 (ttp) cc_final: 0.8855 (ttp) REVERT: C 384 TYR cc_start: 0.8210 (t80) cc_final: 0.7931 (t80) REVERT: C 443 GLU cc_start: 0.8698 (mp0) cc_final: 0.8295 (mp0) REVERT: C 449 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8573 (mt0) REVERT: C 450 MET cc_start: 0.7242 (ptm) cc_final: 0.7011 (ptm) REVERT: C 586 ASP cc_start: 0.7807 (m-30) cc_final: 0.7382 (p0) REVERT: C 710 LYS cc_start: 0.9187 (mmtt) cc_final: 0.8901 (tttt) REVERT: D 6 ARG cc_start: 0.8250 (mpt180) cc_final: 0.7968 (mpt180) REVERT: D 45 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7700 (mp0) REVERT: D 347 GLU cc_start: 0.8869 (mp0) cc_final: 0.8484 (mp0) REVERT: D 426 MET cc_start: 0.8816 (mmm) cc_final: 0.8533 (mmt) REVERT: E 446 LYS cc_start: 0.9167 (tmmt) cc_final: 0.8773 (ptpp) REVERT: A 666 GLU cc_start: 0.8605 (tp30) cc_final: 0.8393 (tp30) REVERT: A 788 ASP cc_start: 0.8872 (m-30) cc_final: 0.8435 (t0) REVERT: G 392 ILE cc_start: 0.9492 (OUTLIER) cc_final: 0.9273 (mp) outliers start: 42 outliers final: 31 residues processed: 200 average time/residue: 0.3330 time to fit residues: 105.0214 Evaluate side-chains 191 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 157 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 295 VAL Chi-restraints excluded: chain G residue 306 CYS Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 392 ILE Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 426 CYS Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 570 MET Chi-restraints excluded: chain G residue 659 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 205 optimal weight: 0.9980 chunk 139 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 210 optimal weight: 0.6980 chunk 170 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 125 optimal weight: 7.9990 chunk 221 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 HIS ** C 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8503 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22129 Z= 0.150 Angle : 0.486 11.199 30200 Z= 0.254 Chirality : 0.036 0.154 3487 Planarity : 0.003 0.044 3594 Dihedral : 16.846 72.785 3663 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.90 % Allowed : 14.32 % Favored : 83.78 % 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: 1.02 (0.17), residues: 2471 helix: 1.55 (0.14), residues: 1459 sheet: -0.49 (0.34), residues: 237 loop : -0.52 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 276 HIS 0.003 0.001 HIS G 284 PHE 0.018 0.001 PHE C 459 TYR 0.027 0.001 TYR C 72 ARG 0.007 0.000 ARG G 385 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 166 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 395 ASP cc_start: 0.8354 (p0) cc_final: 0.8018 (p0) REVERT: C 145 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8227 (mt-10) REVERT: C 323 MET cc_start: 0.9080 (ttp) cc_final: 0.8819 (ttp) REVERT: C 384 TYR cc_start: 0.8132 (t80) cc_final: 0.7853 (t80) REVERT: C 449 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8551 (mt0) REVERT: C 450 MET cc_start: 0.7207 (ptm) cc_final: 0.6968 (ptm) REVERT: C 586 ASP cc_start: 0.7833 (m-30) cc_final: 0.7436 (p0) REVERT: C 658 MET cc_start: 0.8196 (tpt) cc_final: 0.7691 (mmm) REVERT: C 710 LYS cc_start: 0.9173 (mmtt) cc_final: 0.8879 (tttt) REVERT: D 6 ARG cc_start: 0.8279 (mpt180) cc_final: 0.7974 (mpt180) REVERT: D 45 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7611 (mp0) REVERT: D 347 GLU cc_start: 0.8871 (mp0) cc_final: 0.8543 (mp0) REVERT: E 446 LYS cc_start: 0.9153 (tmmt) cc_final: 0.8749 (ptpp) REVERT: A 644 TYR cc_start: 0.9133 (m-10) cc_final: 0.8853 (m-10) REVERT: A 666 GLU cc_start: 0.8547 (tp30) cc_final: 0.8332 (tp30) REVERT: A 788 ASP cc_start: 0.8846 (m-30) cc_final: 0.8399 (t0) REVERT: G 392 ILE cc_start: 0.9468 (OUTLIER) cc_final: 0.9264 (mp) outliers start: 42 outliers final: 26 residues processed: 201 average time/residue: 0.3378 time to fit residues: 108.2515 Evaluate side-chains 187 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 159 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain G residue 306 CYS Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 392 ILE Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 570 MET Chi-restraints excluded: chain G residue 659 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 82 optimal weight: 0.6980 chunk 221 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 chunk 60 optimal weight: 0.4980 chunk 246 optimal weight: 5.9990 chunk 204 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 81 optimal weight: 0.5980 chunk 129 optimal weight: 7.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22129 Z= 0.172 Angle : 0.495 9.367 30200 Z= 0.257 Chirality : 0.037 0.155 3487 Planarity : 0.003 0.044 3594 Dihedral : 16.747 74.260 3663 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.99 % Allowed : 14.69 % Favored : 83.33 % 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: 1.24 (0.18), residues: 2471 helix: 1.67 (0.14), residues: 1467 sheet: -0.34 (0.34), residues: 237 loop : -0.35 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 276 HIS 0.009 0.001 HIS C 580 PHE 0.021 0.001 PHE C 290 TYR 0.033 0.001 TYR C 72 ARG 0.007 0.000 ARG G 385 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 165 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9228 (mmm) cc_final: 0.8885 (mmm) REVERT: B 395 ASP cc_start: 0.8362 (p0) cc_final: 0.8002 (p0) REVERT: B 425 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.9018 (tp) REVERT: C 145 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8258 (mt-10) REVERT: C 323 MET cc_start: 0.9085 (ttp) cc_final: 0.8817 (ttp) REVERT: C 326 PHE cc_start: 0.8629 (m-80) cc_final: 0.8278 (m-10) REVERT: C 443 GLU cc_start: 0.8694 (mp0) cc_final: 0.8296 (mp0) REVERT: C 449 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8558 (mt0) REVERT: C 586 ASP cc_start: 0.7911 (m-30) cc_final: 0.7483 (p0) REVERT: C 658 MET cc_start: 0.8192 (tpt) cc_final: 0.7694 (mmm) REVERT: C 710 LYS cc_start: 0.9155 (mmtt) cc_final: 0.8810 (ptmt) REVERT: D 6 ARG cc_start: 0.8299 (mpt180) cc_final: 0.7979 (mpt180) REVERT: D 45 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7615 (mp0) REVERT: D 95 ASP cc_start: 0.8409 (t0) cc_final: 0.8170 (t0) REVERT: D 347 GLU cc_start: 0.8873 (mp0) cc_final: 0.8539 (mp0) REVERT: E 446 LYS cc_start: 0.9148 (tmmt) cc_final: 0.8735 (ptpp) REVERT: A 644 TYR cc_start: 0.9142 (m-10) cc_final: 0.8833 (m-10) REVERT: A 666 GLU cc_start: 0.8550 (tp30) cc_final: 0.8336 (tp30) REVERT: A 788 ASP cc_start: 0.8862 (m-30) cc_final: 0.8391 (t0) REVERT: G 392 ILE cc_start: 0.9466 (OUTLIER) cc_final: 0.9258 (mp) REVERT: G 433 MET cc_start: 0.8165 (ttm) cc_final: 0.7959 (ttm) outliers start: 44 outliers final: 31 residues processed: 199 average time/residue: 0.3303 time to fit residues: 103.8420 Evaluate side-chains 189 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 155 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain G residue 295 VAL Chi-restraints excluded: chain G residue 306 CYS Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 392 ILE Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 426 CYS Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 570 MET Chi-restraints excluded: chain G residue 659 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 237 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 140 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 207 optimal weight: 0.2980 chunk 137 optimal weight: 5.9990 chunk 245 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 113 optimal weight: 0.2980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22129 Z= 0.150 Angle : 0.485 10.736 30200 Z= 0.253 Chirality : 0.036 0.147 3487 Planarity : 0.003 0.042 3594 Dihedral : 16.614 76.667 3663 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.85 % Allowed : 15.23 % Favored : 82.92 % 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: 1.43 (0.18), residues: 2471 helix: 1.80 (0.14), residues: 1467 sheet: -0.25 (0.34), residues: 237 loop : -0.23 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 276 HIS 0.004 0.000 HIS C 580 PHE 0.020 0.001 PHE C 459 TYR 0.028 0.001 TYR C 72 ARG 0.006 0.000 ARG G 575 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 164 time to evaluate : 2.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9232 (mmm) cc_final: 0.8857 (mmm) REVERT: B 395 ASP cc_start: 0.8304 (p0) cc_final: 0.7943 (p0) REVERT: B 425 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.9023 (tp) REVERT: C 145 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8230 (mt-10) REVERT: C 323 MET cc_start: 0.9114 (ttp) cc_final: 0.8866 (ttp) REVERT: C 384 TYR cc_start: 0.7924 (t80) cc_final: 0.7647 (t80) REVERT: C 449 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8550 (mt0) REVERT: C 586 ASP cc_start: 0.7968 (m-30) cc_final: 0.7513 (p0) REVERT: C 658 MET cc_start: 0.8220 (tpt) cc_final: 0.7725 (mmm) REVERT: C 710 LYS cc_start: 0.9130 (mmtt) cc_final: 0.8795 (ptmt) REVERT: D 6 ARG cc_start: 0.8299 (mpt180) cc_final: 0.7970 (mpt180) REVERT: D 45 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: D 347 GLU cc_start: 0.8866 (mp0) cc_final: 0.8549 (mp0) REVERT: D 426 MET cc_start: 0.8809 (mmm) cc_final: 0.8317 (mmm) REVERT: E 446 LYS cc_start: 0.9134 (tmmt) cc_final: 0.8710 (ptpp) REVERT: A 666 GLU cc_start: 0.8519 (tp30) cc_final: 0.8309 (tp30) REVERT: A 788 ASP cc_start: 0.8849 (m-30) cc_final: 0.8353 (t0) REVERT: G 392 ILE cc_start: 0.9444 (OUTLIER) cc_final: 0.9235 (mp) outliers start: 41 outliers final: 34 residues processed: 193 average time/residue: 0.3163 time to fit residues: 96.8301 Evaluate side-chains 194 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 157 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain G residue 295 VAL Chi-restraints excluded: chain G residue 306 CYS Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 392 ILE Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 426 CYS Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 570 MET Chi-restraints excluded: chain G residue 659 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 152 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 146 optimal weight: 0.6980 chunk 74 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 0.0980 chunk 156 optimal weight: 3.9990 chunk 167 optimal weight: 0.3980 chunk 121 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 193 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 ASN ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22129 Z= 0.134 Angle : 0.487 11.264 30200 Z= 0.252 Chirality : 0.036 0.148 3487 Planarity : 0.003 0.042 3594 Dihedral : 16.529 78.149 3663 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.81 % Allowed : 15.41 % Favored : 82.78 % 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: 1.53 (0.18), residues: 2471 helix: 1.87 (0.14), residues: 1469 sheet: -0.19 (0.35), residues: 237 loop : -0.18 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 276 HIS 0.006 0.000 HIS C 580 PHE 0.021 0.001 PHE C 459 TYR 0.025 0.001 TYR C 72 ARG 0.007 0.000 ARG G 575 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 169 time to evaluate : 2.436 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 333 MET cc_start: 0.9238 (mmm) cc_final: 0.8872 (mmm) REVERT: B 344 MET cc_start: 0.9113 (mmm) cc_final: 0.8894 (tpt) REVERT: B 395 ASP cc_start: 0.8309 (p0) cc_final: 0.7955 (p0) REVERT: B 425 ILE cc_start: 0.9390 (OUTLIER) cc_final: 0.9028 (tp) REVERT: C 145 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8243 (mt-10) REVERT: C 384 TYR cc_start: 0.7861 (t80) cc_final: 0.7657 (t80) REVERT: C 443 GLU cc_start: 0.8704 (mp0) cc_final: 0.8398 (pm20) REVERT: C 449 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8544 (mt0) REVERT: C 586 ASP cc_start: 0.7968 (m-30) cc_final: 0.7497 (p0) REVERT: C 658 MET cc_start: 0.8219 (tpt) cc_final: 0.7723 (mmm) REVERT: C 710 LYS cc_start: 0.9086 (mmtt) cc_final: 0.8776 (ptmt) REVERT: D 6 ARG cc_start: 0.8306 (mpt180) cc_final: 0.7973 (mpt180) REVERT: D 45 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: D 95 ASP cc_start: 0.8414 (t0) cc_final: 0.8163 (t0) REVERT: D 347 GLU cc_start: 0.8868 (mp0) cc_final: 0.8564 (mp0) REVERT: D 426 MET cc_start: 0.8831 (mmm) cc_final: 0.8406 (mmm) REVERT: E 446 LYS cc_start: 0.9144 (tmmt) cc_final: 0.8939 (ptmm) REVERT: A 644 TYR cc_start: 0.9117 (m-10) cc_final: 0.8785 (m-10) REVERT: A 666 GLU cc_start: 0.8500 (tp30) cc_final: 0.8085 (tp30) REVERT: A 788 ASP cc_start: 0.8846 (m-30) cc_final: 0.8343 (t0) REVERT: G 392 ILE cc_start: 0.9445 (OUTLIER) cc_final: 0.9233 (mp) outliers start: 40 outliers final: 32 residues processed: 199 average time/residue: 0.3295 time to fit residues: 103.6620 Evaluate side-chains 193 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 158 time to evaluate : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain G residue 295 VAL Chi-restraints excluded: chain G residue 306 CYS Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 392 ILE Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 570 MET Chi-restraints excluded: chain G residue 659 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 223 optimal weight: 10.0000 chunk 235 optimal weight: 5.9990 chunk 214 optimal weight: 0.1980 chunk 229 optimal weight: 8.9990 chunk 137 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 chunk 179 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 206 optimal weight: 1.9990 chunk 216 optimal weight: 9.9990 chunk 228 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22129 Z= 0.191 Angle : 0.513 10.712 30200 Z= 0.263 Chirality : 0.037 0.158 3487 Planarity : 0.003 0.041 3594 Dihedral : 16.515 81.377 3663 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.76 % Allowed : 15.77 % Favored : 82.47 % 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: 1.59 (0.18), residues: 2471 helix: 1.90 (0.14), residues: 1470 sheet: -0.14 (0.35), residues: 238 loop : -0.12 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 276 HIS 0.008 0.001 HIS C 580 PHE 0.019 0.001 PHE C 459 TYR 0.024 0.001 TYR C 72 ARG 0.009 0.000 ARG G 575 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 160 time to evaluate : 2.282 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: symmetry clash REVERT: B 333 MET cc_start: 0.9243 (mmm) cc_final: 0.8871 (mmm) REVERT: B 344 MET cc_start: 0.9111 (mmm) cc_final: 0.8901 (tpt) REVERT: B 395 ASP cc_start: 0.8321 (p0) cc_final: 0.7948 (p0) REVERT: B 425 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.9018 (tp) REVERT: C 145 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8271 (mt-10) REVERT: C 449 GLN cc_start: 0.8828 (mm-40) cc_final: 0.8549 (mt0) REVERT: C 637 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6845 (mm) REVERT: C 658 MET cc_start: 0.8229 (tpt) cc_final: 0.7740 (mmm) REVERT: D 6 ARG cc_start: 0.8325 (mpt180) cc_final: 0.7976 (mpt180) REVERT: D 45 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7675 (mp0) REVERT: D 95 ASP cc_start: 0.8432 (t0) cc_final: 0.8186 (t0) REVERT: D 347 GLU cc_start: 0.8853 (mp0) cc_final: 0.8513 (mp0) REVERT: D 426 MET cc_start: 0.8788 (mmm) cc_final: 0.8284 (mmm) REVERT: E 446 LYS cc_start: 0.9153 (tmmt) cc_final: 0.8947 (ptmm) REVERT: A 666 GLU cc_start: 0.8540 (tp30) cc_final: 0.8325 (tp30) REVERT: G 392 ILE cc_start: 0.9446 (OUTLIER) cc_final: 0.9241 (mp) outliers start: 39 outliers final: 33 residues processed: 189 average time/residue: 0.3344 time to fit residues: 99.5776 Evaluate side-chains 197 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 160 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain G residue 295 VAL Chi-restraints excluded: chain G residue 306 CYS Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 392 ILE Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 570 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 150 optimal weight: 0.9990 chunk 242 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 168 optimal weight: 0.5980 chunk 254 optimal weight: 7.9990 chunk 233 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 156 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22129 Z= 0.154 Angle : 0.516 14.379 30200 Z= 0.261 Chirality : 0.037 0.295 3487 Planarity : 0.003 0.041 3594 Dihedral : 16.481 84.326 3663 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.72 % Allowed : 15.82 % Favored : 82.47 % 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: 1.64 (0.18), residues: 2471 helix: 1.95 (0.14), residues: 1466 sheet: -0.18 (0.35), residues: 241 loop : -0.09 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 276 HIS 0.006 0.001 HIS C 580 PHE 0.022 0.001 PHE C 459 TYR 0.023 0.001 TYR C 72 ARG 0.009 0.000 ARG G 575 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 166 time to evaluate : 2.430 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 333 MET cc_start: 0.9240 (mmm) cc_final: 0.8866 (mmm) REVERT: B 344 MET cc_start: 0.9109 (mmm) cc_final: 0.8897 (tpt) REVERT: B 395 ASP cc_start: 0.8307 (p0) cc_final: 0.7933 (p0) REVERT: B 425 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.9022 (tp) REVERT: C 145 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8259 (mt-10) REVERT: C 346 LYS cc_start: 0.9355 (mttm) cc_final: 0.9044 (mttm) REVERT: C 443 GLU cc_start: 0.8719 (mp0) cc_final: 0.8374 (pm20) REVERT: C 449 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8540 (mt0) REVERT: C 580 HIS cc_start: 0.6186 (m90) cc_final: 0.5950 (m-70) REVERT: C 586 ASP cc_start: 0.8014 (m-30) cc_final: 0.7569 (p0) REVERT: C 658 MET cc_start: 0.8207 (tpt) cc_final: 0.7709 (mmm) REVERT: C 710 LYS cc_start: 0.9075 (mmtt) cc_final: 0.8777 (ptmt) REVERT: D 6 ARG cc_start: 0.8321 (mpt180) cc_final: 0.7980 (mpt180) REVERT: D 45 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: D 95 ASP cc_start: 0.8407 (t0) cc_final: 0.8159 (t0) REVERT: D 347 GLU cc_start: 0.8854 (mp0) cc_final: 0.8530 (mp0) REVERT: D 426 MET cc_start: 0.8790 (mmm) cc_final: 0.8558 (mmt) REVERT: E 446 LYS cc_start: 0.9159 (tmmt) cc_final: 0.8952 (ptmm) REVERT: F 231 ARG cc_start: 0.8446 (tmm-80) cc_final: 0.7695 (tmm-80) REVERT: A 644 TYR cc_start: 0.9126 (m-10) cc_final: 0.8798 (m-10) REVERT: A 666 GLU cc_start: 0.8504 (tp30) cc_final: 0.8279 (tp30) REVERT: A 788 ASP cc_start: 0.8837 (m-30) cc_final: 0.8343 (t0) REVERT: G 392 ILE cc_start: 0.9437 (OUTLIER) cc_final: 0.9228 (mp) outliers start: 38 outliers final: 32 residues processed: 193 average time/residue: 0.3296 time to fit residues: 100.1825 Evaluate side-chains 194 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 159 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain G residue 295 VAL Chi-restraints excluded: chain G residue 306 CYS Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 392 ILE Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 426 CYS Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 570 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 160 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 186 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 202 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 208 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.092680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.065340 restraints weight = 55133.330| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 3.31 r_work: 0.2894 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22129 Z= 0.145 Angle : 0.510 15.389 30200 Z= 0.259 Chirality : 0.036 0.148 3487 Planarity : 0.003 0.041 3594 Dihedral : 16.402 87.840 3663 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.67 % Allowed : 16.00 % Favored : 82.33 % 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: 1.71 (0.18), residues: 2471 helix: 1.98 (0.14), residues: 1467 sheet: 0.06 (0.35), residues: 232 loop : -0.08 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 228 HIS 0.005 0.000 HIS C 580 PHE 0.021 0.001 PHE C 459 TYR 0.023 0.001 TYR C 72 ARG 0.009 0.000 ARG G 575 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4015.06 seconds wall clock time: 74 minutes 3.25 seconds (4443.25 seconds total)