Starting phenix.real_space_refine on Wed Dec 13 04:27:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eby_28002/12_2023/8eby_28002_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eby_28002/12_2023/8eby_28002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eby_28002/12_2023/8eby_28002.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eby_28002/12_2023/8eby_28002.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eby_28002/12_2023/8eby_28002_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eby_28002/12_2023/8eby_28002_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 6 6.06 5 P 45 5.49 5 S 147 5.16 5 C 14972 2.51 5 N 4102 2.21 5 O 4433 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 109": "NH1" <-> "NH2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A ARG 520": "NH1" <-> "NH2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 574": "NH1" <-> "NH2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A ARG 676": "NH1" <-> "NH2" Residue "A ARG 678": "NH1" <-> "NH2" Residue "A PHE 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 30": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B ARG 112": "NH1" <-> "NH2" Residue "B ARG 166": "NH1" <-> "NH2" Residue "B TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B ARG 334": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B ARG 378": "NH1" <-> "NH2" Residue "B ARG 424": "NH1" <-> "NH2" Residue "B ARG 487": "NH1" <-> "NH2" Residue "B ARG 497": "NH1" <-> "NH2" Residue "B ARG 592": "NH1" <-> "NH2" Residue "B ARG 669": "NH1" <-> "NH2" Residue "B ARG 695": "NH1" <-> "NH2" Residue "D PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 911": "OE1" <-> "OE2" Residue "K TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 211": "NH1" <-> "NH2" Residue "K ARG 237": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 23709 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4882 Classifications: {'peptide': 604} Link IDs: {'CIS': 2, 'PTRANS': 24, 'TRANS': 577} Chain breaks: 2 Chain: "B" Number of atoms: 5457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5457 Classifications: {'peptide': 677} Link IDs: {'PTRANS': 29, 'TRANS': 647} Chain breaks: 1 Chain: "C" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1547 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 183} Chain breaks: 1 Chain: "D" Number of atoms: 3483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3483 Classifications: {'peptide': 434} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 412} Chain breaks: 1 Chain: "E" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2989 Classifications: {'peptide': 380} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 361} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2034 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 1 Chain: "G" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "H" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 409 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "K" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1450 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 166} Chain: "L" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 474 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "M" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 448 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5825 SG CYS B 116 53.297 37.029 41.202 1.00263.29 S ATOM 6134 SG CYS B 155 49.513 33.668 36.833 1.00300.18 S ATOM 5965 SG CYS B 134 51.622 39.585 35.448 1.00303.96 S ATOM 6423 SG CYS B 190 47.149 38.769 39.239 1.00271.00 S ATOM 18036 SG CYS E 345 38.051 62.356 131.419 1.00122.93 S ATOM 18058 SG CYS E 348 40.150 65.336 132.500 1.00116.67 S ATOM 18215 SG CYS E 368 38.606 65.341 129.030 1.00122.84 S ATOM 18236 SG CYS E 371 41.399 62.925 129.836 1.00118.26 S ATOM 18156 SG CYS E 360 36.552 51.504 125.996 1.00129.98 S ATOM 18174 SG CYS E 363 36.939 51.444 129.785 1.00135.09 S ATOM 18323 SG CYS E 382 39.645 52.947 127.641 1.00115.61 S ATOM 18340 SG CYS E 385 39.138 49.194 127.559 1.00119.48 S ATOM 17600 SG CYS E 291 75.688 37.349 121.894 1.00127.66 S ATOM 17622 SG CYS E 294 79.187 35.810 121.632 1.00140.91 S ATOM 17711 SG CYS E 305 78.141 38.296 119.053 1.00128.50 S ATOM 17734 SG CYS E 308 76.426 34.920 119.139 1.00140.97 S ATOM 20236 SG CYS F 268 56.176 37.648 111.865 1.00 96.74 S ATOM 20255 SG CYS F 271 53.681 39.644 113.945 1.00102.67 S ATOM 20340 SG CYS F 282 53.412 35.892 113.821 1.00125.77 S ATOM 20360 SG CYS F 285 52.562 37.945 110.734 1.00134.39 S ATOM 20128 SG CYS F 255 57.007 34.170 124.147 1.00120.27 S ATOM 20145 SG CYS F 257 54.346 31.472 123.794 1.00127.38 S ATOM 20294 SG CYS F 276 58.058 30.496 124.364 1.00121.49 S ATOM 21356 SG CYS K 105 47.369 99.660 21.740 1.00248.15 S ATOM 21380 SG CYS K 108 46.759 99.169 18.020 1.00257.96 S ATOM 21528 SG CYS K 126 49.369 97.058 19.858 1.00238.28 S ATOM 21550 SG CYS K 129 49.984 100.744 19.158 1.00238.81 S Time building chain proxies: 13.10, per 1000 atoms: 0.55 Number of scatterers: 23709 At special positions: 0 Unit cell: (119.52, 155.625, 179.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 Fe 4 26.01 S 147 16.00 P 45 15.00 O 4433 8.00 N 4102 7.00 C 14972 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: 10.36 Conformation dependent library (CDL) restraints added in 4.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B1000 " pdb="FE4 SF4 B1000 " - pdb=" SG CYS B 190 " pdb="FE3 SF4 B1000 " - pdb=" SG CYS B 134 " pdb="FE1 SF4 B1000 " - pdb=" SG CYS B 116 " pdb="FE2 SF4 B1000 " - pdb=" SG CYS B 155 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 371 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 348 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 345 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 368 " pdb=" ZN E 402 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 382 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 360 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 385 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 363 " pdb=" ZN E 403 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 308 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 294 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 305 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 291 " pdb=" ZN F 401 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 271 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 282 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 285 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 268 " pdb=" ZN F 402 " pdb="ZN ZN F 402 " - pdb=" NE2 HIS F 258 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 255 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 257 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 276 " pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 126 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 129 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 105 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 108 " Number of angles added : 33 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5390 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 20 sheets defined 45.3% alpha, 9.6% beta 21 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 10.29 Creating SS restraints... Processing helix chain 'A' and resid 93 through 103 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 153 through 161 Processing helix chain 'A' and resid 182 through 189 removed outlier: 3.831A pdb=" N GLN A 186 " --> pdb=" O PRO A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 196 removed outlier: 4.009A pdb=" N GLU A 196 " --> pdb=" O PRO A 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 192 through 196' Processing helix chain 'A' and resid 274 through 286 removed outlier: 3.533A pdb=" N ILE A 277 " --> pdb=" O GLN A 274 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLU A 278 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS A 284 " --> pdb=" O GLN A 281 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE A 285 " --> pdb=" O LYS A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 327 Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 370 through 381 Processing helix chain 'A' and resid 421 through 432 removed outlier: 3.848A pdb=" N THR A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 446 Processing helix chain 'A' and resid 452 through 457 removed outlier: 4.046A pdb=" N THR A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 483 removed outlier: 3.639A pdb=" N ASN A 481 " --> pdb=" O ILE A 477 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE A 482 " --> pdb=" O VAL A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 498 Processing helix chain 'A' and resid 516 through 524 removed outlier: 3.881A pdb=" N ARG A 520 " --> pdb=" O PRO A 516 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLU A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 535 Processing helix chain 'A' and resid 538 through 553 Processing helix chain 'A' and resid 565 through 573 removed outlier: 4.122A pdb=" N GLU A 570 " --> pdb=" O PHE A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 597 removed outlier: 4.100A pdb=" N LYS A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 642 Processing helix chain 'A' and resid 668 through 676 Processing helix chain 'A' and resid 678 through 683 Processing helix chain 'A' and resid 706 through 717 removed outlier: 3.751A pdb=" N LEU A 713 " --> pdb=" O GLN A 709 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLN A 714 " --> pdb=" O GLN A 710 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 34 Processing helix chain 'B' and resid 48 through 62 Processing helix chain 'B' and resid 77 through 98 Processing helix chain 'B' and resid 119 through 122 No H-bonds generated for 'chain 'B' and resid 119 through 122' Processing helix chain 'B' and resid 127 through 137 removed outlier: 4.646A pdb=" N ASP B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLY B 132 " --> pdb=" O LYS B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 147 removed outlier: 3.949A pdb=" N GLN B 147 " --> pdb=" O ARG B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 164 removed outlier: 4.650A pdb=" N ALA B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 187 Processing helix chain 'B' and resid 191 through 199 Processing helix chain 'B' and resid 209 through 213 removed outlier: 4.264A pdb=" N LEU B 213 " --> pdb=" O HIS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 221 removed outlier: 3.871A pdb=" N ASP B 219 " --> pdb=" O PRO B 215 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU B 220 " --> pdb=" O LYS B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 247 removed outlier: 3.573A pdb=" N MET B 247 " --> pdb=" O CYS B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 271 removed outlier: 3.994A pdb=" N GLU B 264 " --> pdb=" O GLN B 260 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 334 removed outlier: 3.693A pdb=" N GLY B 331 " --> pdb=" O GLU B 327 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 345 removed outlier: 3.844A pdb=" N VAL B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG B 343 " --> pdb=" O TYR B 339 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU B 344 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG B 345 " --> pdb=" O LYS B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 364 Processing helix chain 'B' and resid 370 through 379 removed outlier: 3.643A pdb=" N PHE B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLU B 377 " --> pdb=" O ARG B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 386 Processing helix chain 'B' and resid 395 through 409 Processing helix chain 'B' and resid 442 through 448 Proline residue: B 446 - end of helix No H-bonds generated for 'chain 'B' and resid 442 through 448' Processing helix chain 'B' and resid 467 through 470 No H-bonds generated for 'chain 'B' and resid 467 through 470' Processing helix chain 'B' and resid 508 through 510 No H-bonds generated for 'chain 'B' and resid 508 through 510' Processing helix chain 'B' and resid 514 through 528 Processing helix chain 'B' and resid 542 through 554 Processing helix chain 'B' and resid 558 through 564 removed outlier: 3.735A pdb=" N ASN B 564 " --> pdb=" O ASN B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 589 Processing helix chain 'B' and resid 603 through 607 Processing helix chain 'B' and resid 633 through 643 Processing helix chain 'B' and resid 648 through 667 removed outlier: 4.228A pdb=" N ARG B 666 " --> pdb=" O GLN B 662 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ALA B 667 " --> pdb=" O CYS B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 685 Processing helix chain 'B' and resid 687 through 692 removed outlier: 4.286A pdb=" N LYS B 692 " --> pdb=" O ASP B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 698 No H-bonds generated for 'chain 'B' and resid 695 through 698' Processing helix chain 'B' and resid 710 through 724 Processing helix chain 'C' and resid 112 through 120 removed outlier: 3.546A pdb=" N MET C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 139 through 146 removed outlier: 3.589A pdb=" N ASN C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG C 146 " --> pdb=" O PHE C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 412 Processing helix chain 'C' and resid 419 through 421 No H-bonds generated for 'chain 'C' and resid 419 through 421' Processing helix chain 'C' and resid 424 through 434 Processing helix chain 'C' and resid 455 through 478 removed outlier: 3.503A pdb=" N GLU C 460 " --> pdb=" O ASP C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 515 removed outlier: 4.131A pdb=" N GLU C 488 " --> pdb=" O PRO C 484 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS C 489 " --> pdb=" O PHE C 485 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N CYS C 506 " --> pdb=" O VAL C 502 " (cutoff:3.500A) Proline residue: C 507 - end of helix Processing helix chain 'C' and resid 521 through 546 removed outlier: 3.833A pdb=" N ILE C 525 " --> pdb=" O LEU C 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 28 through 36 removed outlier: 3.809A pdb=" N GLY D 36 " --> pdb=" O ASP D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 46 Processing helix chain 'D' and resid 50 through 61 removed outlier: 3.545A pdb=" N ASN D 54 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N PHE D 61 " --> pdb=" O MET D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 74 removed outlier: 3.699A pdb=" N TRP D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 93 Processing helix chain 'D' and resid 112 through 122 Processing helix chain 'D' and resid 145 through 164 Processing helix chain 'D' and resid 173 through 181 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 208 through 226 removed outlier: 4.592A pdb=" N GLN D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N SER D 225 " --> pdb=" O GLN D 221 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG D 226 " --> pdb=" O THR D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 241 Processing helix chain 'D' and resid 256 through 268 Processing helix chain 'D' and resid 285 through 291 removed outlier: 4.330A pdb=" N SER D 291 " --> pdb=" O ALA D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 330 Processing helix chain 'D' and resid 348 through 356 Processing helix chain 'D' and resid 361 through 370 Processing helix chain 'D' and resid 374 through 378 Processing helix chain 'D' and resid 385 through 398 removed outlier: 4.145A pdb=" N ARG D 398 " --> pdb=" O TRP D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 428 Processing helix chain 'D' and resid 445 through 461 removed outlier: 4.524A pdb=" N SER D 449 " --> pdb=" O PRO D 445 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASP D 450 " --> pdb=" O ALA D 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 21 removed outlier: 3.553A pdb=" N ILE E 21 " --> pdb=" O THR E 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 18 through 21' Processing helix chain 'E' and resid 29 through 41 Processing helix chain 'E' and resid 69 through 72 Processing helix chain 'E' and resid 80 through 98 Processing helix chain 'E' and resid 124 through 136 removed outlier: 4.513A pdb=" N ASP E 136 " --> pdb=" O LYS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 158 removed outlier: 4.639A pdb=" N HIS E 158 " --> pdb=" O GLN E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 192 Processing helix chain 'E' and resid 206 through 215 Processing helix chain 'E' and resid 225 through 236 Processing helix chain 'E' and resid 273 through 277 removed outlier: 3.681A pdb=" N ASP E 277 " --> pdb=" O MET E 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 273 through 277' Processing helix chain 'E' and resid 315 through 325 removed outlier: 4.443A pdb=" N SER E 321 " --> pdb=" O HIS E 317 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TYR E 322 " --> pdb=" O LEU E 318 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N HIS E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N HIS E 324 " --> pdb=" O ARG E 320 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU E 325 " --> pdb=" O SER E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 377 Processing helix chain 'E' and resid 383 through 386 No H-bonds generated for 'chain 'E' and resid 383 through 386' Processing helix chain 'F' and resid 19 through 27 Processing helix chain 'F' and resid 34 through 51 Processing helix chain 'F' and resid 102 through 120 Processing helix chain 'F' and resid 133 through 150 removed outlier: 3.576A pdb=" N GLU F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 186 Processing helix chain 'F' and resid 201 through 210 Processing helix chain 'F' and resid 220 through 230 removed outlier: 4.705A pdb=" N LEU F 224 " --> pdb=" O PRO F 221 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL F 230 " --> pdb=" O LEU F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 240 removed outlier: 3.958A pdb=" N GLN F 240 " --> pdb=" O ASP F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 287 Processing helix chain 'G' and resid 14 through 26 Processing helix chain 'G' and resid 47 through 63 removed outlier: 3.695A pdb=" N VAL G 50 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ASN G 51 " --> pdb=" O GLU G 48 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL G 52 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP G 62 " --> pdb=" O GLU G 59 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN G 63 " --> pdb=" O LEU G 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 890 through 901 Processing helix chain 'H' and resid 909 through 914 Processing helix chain 'H' and resid 924 through 933 Processing helix chain 'H' and resid 936 through 938 No H-bonds generated for 'chain 'H' and resid 936 through 938' Processing helix chain 'K' and resid 116 through 121 Processing helix chain 'K' and resid 141 through 148 Processing helix chain 'K' and resid 152 through 156 Processing helix chain 'K' and resid 183 through 194 Processing helix chain 'K' and resid 200 through 231 removed outlier: 4.078A pdb=" N LEU K 226 " --> pdb=" O LYS K 222 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG K 228 " --> pdb=" O LYS K 224 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ALA K 229 " --> pdb=" O GLU K 225 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL K 230 " --> pdb=" O LEU K 226 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG K 231 " --> pdb=" O ARG K 227 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 76 through 78 removed outlier: 5.381A pdb=" N LYS A 117 " --> pdb=" O PRO A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 166 through 171 Processing sheet with id= C, first strand: chain 'A' and resid 438 through 441 removed outlier: 6.412A pdb=" N GLY A 336 " --> pdb=" O GLY A 465 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N THR A 467 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE A 338 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N VAL A 339 " --> pdb=" O PRO A 486 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N LEU A 488 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 361 through 365 removed outlier: 4.667A pdb=" N THR A 409 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 688 through 690 removed outlier: 3.530A pdb=" N ILE A 690 " --> pdb=" O GLU A 509 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP A 511 " --> pdb=" O ILE A 690 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA A 657 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N ALA A 508 " --> pdb=" O ALA A 657 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE A 659 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL A 510 " --> pdb=" O PHE A 659 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N SER A 661 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N CYS A 512 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL A 663 " --> pdb=" O CYS A 512 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 623 " --> pdb=" O PHE A 658 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 2 through 5 Processing sheet with id= G, first strand: chain 'B' and resid 38 through 41 removed outlier: 3.806A pdb=" N SER B 458 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR B 457 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LYS B 69 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N VAL B 232 " --> pdb=" O LYS B 69 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE B 71 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ASP B 234 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N CYS B 73 " --> pdb=" O ASP B 234 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 106 through 108 removed outlier: 6.922A pdb=" N VAL B 204 " --> pdb=" O LEU B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 414 through 419 Processing sheet with id= J, first strand: chain 'B' and resid 490 through 495 removed outlier: 8.258A pdb=" N GLY B 675 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N MET B 493 " --> pdb=" O GLY B 675 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N MET B 677 " --> pdb=" O MET B 493 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE B 495 " --> pdb=" O MET B 677 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N PHE B 679 " --> pdb=" O ILE B 495 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU B 566 " --> pdb=" O ILE B 595 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU B 597 " --> pdb=" O LEU B 566 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N PHE B 568 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N VAL B 599 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 96 through 100 removed outlier: 3.627A pdb=" N ILE D 109 " --> pdb=" O HIS D 97 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 248 through 250 Processing sheet with id= M, first strand: chain 'D' and resid 307 through 310 removed outlier: 3.757A pdb=" N ARG D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLN D 345 " --> pdb=" O MET D 334 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N MET D 334 " --> pdb=" O GLN D 345 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 407 through 409 removed outlier: 3.644A pdb=" N PHE D 433 " --> pdb=" O VAL D 442 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 113 through 118 removed outlier: 6.683A pdb=" N ILE E 106 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N SER E 164 " --> pdb=" O HIS E 60 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N TYR E 62 " --> pdb=" O SER E 164 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLU E 166 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N VAL E 64 " --> pdb=" O GLU E 166 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU E 168 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ASP E 66 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ILE E 170 " --> pdb=" O ASP E 66 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARG E 195 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE E 169 " --> pdb=" O ARG E 195 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N SER E 197 " --> pdb=" O ILE E 169 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 332 through 335 Processing sheet with id= Q, first strand: chain 'F' and resid 67 through 69 removed outlier: 6.343A pdb=" N GLU F 156 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LEU F 10 " --> pdb=" O GLU F 156 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LYS F 158 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL F 12 " --> pdb=" O LYS F 158 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ARG F 160 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL F 14 " --> pdb=" O ARG F 160 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU F 162 " --> pdb=" O VAL F 14 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ASP F 16 " --> pdb=" O LEU F 162 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE F 164 " --> pdb=" O ASP F 16 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU F 190 " --> pdb=" O ILE F 161 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL F 163 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP F 192 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LYS F 165 " --> pdb=" O ASP F 192 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N CYS F 194 " --> pdb=" O LYS F 165 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 8 through 11 removed outlier: 3.776A pdb=" N GLN G 36 " --> pdb=" O PHE G 44 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'K' and resid 138 through 140 Processing sheet with id= T, first strand: chain 'K' and resid 250 through 252 removed outlier: 3.798A pdb=" N MET K 256 " --> pdb=" O LEU K 252 " (cutoff:3.500A) 866 hydrogen bonds defined for protein. 2430 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 8.06 Time building geometry restraints manager: 10.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 10205 1.43 - 1.64: 13862 1.64 - 1.86: 216 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 24295 Sorted by residual: bond pdb=" C PRO B 354 " pdb=" N PRO B 355 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.36e+00 bond pdb=" N LYS H 917 " pdb=" CA LYS H 917 " ideal model delta sigma weight residual 1.459 1.470 -0.012 1.16e-02 7.43e+03 1.02e+00 bond pdb=" CA VAL C 453 " pdb=" CB VAL C 453 " ideal model delta sigma weight residual 1.537 1.549 -0.012 1.29e-02 6.01e+03 8.70e-01 bond pdb=" C3' DA L 16 " pdb=" O3' DA L 16 " ideal model delta sigma weight residual 1.422 1.450 -0.028 3.00e-02 1.11e+03 8.60e-01 bond pdb=" N PRO A 304 " pdb=" CA PRO A 304 " ideal model delta sigma weight residual 1.469 1.480 -0.011 1.28e-02 6.10e+03 7.61e-01 ... (remaining 24290 not shown) Histogram of bond angle deviations from ideal: 73.70 - 85.77: 12 85.77 - 97.83: 0 97.83 - 109.89: 3199 109.89 - 121.95: 24942 121.95 - 134.01: 4882 Bond angle restraints: 33035 Sorted by residual: angle pdb=" N GLN H 906 " pdb=" CA GLN H 906 " pdb=" C GLN H 906 " ideal model delta sigma weight residual 114.62 110.61 4.01 1.14e+00 7.69e-01 1.24e+01 angle pdb=" C LYS H 917 " pdb=" CA LYS H 917 " pdb=" CB LYS H 917 " ideal model delta sigma weight residual 110.92 115.78 -4.86 1.59e+00 3.96e-01 9.36e+00 angle pdb=" CA GLN K 197 " pdb=" C GLN K 197 " pdb=" N GLU K 198 " ideal model delta sigma weight residual 118.15 113.06 5.09 1.80e+00 3.09e-01 7.98e+00 angle pdb=" C LEU H 916 " pdb=" N LYS H 917 " pdb=" CA LYS H 917 " ideal model delta sigma weight residual 120.79 124.67 -3.88 1.39e+00 5.18e-01 7.79e+00 angle pdb=" C ASP B 423 " pdb=" N ARG B 424 " pdb=" CA ARG B 424 " ideal model delta sigma weight residual 121.54 126.73 -5.19 1.91e+00 2.74e-01 7.39e+00 ... (remaining 33030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.42: 14191 28.42 - 56.85: 393 56.85 - 85.27: 25 85.27 - 113.70: 1 113.70 - 142.12: 1 Dihedral angle restraints: 14611 sinusoidal: 6297 harmonic: 8314 Sorted by residual: dihedral pdb=" CA ASP A 70 " pdb=" C ASP A 70 " pdb=" N HIS A 71 " pdb=" CA HIS A 71 " ideal model delta harmonic sigma weight residual 0.00 -22.24 22.24 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" C4' DA L 9 " pdb=" C3' DA L 9 " pdb=" O3' DA L 9 " pdb=" P DC L 10 " ideal model delta sinusoidal sigma weight residual 220.00 77.88 142.12 1 3.50e+01 8.16e-04 1.40e+01 dihedral pdb=" CA ASP A 81 " pdb=" C ASP A 81 " pdb=" N GLY A 82 " pdb=" CA GLY A 82 " ideal model delta harmonic sigma weight residual 180.00 161.85 18.15 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 14608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2339 0.027 - 0.054: 871 0.054 - 0.081: 255 0.081 - 0.108: 190 0.108 - 0.135: 41 Chirality restraints: 3696 Sorted by residual: chirality pdb=" CB VAL C 453 " pdb=" CA VAL C 453 " pdb=" CG1 VAL C 453 " pdb=" CG2 VAL C 453 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CB VAL A 92 " pdb=" CA VAL A 92 " pdb=" CG1 VAL A 92 " pdb=" CG2 VAL A 92 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA ILE B 535 " pdb=" N ILE B 535 " pdb=" C ILE B 535 " pdb=" CB ILE B 535 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 3693 not shown) Planarity restraints: 4058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 582 " -0.039 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO A 583 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 353 " -0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO B 354 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 354 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 354 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 373 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.80e+00 pdb=" N PRO D 374 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO D 374 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 374 " 0.019 5.00e-02 4.00e+02 ... (remaining 4055 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 507 2.69 - 3.25: 23429 3.25 - 3.80: 37907 3.80 - 4.35: 49117 4.35 - 4.90: 79200 Nonbonded interactions: 190160 Sorted by model distance: nonbonded pdb=" O ILE H 899 " pdb=" OG SER H 903 " model vdw 2.142 2.440 nonbonded pdb=" O PHE A 378 " pdb=" OG SER A 382 " model vdw 2.184 2.440 nonbonded pdb=" O LEU B 382 " pdb=" OG1 THR B 385 " model vdw 2.225 2.440 nonbonded pdb=" OG SER E 243 " pdb=" O ALA F 288 " model vdw 2.231 2.440 nonbonded pdb=" O LEU E 30 " pdb=" OG1 THR E 33 " model vdw 2.239 2.440 ... (remaining 190155 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 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: 0.020 Extract box with map and model: 6.630 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 78.410 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.090 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 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 : 0.002 0.037 24295 Z= 0.134 Angle : 0.472 8.097 33035 Z= 0.274 Chirality : 0.037 0.135 3696 Planarity : 0.003 0.059 4058 Dihedral : 11.969 142.123 9221 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.32 % Favored : 95.65 % Rotamer: Outliers : 2.23 % Allowed : 5.90 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % 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: 0.93 (0.17), residues: 2804 helix: 1.97 (0.15), residues: 1316 sheet: 0.45 (0.29), residues: 360 loop : -0.98 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 511 HIS 0.004 0.000 HIS B 729 PHE 0.010 0.001 PHE A 482 TYR 0.012 0.001 TYR A 534 ARG 0.003 0.000 ARG A 676 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 956 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 900 time to evaluate : 2.550 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: 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: 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 outliers start: 56 outliers final: 18 residues processed: 941 average time/residue: 0.4240 time to fit residues: 579.1722 Evaluate side-chains 760 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 742 time to evaluate : 2.852 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2249 time to fit residues: 11.5006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 239 optimal weight: 0.0870 chunk 215 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 165 optimal weight: 0.0060 chunk 257 optimal weight: 1.9990 overall best weight: 1.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 ASN B 210 HIS B 238 ASN B 241 ASN B 560 ASN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 HIS B 707 ASN ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 GLN ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN ** E 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN F 185 GLN F 248 HIS ** H 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 146 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 24295 Z= 0.336 Angle : 0.659 9.906 33035 Z= 0.341 Chirality : 0.045 0.198 3696 Planarity : 0.005 0.071 4058 Dihedral : 12.775 142.763 3575 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.63 % Favored : 94.33 % Rotamer: Outliers : 4.50 % Allowed : 16.02 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % 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: 0.19 (0.16), residues: 2804 helix: 1.19 (0.14), residues: 1329 sheet: 0.11 (0.27), residues: 373 loop : -1.16 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 11 HIS 0.021 0.002 HIS D 424 PHE 0.021 0.002 PHE A 703 TYR 0.024 0.002 TYR K 246 ARG 0.008 0.001 ARG D 276 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 785 time to evaluate : 2.694 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: 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: symmetry clash outliers start: 113 outliers final: 61 residues processed: 841 average time/residue: 0.4136 time to fit residues: 510.0181 Evaluate side-chains 814 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 753 time to evaluate : 2.468 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.2096 time to fit residues: 27.4410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 143 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 214 optimal weight: 5.9990 chunk 175 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 258 optimal weight: 5.9990 chunk 279 optimal weight: 4.9990 chunk 230 optimal weight: 0.6980 chunk 256 optimal weight: 0.1980 chunk 88 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 ASN A 564 ASN ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 HIS ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 349 GLN F 48 HIS F 155 GLN F 179 ASN F 185 GLN F 188 ASN F 205 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24295 Z= 0.236 Angle : 0.604 9.150 33035 Z= 0.307 Chirality : 0.042 0.205 3696 Planarity : 0.004 0.105 4058 Dihedral : 12.789 146.280 3575 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.67 % Favored : 95.29 % Rotamer: Outliers : 2.71 % Allowed : 20.17 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % 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: 0.16 (0.16), residues: 2804 helix: 1.19 (0.15), residues: 1319 sheet: -0.04 (0.26), residues: 385 loop : -1.15 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 55 HIS 0.018 0.001 HIS C 474 PHE 0.015 0.002 PHE A 659 TYR 0.022 0.002 TYR A 61 ARG 0.014 0.001 ARG D 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 762 time to evaluate : 2.886 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 36 residues processed: 790 average time/residue: 0.4450 time to fit residues: 515.1048 Evaluate side-chains 780 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 744 time to evaluate : 2.778 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.3338 time to fit residues: 24.9808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 255 optimal weight: 2.9990 chunk 194 optimal weight: 0.5980 chunk 134 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 123 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 259 optimal weight: 0.5980 chunk 274 optimal weight: 9.9990 chunk 135 optimal weight: 6.9990 chunk 245 optimal weight: 0.0070 chunk 73 optimal weight: 0.7980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 499 ASN A 555 ASN ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN B 519 ASN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN F 205 GLN ** H 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24295 Z= 0.198 Angle : 0.604 9.322 33035 Z= 0.306 Chirality : 0.042 0.397 3696 Planarity : 0.004 0.059 4058 Dihedral : 12.828 147.722 3575 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.24 % Favored : 94.72 % Rotamer: Outliers : 2.75 % Allowed : 21.36 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % 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: 0.15 (0.16), residues: 2804 helix: 1.16 (0.15), residues: 1317 sheet: -0.04 (0.27), residues: 377 loop : -1.13 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP D 55 HIS 0.016 0.001 HIS C 474 PHE 0.018 0.001 PHE A 703 TYR 0.021 0.002 TYR A 581 ARG 0.009 0.001 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 746 time to evaluate : 2.731 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: 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: symmetry clash outliers start: 69 outliers final: 32 residues processed: 773 average time/residue: 0.4351 time to fit residues: 489.7769 Evaluate side-chains 754 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 722 time to evaluate : 2.662 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.2610 time to fit residues: 19.0745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 228 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 204 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 189 optimal weight: 0.0020 chunk 0 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 246 optimal weight: 0.1980 chunk 69 optimal weight: 6.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 HIS A 481 ASN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 ASN ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 ASN E 256 GLN ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24295 Z= 0.209 Angle : 0.619 10.188 33035 Z= 0.314 Chirality : 0.042 0.196 3696 Planarity : 0.004 0.107 4058 Dihedral : 12.932 148.303 3575 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.03 % Favored : 94.94 % Rotamer: Outliers : 2.03 % Allowed : 22.88 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % 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: 0.11 (0.16), residues: 2804 helix: 1.12 (0.15), residues: 1318 sheet: -0.02 (0.27), residues: 364 loop : -1.13 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP D 55 HIS 0.019 0.001 HIS D 424 PHE 0.038 0.002 PHE A 392 TYR 0.024 0.002 TYR A 163 ARG 0.013 0.001 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 742 time to evaluate : 2.719 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 27 residues processed: 766 average time/residue: 0.4451 time to fit residues: 496.9562 Evaluate side-chains 754 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 727 time to evaluate : 2.670 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2615 time to fit residues: 16.0554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 92 optimal weight: 7.9990 chunk 247 optimal weight: 0.9980 chunk 54 optimal weight: 0.3980 chunk 161 optimal weight: 0.0030 chunk 67 optimal weight: 3.9990 chunk 274 optimal weight: 10.0000 chunk 228 optimal weight: 0.9990 chunk 127 optimal weight: 20.0000 chunk 22 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 ASN A 564 ASN ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN B 519 ASN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 HIS ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 HIS F 205 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24295 Z= 0.260 Angle : 0.648 10.155 33035 Z= 0.328 Chirality : 0.043 0.294 3696 Planarity : 0.004 0.081 4058 Dihedral : 13.021 148.317 3575 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.39 % Favored : 94.58 % Rotamer: Outliers : 2.59 % Allowed : 23.56 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % 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: 0.00 (0.16), residues: 2804 helix: 1.01 (0.15), residues: 1332 sheet: -0.12 (0.27), residues: 358 loop : -1.16 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 55 HIS 0.013 0.001 HIS D 424 PHE 0.039 0.002 PHE A 392 TYR 0.048 0.002 TYR A 581 ARG 0.014 0.001 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 753 time to evaluate : 2.675 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 outliers start: 65 outliers final: 40 residues processed: 771 average time/residue: 0.4463 time to fit residues: 500.9613 Evaluate side-chains 771 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 731 time to evaluate : 2.637 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.2442 time to fit residues: 20.8159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 264 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 231 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 273 optimal weight: 0.8980 chunk 171 optimal weight: 0.0070 chunk 166 optimal weight: 0.7980 chunk 126 optimal weight: 0.4980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 683 GLN B 37 HIS ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN ** H 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24295 Z= 0.221 Angle : 0.662 11.998 33035 Z= 0.333 Chirality : 0.043 0.205 3696 Planarity : 0.004 0.063 4058 Dihedral : 12.983 148.753 3575 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.28 % Favored : 94.69 % Rotamer: Outliers : 1.20 % Allowed : 25.43 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % 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: -0.05 (0.16), residues: 2804 helix: 0.92 (0.15), residues: 1332 sheet: -0.19 (0.28), residues: 344 loop : -1.10 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 55 HIS 0.014 0.001 HIS D 424 PHE 0.034 0.002 PHE A 270 TYR 0.047 0.002 TYR A 581 ARG 0.021 0.001 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 738 time to evaluate : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 14 residues processed: 748 average time/residue: 0.4451 time to fit residues: 483.1506 Evaluate side-chains 740 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 726 time to evaluate : 2.505 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3085 time to fit residues: 10.8074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 169 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 82 optimal weight: 0.2980 chunk 53 optimal weight: 0.3980 chunk 174 optimal weight: 1.9990 chunk 186 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 215 optimal weight: 7.9990 chunk 249 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 ASN B 37 HIS B 519 ASN ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN F 237 GLN ** H 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24295 Z= 0.266 Angle : 0.715 13.105 33035 Z= 0.360 Chirality : 0.044 0.192 3696 Planarity : 0.004 0.064 4058 Dihedral : 12.947 148.147 3575 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.85 % Favored : 94.12 % Rotamer: Outliers : 1.32 % Allowed : 26.54 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % 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: -0.23 (0.16), residues: 2804 helix: 0.78 (0.15), residues: 1339 sheet: -0.38 (0.27), residues: 349 loop : -1.16 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 511 HIS 0.014 0.001 HIS D 424 PHE 0.046 0.002 PHE A 392 TYR 0.034 0.002 TYR A 581 ARG 0.019 0.001 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 754 time to evaluate : 2.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 21 residues processed: 766 average time/residue: 0.4345 time to fit residues: 487.9603 Evaluate side-chains 769 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 748 time to evaluate : 2.641 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2309 time to fit residues: 12.7127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 262 optimal weight: 0.9980 chunk 239 optimal weight: 1.9990 chunk 255 optimal weight: 0.8980 chunk 153 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 230 optimal weight: 0.8980 chunk 241 optimal weight: 0.9990 chunk 254 optimal weight: 2.9990 chunk 167 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 415 HIS B 37 HIS ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 HIS D 181 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN F 205 GLN G 27 ASN ** H 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24295 Z= 0.246 Angle : 0.724 14.489 33035 Z= 0.364 Chirality : 0.044 0.188 3696 Planarity : 0.005 0.097 4058 Dihedral : 12.898 148.572 3575 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.63 % Favored : 94.33 % Rotamer: Outliers : 0.80 % Allowed : 27.10 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % 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: -0.27 (0.16), residues: 2804 helix: 0.70 (0.15), residues: 1334 sheet: -0.35 (0.27), residues: 340 loop : -1.13 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP D 213 HIS 0.013 0.001 HIS D 424 PHE 0.046 0.002 PHE A 392 TYR 0.026 0.002 TYR A 581 ARG 0.013 0.001 ARG F 252 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 763 time to evaluate : 2.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 767 average time/residue: 0.4619 time to fit residues: 519.6016 Evaluate side-chains 761 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 750 time to evaluate : 2.499 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2578 time to fit residues: 8.4271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 269 optimal weight: 0.7980 chunk 164 optimal weight: 0.5980 chunk 127 optimal weight: 20.0000 chunk 187 optimal weight: 0.0040 chunk 282 optimal weight: 1.9990 chunk 260 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 174 optimal weight: 0.1980 chunk 138 optimal weight: 6.9990 chunk 178 optimal weight: 0.7980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 GLN A 564 ASN B 37 HIS B 499 ASN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 GLN D 97 HIS ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 HIS F 205 GLN H 893 GLN ** K 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24295 Z= 0.219 Angle : 0.746 17.766 33035 Z= 0.373 Chirality : 0.043 0.206 3696 Planarity : 0.004 0.064 4058 Dihedral : 12.856 148.515 3575 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.53 % Favored : 94.44 % Rotamer: Outliers : 0.56 % Allowed : 27.82 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.16), residues: 2804 helix: 0.67 (0.15), residues: 1322 sheet: -0.37 (0.27), residues: 339 loop : -1.15 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.002 TRP D 213 HIS 0.013 0.001 HIS D 424 PHE 0.027 0.002 PHE B 720 TYR 0.023 0.001 TYR A 581 ARG 0.012 0.001 ARG A 298 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 752 time to evaluate : 2.886 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 outliers start: 14 outliers final: 8 residues processed: 753 average time/residue: 0.4506 time to fit residues: 493.3115 Evaluate side-chains 748 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 740 time to evaluate : 2.828 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2885 time to fit residues: 8.0272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 240 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 207 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 225 optimal weight: 0.8980 chunk 94 optimal weight: 0.4980 chunk 231 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 198 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN A 415 HIS B 37 HIS B 328 HIS B 519 ASN B 585 GLN B 698 GLN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 HIS ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN ** F 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.150057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.121839 restraints weight = 40347.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.125780 restraints weight = 19136.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.128298 restraints weight = 11593.106| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.5379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24295 Z= 0.244 Angle : 0.752 12.438 33035 Z= 0.377 Chirality : 0.044 0.220 3696 Planarity : 0.004 0.062 4058 Dihedral : 12.891 148.252 3575 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.71 % Favored : 94.26 % Rotamer: Outliers : 0.72 % Allowed : 28.26 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.16), residues: 2804 helix: 0.69 (0.15), residues: 1319 sheet: -0.46 (0.27), residues: 349 loop : -1.16 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.003 TRP D 213 HIS 0.010 0.001 HIS K 136 PHE 0.029 0.002 PHE A 392 TYR 0.032 0.002 TYR A 581 ARG 0.013 0.001 ARG A 298 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7830.19 seconds wall clock time: 140 minutes 59.43 seconds (8459.43 seconds total)