Starting phenix.real_space_refine on Sun Sep 29 20:33:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebu_27998/09_2024/8ebu_27998.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebu_27998/09_2024/8ebu_27998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebu_27998/09_2024/8ebu_27998.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebu_27998/09_2024/8ebu_27998.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebu_27998/09_2024/8ebu_27998.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebu_27998/09_2024/8ebu_27998.cif" } resolution = 3.3 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= 0.020 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 47 5.49 5 S 146 5.16 5 C 14864 2.51 5 N 4071 2.21 5 O 4405 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23543 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: {'PTRANS': 24, 'TRANS': 579} 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: 1444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1444 Classifications: {'peptide': 179} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 172} 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: {'PTRANS': 21, '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: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 303 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain breaks: 1 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: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 496 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "M" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 469 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} 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 55.952 39.988 41.090 1.00125.15 S ATOM 6134 SG CYS B 155 52.333 36.397 36.791 1.00126.77 S ATOM 5965 SG CYS B 134 53.794 42.600 35.650 1.00119.97 S ATOM 6423 SG CYS B 190 49.618 41.350 39.627 1.00118.76 S ATOM 17933 SG CYS E 345 41.827 61.151 132.535 1.00 53.91 S ATOM 17955 SG CYS E 348 43.604 64.300 133.735 1.00 43.62 S ATOM 18112 SG CYS E 368 41.879 64.252 130.312 1.00 45.52 S ATOM 18133 SG CYS E 371 45.038 62.236 130.910 1.00 40.96 S ATOM 18053 SG CYS E 360 40.833 50.582 126.921 1.00 57.69 S ATOM 18071 SG CYS E 363 41.126 50.067 130.685 1.00 61.60 S ATOM 18220 SG CYS E 382 43.731 52.125 128.803 1.00 43.88 S ATOM 18237 SG CYS E 385 43.624 48.395 128.291 1.00 42.71 S ATOM 17497 SG CYS E 291 80.132 38.822 120.915 1.00 50.76 S ATOM 17519 SG CYS E 294 83.655 37.423 120.505 1.00 63.45 S ATOM 17608 SG CYS E 305 82.372 39.983 118.017 1.00 52.10 S ATOM 17631 SG CYS E 308 80.907 36.507 118.037 1.00 57.40 S ATOM 20133 SG CYS F 268 60.437 38.234 111.588 1.00 32.82 S ATOM 20152 SG CYS F 271 57.912 40.031 113.751 1.00 35.10 S ATOM 20237 SG CYS F 282 57.928 36.223 113.703 1.00 69.28 S ATOM 20257 SG CYS F 285 56.763 38.118 110.659 1.00 68.43 S ATOM 20025 SG CYS F 255 62.252 34.521 123.735 1.00 47.32 S ATOM 20042 SG CYS F 257 59.734 31.713 123.202 1.00 56.61 S ATOM 20191 SG CYS F 276 63.496 30.887 123.579 1.00 49.54 S ATOM 21147 SG CYS K 105 44.962 102.777 24.284 1.00103.00 S ATOM 21171 SG CYS K 108 44.497 102.477 20.518 1.00 98.85 S ATOM 21319 SG CYS K 126 47.124 100.350 22.324 1.00 98.15 S ATOM 21341 SG CYS K 129 47.618 104.079 21.816 1.00103.44 S Time building chain proxies: 12.98, per 1000 atoms: 0.55 Number of scatterers: 23543 At special positions: 0 Unit cell: (119.52, 156.87, 181.77, 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 146 16.00 P 47 15.00 O 4405 8.00 N 4071 7.00 C 14864 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.75 Conformation dependent library (CDL) restraints added in 2.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B1000 " pdb="FE3 SF4 B1000 " - pdb=" SG CYS B 134 " pdb="FE4 SF4 B1000 " - pdb=" SG CYS B 190 " pdb="FE2 SF4 B1000 " - pdb=" SG CYS B 155 " pdb="FE1 SF4 B1000 " - pdb=" SG CYS B 116 " 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 345 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 348 " 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 268 " 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 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 129 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 126 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 108 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 105 " Number of angles added : 33 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5342 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 23 sheets defined 51.2% alpha, 10.7% beta 20 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 7.72 Creating SS restraints... Processing helix chain 'A' and resid 92 through 104 removed outlier: 3.518A pdb=" N ALA A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 129 Processing helix chain 'A' and resid 132 through 143 Processing helix chain 'A' and resid 152 through 162 removed outlier: 3.995A pdb=" N SER A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 190 removed outlier: 4.347A pdb=" N ILE A 185 " --> pdb=" O HIS A 181 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN A 186 " --> pdb=" O PRO A 182 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 196 removed outlier: 3.649A pdb=" N ARG A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU A 196 " --> pdb=" O PRO A 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 191 through 196' Processing helix chain 'A' and resid 199 through 203 removed outlier: 4.205A pdb=" N GLU A 203 " --> pdb=" O ARG A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 276 through 287 removed outlier: 3.636A pdb=" N LEU A 280 " --> pdb=" O MET A 276 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 285 " --> pdb=" O GLN A 281 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N HIS A 286 " --> pdb=" O LYS A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 328 Processing helix chain 'A' and resid 346 through 358 Processing helix chain 'A' and resid 369 through 382 Processing helix chain 'A' and resid 420 through 431 Processing helix chain 'A' and resid 443 through 446 Processing helix chain 'A' and resid 451 through 458 removed outlier: 4.034A pdb=" N LEU A 455 " --> pdb=" O PHE A 451 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 484 removed outlier: 4.260A pdb=" N PHE A 482 " --> pdb=" O VAL A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 499 Processing helix chain 'A' and resid 515 through 525 removed outlier: 3.509A pdb=" N ARG A 520 " --> pdb=" O PRO A 516 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 536 removed outlier: 3.542A pdb=" N TYR A 534 " --> pdb=" O ARG A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 554 removed outlier: 3.545A pdb=" N ARG A 554 " --> pdb=" O PHE A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 576 removed outlier: 3.886A pdb=" N GLU A 570 " --> pdb=" O PHE A 566 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG A 574 " --> pdb=" O GLU A 570 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A 575 " --> pdb=" O TYR A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 598 removed outlier: 4.062A pdb=" N LYS A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N HIS A 598 " --> pdb=" O GLN A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 642 Processing helix chain 'A' and resid 667 through 677 removed outlier: 4.127A pdb=" N ALA A 671 " --> pdb=" O THR A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 684 Processing helix chain 'A' and resid 705 through 717 removed outlier: 3.686A pdb=" N GLN A 709 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 713 " --> pdb=" O GLN A 709 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN A 714 " --> pdb=" O GLN A 710 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 35 Processing helix chain 'B' and resid 47 through 63 removed outlier: 3.579A pdb=" N SER B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 99 Processing helix chain 'B' and resid 129 through 138 Processing helix chain 'B' and resid 139 through 147 removed outlier: 3.877A pdb=" N GLN B 147 " --> pdb=" O ARG B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 165 removed outlier: 4.570A pdb=" N ALA B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 188 Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 214 through 222 removed outlier: 3.913A pdb=" N ASP B 219 " --> pdb=" O PRO B 215 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU B 220 " --> pdb=" O LYS B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.982A pdb=" N MET B 247 " --> pdb=" O CYS B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 272 removed outlier: 4.029A pdb=" N GLU B 264 " --> pdb=" O GLN B 260 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG B 272 " --> pdb=" O LYS B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 331 removed outlier: 3.971A pdb=" N GLY B 331 " --> pdb=" O GLU B 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 327 through 331' Processing helix chain 'B' and resid 335 through 346 removed outlier: 4.099A pdb=" N TYR B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG B 343 " --> pdb=" O TYR B 339 " (cutoff:3.500A) removed outlier: 3.873A 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 355 through 365 removed outlier: 4.293A pdb=" N SER B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN B 363 " --> pdb=" O SER B 359 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG B 364 " --> pdb=" O GLY B 360 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL B 365 " --> pdb=" O LEU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 374 through 387 removed outlier: 3.875A pdb=" N ARG B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER B 381 " --> pdb=" O GLU B 377 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N HIS B 384 " --> pdb=" O ARG B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 410 removed outlier: 3.542A pdb=" N THR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 449 Processing helix chain 'B' and resid 466 through 471 Processing helix chain 'B' and resid 507 through 511 Processing helix chain 'B' and resid 513 through 528 Processing helix chain 'B' and resid 541 through 555 Processing helix chain 'B' and resid 557 through 563 Processing helix chain 'B' and resid 573 through 590 removed outlier: 3.834A pdb=" N ASN B 590 " --> pdb=" O GLU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 608 removed outlier: 4.235A pdb=" N GLU B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE B 608 " --> pdb=" O VAL B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 644 Processing helix chain 'B' and resid 647 through 665 Processing helix chain 'B' and resid 666 through 668 No H-bonds generated for 'chain 'B' and resid 666 through 668' Processing helix chain 'B' and resid 682 through 685 Processing helix chain 'B' and resid 686 through 691 Processing helix chain 'B' and resid 694 through 699 removed outlier: 3.792A pdb=" N GLU B 699 " --> pdb=" O ARG B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 725 Processing helix chain 'C' and resid 124 through 133 Processing helix chain 'C' and resid 138 through 147 removed outlier: 3.629A pdb=" N ASN C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG C 146 " --> pdb=" O PHE C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 413 removed outlier: 4.008A pdb=" N ALA C 413 " --> pdb=" O GLN C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 435 Processing helix chain 'C' and resid 454 through 479 Processing helix chain 'C' and resid 483 through 516 removed outlier: 3.854A pdb=" N GLU C 487 " --> pdb=" O THR C 483 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU C 488 " --> pdb=" O PRO C 484 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS C 489 " --> pdb=" O PHE C 485 " (cutoff:3.500A) removed outlier: 4.412A 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 520 through 547 removed outlier: 4.231A pdb=" N HIS C 524 " --> pdb=" O ASN C 520 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE C 525 " --> pdb=" O LEU C 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 25 removed outlier: 3.551A pdb=" N PHE D 22 " --> pdb=" O ASN D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 35 Processing helix chain 'D' and resid 37 through 48 Processing helix chain 'D' and resid 49 through 59 removed outlier: 3.687A pdb=" N ASN D 54 " --> pdb=" O SER D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 73 Processing helix chain 'D' and resid 79 through 93 Processing helix chain 'D' and resid 111 through 123 Processing helix chain 'D' and resid 144 through 165 Processing helix chain 'D' and resid 172 through 182 Processing helix chain 'D' and resid 197 through 206 Processing helix chain 'D' and resid 207 through 223 Processing helix chain 'D' and resid 224 through 226 No H-bonds generated for 'chain 'D' and resid 224 through 226' Processing helix chain 'D' and resid 229 through 242 Processing helix chain 'D' and resid 255 through 269 Processing helix chain 'D' and resid 284 through 289 Processing helix chain 'D' and resid 321 through 330 Processing helix chain 'D' and resid 347 through 357 Processing helix chain 'D' and resid 360 through 371 Processing helix chain 'D' and resid 375 through 379 removed outlier: 3.565A pdb=" N GLN D 379 " --> pdb=" O MET D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 399 removed outlier: 4.234A pdb=" N ARG D 398 " --> pdb=" O TRP D 394 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP D 399 " --> pdb=" O GLU D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 429 Processing helix chain 'D' and resid 444 through 462 removed outlier: 4.343A pdb=" N SER D 449 " --> pdb=" O PRO D 445 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP D 450 " --> pdb=" O ALA D 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 21 removed outlier: 3.566A pdb=" N GLU E 20 " --> pdb=" O ARG E 17 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE E 21 " --> pdb=" O THR E 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 17 through 21' Processing helix chain 'E' and resid 29 through 42 removed outlier: 3.697A pdb=" N LYS E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 79 through 99 Processing helix chain 'E' and resid 123 through 136 removed outlier: 3.718A pdb=" N HIS E 127 " --> pdb=" O ASN E 123 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASP E 136 " --> pdb=" O LYS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 157 Processing helix chain 'E' and resid 181 through 192 removed outlier: 4.026A pdb=" N LEU E 185 " --> pdb=" O ASN E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 216 Processing helix chain 'E' and resid 224 through 237 removed outlier: 3.740A pdb=" N SER E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 277 removed outlier: 4.008A pdb=" N ASP E 277 " --> pdb=" O MET E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 320 Processing helix chain 'E' and resid 321 through 326 removed outlier: 4.165A pdb=" N LEU E 325 " --> pdb=" O SER E 321 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE E 326 " --> pdb=" O TYR E 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 321 through 326' Processing helix chain 'E' and resid 368 through 378 Processing helix chain 'E' and resid 382 through 387 removed outlier: 3.682A pdb=" N HIS E 387 " --> pdb=" O PRO E 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 29 Processing helix chain 'F' and resid 33 through 52 removed outlier: 4.025A pdb=" N ASN F 52 " --> pdb=" O HIS F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 121 Processing helix chain 'F' and resid 132 through 151 Processing helix chain 'F' and resid 173 through 187 Processing helix chain 'F' and resid 200 through 211 Processing helix chain 'F' and resid 219 through 221 No H-bonds generated for 'chain 'F' and resid 219 through 221' Processing helix chain 'F' and resid 222 through 230 Processing helix chain 'F' and resid 234 through 241 removed outlier: 3.888A 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 13 through 27 Processing helix chain 'G' and resid 49 through 64 removed outlier: 3.829A pdb=" N LEU G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN G 64 " --> pdb=" O LEU G 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 890 through 902 removed outlier: 3.588A pdb=" N ALA H 894 " --> pdb=" O THR H 890 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA H 902 " --> pdb=" O ARG H 898 " (cutoff:3.500A) Processing helix chain 'H' and resid 908 through 916 Processing helix chain 'H' and resid 935 through 939 Processing helix chain 'K' and resid 115 through 122 Processing helix chain 'K' and resid 141 through 149 Processing helix chain 'K' and resid 151 through 157 Processing helix chain 'K' and resid 183 through 195 Processing helix chain 'K' and resid 196 through 232 removed outlier: 4.018A pdb=" N LEU K 226 " --> pdb=" O LYS K 222 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG K 228 " --> pdb=" O LYS K 224 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ALA K 229 " --> pdb=" O GLU K 225 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL K 230 " --> pdb=" O LEU K 226 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG K 231 " --> pdb=" O ARG K 227 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.733A pdb=" N VAL D 343 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 5.686A pdb=" N LYS A 117 " --> pdb=" O PRO A 106 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 171 removed outlier: 3.573A pdb=" N VAL A 268 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 294 through 295 Processing sheet with id=AA5, first strand: chain 'A' and resid 389 through 392 removed outlier: 4.296A pdb=" N THR A 409 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N CYS A 361 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N SER A 408 " --> pdb=" O CYS A 361 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N VAL A 363 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU A 362 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ASP A 441 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU A 364 " --> pdb=" O ASP A 441 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N VAL A 337 " --> pdb=" O LYS A 487 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 579 through 580 removed outlier: 6.570A pdb=" N ILE A 558 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ILE A 607 " --> pdb=" O ILE A 558 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL A 560 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LEU A 623 " --> pdb=" O TYR A 660 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU A 662 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLN A 625 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N SER A 664 " --> pdb=" O GLN A 625 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 688 " --> pdb=" O CYS A 507 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 2 through 5 Processing sheet with id=AA8, first strand: chain 'B' and resid 38 through 41 removed outlier: 3.656A pdb=" N SER B 458 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LYS B 69 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N VAL B 232 " --> pdb=" O LYS B 69 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE B 71 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ASP B 234 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N CYS B 73 " --> pdb=" O ASP B 234 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU B 70 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU B 107 " --> pdb=" O VAL B 206 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 250 through 251 Processing sheet with id=AB1, first strand: chain 'B' and resid 490 through 495 removed outlier: 3.586A pdb=" N CYS B 491 " --> pdb=" O GLY B 675 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET B 677 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL B 618 " --> pdb=" O VAL B 678 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ALA B 680 " --> pdb=" O VAL B 618 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N MET B 620 " --> pdb=" O ALA B 680 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL B 536 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N PHE B 621 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N PHE B 538 " --> pdb=" O PHE B 621 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE B 535 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N SER B 598 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA B 537 " --> pdb=" O SER B 598 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU B 566 " --> pdb=" O ILE B 595 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LEU B 597 " --> pdb=" O LEU B 566 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE B 568 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N VAL B 599 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 66 through 67 removed outlier: 3.668A pdb=" N ILE D 109 " --> pdb=" O HIS D 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 185 through 186 Processing sheet with id=AB4, first strand: chain 'D' and resid 249 through 250 Processing sheet with id=AB5, first strand: chain 'D' and resid 431 through 435 removed outlier: 6.503A pdb=" N VAL D 442 " --> pdb=" O VAL D 432 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU D 434 " --> pdb=" O LEU D 440 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU D 440 " --> pdb=" O GLU D 434 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET D 441 " --> pdb=" O TYR D 409 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN G 36 " --> pdb=" O PHE G 44 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 113 through 121 removed outlier: 6.714A pdb=" N ILE E 106 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N GLU E 119 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ILE E 104 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N HIS E 60 " --> pdb=" O GLU E 166 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU E 168 " --> pdb=" O HIS E 60 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N TYR E 62 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE E 170 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL E 64 " --> pdb=" O ILE E 170 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG E 165 " --> pdb=" O ARG E 195 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N SER E 197 " --> pdb=" O ARG E 165 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL E 167 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE E 199 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE E 169 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 303 through 304 removed outlier: 3.568A pdb=" N LEU E 312 " --> pdb=" O VAL E 303 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR E 311 " --> pdb=" O ARG E 251 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 257 through 258 Processing sheet with id=AB9, first strand: chain 'E' and resid 332 through 335 Processing sheet with id=AC1, first strand: chain 'F' and resid 67 through 69 removed outlier: 7.626A pdb=" N LYS F 56 " --> pdb=" O GLU F 7 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASN F 9 " --> pdb=" O LYS F 56 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ALA F 58 " --> pdb=" O ASN F 9 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU F 11 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ILE F 60 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE F 13 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N SER F 62 " --> pdb=" O ILE F 13 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL F 15 " --> pdb=" O SER F 62 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU F 8 " --> pdb=" O GLU F 156 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 253 through 254 removed outlier: 3.847A pdb=" N ALA F 253 " --> pdb=" O ILE F 262 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 103 through 104 Processing sheet with id=AC4, first strand: chain 'K' and resid 138 through 140 Processing sheet with id=AC5, first strand: chain 'K' and resid 250 through 251 1033 hydrogen bonds defined for protein. 2976 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 9.04 Time building geometry restraints manager: 6.72 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: 10158 1.43 - 1.64: 13748 1.64 - 1.86: 214 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 24132 Sorted by residual: bond pdb=" C PRO B 354 " pdb=" N PRO B 355 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.52e+00 bond pdb=" CA GLY A 465 " pdb=" C GLY A 465 " ideal model delta sigma weight residual 1.520 1.513 0.007 7.30e-03 1.88e+04 1.03e+00 bond pdb=" N SER E 245 " pdb=" CA SER E 245 " ideal model delta sigma weight residual 1.468 1.456 0.012 1.24e-02 6.50e+03 9.80e-01 bond pdb=" CA LEU D 100 " pdb=" CB LEU D 100 " ideal model delta sigma weight residual 1.524 1.537 -0.013 1.37e-02 5.33e+03 9.34e-01 bond pdb=" C3' DA L 16 " pdb=" O3' DA L 16 " ideal model delta sigma weight residual 1.422 1.451 -0.029 3.00e-02 1.11e+03 9.33e-01 ... (remaining 24127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 32375 1.64 - 3.29: 391 3.29 - 4.93: 53 4.93 - 6.58: 8 6.58 - 8.22: 4 Bond angle restraints: 32831 Sorted by residual: angle pdb=" C HIS B 612 " pdb=" N HIS B 613 " pdb=" CA HIS B 613 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" N ILE B 504 " pdb=" CA ILE B 504 " pdb=" C ILE B 504 " ideal model delta sigma weight residual 111.91 109.01 2.90 8.90e-01 1.26e+00 1.06e+01 angle pdb=" CA GLY F 126 " pdb=" C GLY F 126 " pdb=" N GLN F 127 " ideal model delta sigma weight residual 114.23 116.90 -2.67 8.80e-01 1.29e+00 9.22e+00 angle pdb=" N GLN H 906 " pdb=" CA GLN H 906 " pdb=" C GLN H 906 " ideal model delta sigma weight residual 114.62 111.29 3.33 1.14e+00 7.69e-01 8.54e+00 angle pdb=" C ASP B 423 " pdb=" N ARG B 424 " pdb=" CA ARG B 424 " ideal model delta sigma weight residual 121.54 126.60 -5.06 1.91e+00 2.74e-01 7.01e+00 ... (remaining 32826 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.16: 14166 35.16 - 70.31: 309 70.31 - 105.47: 9 105.47 - 140.63: 2 140.63 - 175.79: 3 Dihedral angle restraints: 14489 sinusoidal: 6250 harmonic: 8239 Sorted by residual: dihedral pdb=" C4' DT L 23 " pdb=" C3' DT L 23 " pdb=" O3' DT L 23 " pdb=" P DG L 24 " ideal model delta sinusoidal sigma weight residual -140.00 35.79 -175.79 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG L 21 " pdb=" C3' DG L 21 " pdb=" O3' DG L 21 " pdb=" P DC L 22 " ideal model delta sinusoidal sigma weight residual 220.00 71.20 148.80 1 3.50e+01 8.16e-04 1.45e+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 77.21 142.79 1 3.50e+01 8.16e-04 1.41e+01 ... (remaining 14486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2418 0.029 - 0.058: 830 0.058 - 0.087: 229 0.087 - 0.116: 180 0.116 - 0.145: 20 Chirality restraints: 3677 Sorted by residual: 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 -2.48 -0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA ILE B 595 " pdb=" N ILE B 595 " pdb=" C ILE B 595 " pdb=" CB ILE B 595 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-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 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 3674 not shown) Planarity restraints: 4022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 582 " -0.034 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO A 583 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 353 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO B 354 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 354 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 354 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 613 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.12e+00 pdb=" C HIS B 613 " -0.025 2.00e-02 2.50e+03 pdb=" O HIS B 613 " 0.009 2.00e-02 2.50e+03 pdb=" N TYR B 614 " 0.009 2.00e-02 2.50e+03 ... (remaining 4019 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1188 2.73 - 3.27: 23639 3.27 - 3.82: 39599 3.82 - 4.36: 46644 4.36 - 4.90: 78802 Nonbonded interactions: 189872 Sorted by model distance: nonbonded pdb=" O PHE A 378 " pdb=" OG SER A 382 " model vdw 2.188 3.040 nonbonded pdb=" O ASP A 309 " pdb=" OG1 THR A 383 " model vdw 2.213 3.040 nonbonded pdb=" OG SER E 243 " pdb=" O ALA F 288 " model vdw 2.214 3.040 nonbonded pdb=" OG1 THR B 482 " pdb=" OE2 GLU B 699 " model vdw 2.222 3.040 nonbonded pdb=" OG1 THR B 76 " pdb=" OE1 GLU B 79 " model vdw 2.223 3.040 ... (remaining 189867 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.870 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 65.240 Find NCS groups from input model: 0.320 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: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 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 0.035 24132 Z= 0.138 Angle : 0.492 8.224 32831 Z= 0.287 Chirality : 0.038 0.145 3677 Planarity : 0.003 0.052 4022 Dihedral : 13.040 175.786 9147 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.02 % Allowed : 6.23 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.17), residues: 2776 helix: 1.86 (0.15), residues: 1288 sheet: 0.52 (0.29), residues: 365 loop : -0.99 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 511 HIS 0.005 0.001 HIS B 613 PHE 0.011 0.001 PHE A 659 TYR 0.013 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) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1001 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 926 time to evaluate : 2.553 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: A 60 ASP cc_start: 0.7259 (p0) cc_final: 0.7054 (p0) REVERT: A 98 ASP cc_start: 0.6531 (m-30) cc_final: 0.6281 (m-30) REVERT: A 105 GLU cc_start: 0.7293 (pm20) cc_final: 0.7029 (pm20) REVERT: A 117 LYS cc_start: 0.8127 (tttt) cc_final: 0.7890 (ttpt) REVERT: A 153 MET cc_start: 0.6019 (mmm) cc_final: 0.5796 (mmm) REVERT: A 165 LYS cc_start: 0.7573 (mttm) cc_final: 0.7273 (mttp) REVERT: A 183 ASP cc_start: 0.7799 (p0) cc_final: 0.7484 (p0) REVERT: A 273 LYS cc_start: 0.7677 (ttmt) cc_final: 0.7338 (mtmt) REVERT: A 282 LYS cc_start: 0.8300 (tttt) cc_final: 0.8032 (ttmm) REVERT: A 298 ARG cc_start: 0.7272 (mmm160) cc_final: 0.7054 (tpp80) REVERT: A 308 ILE cc_start: 0.7416 (tp) cc_final: 0.7162 (tt) REVERT: A 309 ASP cc_start: 0.5594 (p0) cc_final: 0.4964 (p0) REVERT: A 316 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7470 (pp) REVERT: A 321 GLU cc_start: 0.7010 (mm-30) cc_final: 0.6733 (mm-30) REVERT: A 351 VAL cc_start: 0.8150 (t) cc_final: 0.7280 (p) REVERT: A 419 ARG cc_start: 0.7287 (ttm170) cc_final: 0.7068 (ttm110) REVERT: A 424 GLU cc_start: 0.7545 (tp30) cc_final: 0.7210 (tp30) REVERT: A 487 LYS cc_start: 0.8271 (ttmt) cc_final: 0.8016 (ttpp) REVERT: A 506 GLN cc_start: 0.8186 (tt0) cc_final: 0.7805 (tt0) REVERT: A 509 GLU cc_start: 0.6604 (tm-30) cc_final: 0.5969 (tm-30) REVERT: A 570 GLU cc_start: 0.5539 (OUTLIER) cc_final: 0.5325 (pm20) REVERT: A 658 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7450 (p90) REVERT: A 659 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.7329 (p90) REVERT: B 27 GLU cc_start: 0.7079 (tm-30) cc_final: 0.6870 (tm-30) REVERT: B 40 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7969 (mm) REVERT: B 53 LEU cc_start: 0.7805 (mt) cc_final: 0.6938 (mm) REVERT: B 61 ARG cc_start: 0.6473 (tpm170) cc_final: 0.5875 (tpm170) REVERT: B 63 TYR cc_start: 0.7192 (m-80) cc_final: 0.6872 (m-80) REVERT: B 73 CYS cc_start: 0.6744 (m) cc_final: 0.6530 (m) REVERT: B 133 LYS cc_start: 0.7643 (mttt) cc_final: 0.7388 (tppt) REVERT: B 176 ASN cc_start: 0.6132 (t0) cc_final: 0.5744 (t0) REVERT: B 212 LEU cc_start: 0.8228 (mt) cc_final: 0.7842 (mt) REVERT: B 241 ASN cc_start: 0.7150 (m110) cc_final: 0.6821 (m110) REVERT: B 259 CYS cc_start: 0.6510 (m) cc_final: 0.6285 (m) REVERT: B 262 ASN cc_start: 0.7210 (p0) cc_final: 0.6736 (p0) REVERT: B 338 GLU cc_start: 0.6639 (pm20) cc_final: 0.6243 (mp0) REVERT: B 341 LYS cc_start: 0.7158 (mtmm) cc_final: 0.6891 (mttt) REVERT: B 363 GLN cc_start: 0.7092 (mm-40) cc_final: 0.6854 (mm-40) REVERT: B 437 CYS cc_start: 0.6652 (t) cc_final: 0.6161 (t) REVERT: B 505 SER cc_start: 0.7324 (t) cc_final: 0.6658 (p) REVERT: B 518 ARG cc_start: 0.7454 (mtp85) cc_final: 0.7113 (mtp85) REVERT: B 533 ASP cc_start: 0.7124 (p0) cc_final: 0.6713 (p0) REVERT: B 563 ARG cc_start: 0.6952 (ptp90) cc_final: 0.6669 (ptp90) REVERT: B 583 LYS cc_start: 0.7653 (ptpp) cc_final: 0.7200 (mtmm) REVERT: B 592 ARG cc_start: 0.7616 (tpt90) cc_final: 0.6859 (mmm160) REVERT: B 668 ILE cc_start: 0.7805 (mm) cc_final: 0.7418 (mt) REVERT: B 673 ASP cc_start: 0.7573 (t0) cc_final: 0.7353 (t0) REVERT: B 682 LYS cc_start: 0.7832 (pttp) cc_final: 0.7599 (pttp) REVERT: B 711 ASP cc_start: 0.6879 (m-30) cc_final: 0.6506 (m-30) REVERT: B 722 ARG cc_start: 0.7955 (ttm-80) cc_final: 0.7612 (ttm-80) REVERT: C 430 THR cc_start: 0.8231 (m) cc_final: 0.7876 (p) REVERT: C 442 GLN cc_start: 0.2609 (OUTLIER) cc_final: 0.2167 (pt0) REVERT: C 524 HIS cc_start: 0.7499 (t-170) cc_final: 0.6624 (t-90) REVERT: C 528 MET cc_start: 0.7329 (mtp) cc_final: 0.6932 (mtm) REVERT: C 545 MET cc_start: 0.5252 (mtt) cc_final: 0.5051 (mtt) REVERT: D 47 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6705 (mm-30) REVERT: D 77 LYS cc_start: 0.7739 (mttt) cc_final: 0.7512 (mttt) REVERT: D 123 LEU cc_start: 0.8164 (mt) cc_final: 0.7951 (mp) REVERT: D 204 LEU cc_start: 0.8119 (mt) cc_final: 0.7817 (mt) REVERT: D 215 PHE cc_start: 0.7578 (t80) cc_final: 0.7137 (t80) REVERT: D 244 THR cc_start: 0.8418 (m) cc_final: 0.8056 (p) REVERT: D 249 TYR cc_start: 0.8031 (m-80) cc_final: 0.7812 (m-80) REVERT: D 261 PHE cc_start: 0.8472 (t80) cc_final: 0.8119 (t80) REVERT: D 263 GLN cc_start: 0.6903 (mm-40) cc_final: 0.6529 (mm110) REVERT: D 264 HIS cc_start: 0.7584 (m170) cc_final: 0.7143 (m170) REVERT: D 267 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7175 (mt-10) REVERT: D 312 ASN cc_start: 0.8123 (p0) cc_final: 0.7893 (p0) REVERT: D 313 TYR cc_start: 0.7999 (m-80) cc_final: 0.7684 (m-80) REVERT: D 390 GLN cc_start: 0.8238 (tp40) cc_final: 0.7574 (tp-100) REVERT: D 395 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6847 (tm-30) REVERT: D 397 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6881 (mm-30) REVERT: D 407 VAL cc_start: 0.8210 (t) cc_final: 0.7968 (m) REVERT: D 418 PHE cc_start: 0.6911 (t80) cc_final: 0.6629 (t80) REVERT: D 421 LEU cc_start: 0.8768 (tp) cc_final: 0.8435 (tt) REVERT: D 439 ARG cc_start: 0.8128 (mtm180) cc_final: 0.7766 (mtm180) REVERT: D 450 ASP cc_start: 0.6775 (t0) cc_final: 0.6465 (t0) REVERT: D 452 LYS cc_start: 0.7123 (tttt) cc_final: 0.6360 (ttmt) REVERT: E 35 GLU cc_start: 0.7009 (tt0) cc_final: 0.6802 (tt0) REVERT: E 37 ILE cc_start: 0.8330 (mm) cc_final: 0.8095 (mm) REVERT: E 38 LEU cc_start: 0.7988 (mt) cc_final: 0.7724 (mt) REVERT: E 111 SER cc_start: 0.8175 (m) cc_final: 0.7671 (p) REVERT: E 132 LYS cc_start: 0.7105 (mttt) cc_final: 0.6808 (ttmm) REVERT: E 159 MET cc_start: 0.8128 (mmt) cc_final: 0.7848 (mmp) REVERT: E 224 ASP cc_start: 0.6402 (p0) cc_final: 0.6189 (p0) REVERT: E 226 SER cc_start: 0.7531 (p) cc_final: 0.7270 (p) REVERT: E 251 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7406 (mmm160) REVERT: E 328 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7280 (tt) REVERT: E 336 LEU cc_start: 0.7981 (tp) cc_final: 0.7744 (tt) REVERT: E 357 VAL cc_start: 0.7469 (t) cc_final: 0.7235 (p) REVERT: F 39 ASP cc_start: 0.6316 (m-30) cc_final: 0.6030 (m-30) REVERT: F 108 ASN cc_start: 0.8272 (m110) cc_final: 0.7857 (m-40) REVERT: F 139 LYS cc_start: 0.8718 (mttt) cc_final: 0.8326 (mtmt) REVERT: F 178 MET cc_start: 0.7388 (mmm) cc_final: 0.7133 (mmt) REVERT: F 208 ASP cc_start: 0.6119 (t70) cc_final: 0.5851 (t0) REVERT: F 224 LEU cc_start: 0.8332 (tp) cc_final: 0.8108 (tp) REVERT: F 240 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.7109 (mp10) REVERT: G 61 MET cc_start: 0.6713 (tpp) cc_final: 0.6282 (mmm) REVERT: K 118 MET cc_start: 0.6203 (tpp) cc_final: 0.5783 (tpp) REVERT: K 151 LYS cc_start: 0.7890 (mttt) cc_final: 0.7506 (mttt) REVERT: K 164 PHE cc_start: 0.8162 (p90) cc_final: 0.7951 (p90) REVERT: K 209 GLU cc_start: 0.7521 (tp30) cc_final: 0.7050 (tp30) REVERT: K 213 LYS cc_start: 0.7885 (tptt) cc_final: 0.7399 (tptt) outliers start: 75 outliers final: 30 residues processed: 979 average time/residue: 0.4342 time to fit residues: 621.2324 Evaluate side-chains 808 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 769 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain B residue 712 GLU Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 251 ARG Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 236 ASP Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain H residue 908 ARG Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 236 optimal weight: 0.8980 chunk 212 optimal weight: 0.8980 chunk 117 optimal weight: 0.0980 chunk 72 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 254 optimal weight: 0.0870 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 190 GLN ** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 ASN A 668 GLN A 677 GLN B 210 HIS B 238 ASN ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 ASN C 145 ASN ** C 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN D 117 ASN D 141 HIS D 177 GLN D 202 GLN D 260 ASN D 273 GLN D 363 GLN E 332 GLN E 365 ASN ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN F 179 ASN G 42 HIS K 119 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24132 Z= 0.217 Angle : 0.611 9.808 32831 Z= 0.318 Chirality : 0.043 0.215 3677 Planarity : 0.004 0.047 4022 Dihedral : 14.336 178.660 3646 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.90 % Allowed : 16.12 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.16), residues: 2776 helix: 1.60 (0.15), residues: 1326 sheet: 0.18 (0.27), residues: 383 loop : -1.10 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 511 HIS 0.024 0.001 HIS C 474 PHE 0.031 0.002 PHE D 215 TYR 0.018 0.001 TYR A 534 ARG 0.008 0.001 ARG K 227 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 813 time to evaluate : 2.354 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: A 117 LYS cc_start: 0.8030 (tttt) cc_final: 0.7507 (ttpt) REVERT: A 131 LEU cc_start: 0.8074 (mp) cc_final: 0.7762 (mp) REVERT: A 157 LYS cc_start: 0.8051 (tppt) cc_final: 0.7819 (ttmm) REVERT: A 165 LYS cc_start: 0.7710 (mttm) cc_final: 0.7463 (mttp) REVERT: A 282 LYS cc_start: 0.8592 (tttt) cc_final: 0.8062 (ttmm) REVERT: A 309 ASP cc_start: 0.5746 (p0) cc_final: 0.5314 (p0) REVERT: A 316 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7957 (pp) REVERT: A 334 ARG cc_start: 0.7268 (ptp-170) cc_final: 0.6951 (ptp-170) REVERT: A 375 LYS cc_start: 0.8360 (ttpt) cc_final: 0.8094 (ttmm) REVERT: A 446 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7768 (mm) REVERT: A 454 VAL cc_start: 0.8518 (t) cc_final: 0.8316 (p) REVERT: A 506 GLN cc_start: 0.7913 (tt0) cc_final: 0.7474 (tt0) REVERT: A 570 GLU cc_start: 0.5914 (OUTLIER) cc_final: 0.5484 (pm20) REVERT: A 625 GLN cc_start: 0.7484 (pt0) cc_final: 0.6537 (pt0) REVERT: A 658 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.7411 (p90) REVERT: A 659 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.6606 (p90) REVERT: B 12 PHE cc_start: 0.6794 (t80) cc_final: 0.6303 (m-80) REVERT: B 27 GLU cc_start: 0.7112 (tm-30) cc_final: 0.6879 (tm-30) REVERT: B 28 LEU cc_start: 0.7258 (tp) cc_final: 0.7028 (mt) REVERT: B 53 LEU cc_start: 0.7938 (mt) cc_final: 0.7087 (mm) REVERT: B 57 MET cc_start: 0.7162 (mmt) cc_final: 0.6778 (mmt) REVERT: B 61 ARG cc_start: 0.6550 (tpm170) cc_final: 0.5939 (tpm170) REVERT: B 176 ASN cc_start: 0.6053 (t0) cc_final: 0.5834 (t0) REVERT: B 238 ASN cc_start: 0.8017 (m-40) cc_final: 0.7723 (m110) REVERT: B 244 ILE cc_start: 0.8509 (tp) cc_final: 0.8252 (tp) REVERT: B 262 ASN cc_start: 0.7168 (p0) cc_final: 0.6807 (p0) REVERT: B 363 GLN cc_start: 0.7161 (mm-40) cc_final: 0.6933 (mm-40) REVERT: B 469 LYS cc_start: 0.7149 (ptpt) cc_final: 0.6920 (ptpp) REVERT: B 487 ARG cc_start: 0.6131 (ptt-90) cc_final: 0.5469 (ptt180) REVERT: B 511 ARG cc_start: 0.7739 (mtp85) cc_final: 0.7417 (mtt180) REVERT: B 570 GLU cc_start: 0.6500 (tm-30) cc_final: 0.6291 (tm-30) REVERT: B 583 LYS cc_start: 0.7601 (ptpp) cc_final: 0.7259 (mtmm) REVERT: B 589 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6915 (tp30) REVERT: B 603 LYS cc_start: 0.7161 (ptmm) cc_final: 0.6859 (ptmm) REVERT: B 668 ILE cc_start: 0.7921 (mm) cc_final: 0.7607 (mt) REVERT: B 672 THR cc_start: 0.7792 (p) cc_final: 0.7393 (m) REVERT: B 681 ASP cc_start: 0.7961 (t0) cc_final: 0.7389 (t70) REVERT: B 682 LYS cc_start: 0.7947 (pttp) cc_final: 0.7485 (ttpp) REVERT: C 441 MET cc_start: 0.5190 (mmm) cc_final: 0.4860 (mmt) REVERT: C 442 GLN cc_start: 0.2702 (OUTLIER) cc_final: 0.1928 (pt0) REVERT: C 474 HIS cc_start: 0.6745 (m-70) cc_final: 0.6502 (m-70) REVERT: C 528 MET cc_start: 0.7346 (mtp) cc_final: 0.7116 (mtm) REVERT: C 529 LEU cc_start: 0.8685 (mt) cc_final: 0.7753 (mt) REVERT: C 545 MET cc_start: 0.5627 (mtt) cc_final: 0.5344 (mtt) REVERT: D 53 LYS cc_start: 0.8845 (mtmt) cc_final: 0.8357 (mtmm) REVERT: D 57 MET cc_start: 0.8077 (mmm) cc_final: 0.7860 (mmm) REVERT: D 89 LEU cc_start: 0.8456 (tp) cc_final: 0.8172 (tt) REVERT: D 113 ILE cc_start: 0.7406 (OUTLIER) cc_final: 0.7147 (mp) REVERT: D 115 ARG cc_start: 0.7825 (ttt-90) cc_final: 0.7592 (ttt-90) REVERT: D 117 ASN cc_start: 0.7303 (m-40) cc_final: 0.7059 (m-40) REVERT: D 120 ILE cc_start: 0.8219 (mt) cc_final: 0.7964 (mm) REVERT: D 139 ASP cc_start: 0.6336 (t0) cc_final: 0.5798 (t0) REVERT: D 156 TRP cc_start: 0.8554 (t-100) cc_final: 0.8248 (t-100) REVERT: D 177 GLN cc_start: 0.7606 (mt0) cc_final: 0.7016 (tm-30) REVERT: D 180 SER cc_start: 0.8136 (m) cc_final: 0.7630 (p) REVERT: D 185 MET cc_start: 0.7121 (mtm) cc_final: 0.6880 (mpp) REVERT: D 216 MET cc_start: 0.8046 (tpp) cc_final: 0.7803 (mmp) REVERT: D 243 SER cc_start: 0.8504 (m) cc_final: 0.8110 (m) REVERT: D 249 TYR cc_start: 0.7940 (m-80) cc_final: 0.7613 (m-80) REVERT: D 261 PHE cc_start: 0.8527 (t80) cc_final: 0.8220 (t80) REVERT: D 282 TYR cc_start: 0.7705 (m-80) cc_final: 0.7209 (m-80) REVERT: D 312 ASN cc_start: 0.8137 (p0) cc_final: 0.7923 (p0) REVERT: D 313 TYR cc_start: 0.8112 (m-80) cc_final: 0.7879 (m-80) REVERT: D 365 ILE cc_start: 0.8339 (mt) cc_final: 0.8078 (mm) REVERT: D 395 GLU cc_start: 0.7059 (tm-30) cc_final: 0.6825 (tm-30) REVERT: D 402 ARG cc_start: 0.5996 (mpt180) cc_final: 0.5490 (mtt90) REVERT: D 407 VAL cc_start: 0.8421 (t) cc_final: 0.8111 (m) REVERT: D 439 ARG cc_start: 0.8211 (mtm180) cc_final: 0.7997 (mtm-85) REVERT: E 37 ILE cc_start: 0.8307 (mm) cc_final: 0.8043 (mm) REVERT: E 38 LEU cc_start: 0.8016 (mt) cc_final: 0.7738 (mt) REVERT: E 40 LYS cc_start: 0.8050 (tppt) cc_final: 0.7849 (mmmm) REVERT: E 66 ASP cc_start: 0.7434 (t0) cc_final: 0.7202 (t0) REVERT: E 172 SER cc_start: 0.8039 (t) cc_final: 0.7783 (p) REVERT: E 328 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7344 (tt) REVERT: E 366 VAL cc_start: 0.8053 (OUTLIER) cc_final: 0.7657 (m) REVERT: F 39 ASP cc_start: 0.6513 (m-30) cc_final: 0.6238 (m-30) REVERT: F 55 ASN cc_start: 0.8106 (m-40) cc_final: 0.7714 (m-40) REVERT: F 116 LYS cc_start: 0.8809 (mmmm) cc_final: 0.8456 (mtpp) REVERT: F 139 LYS cc_start: 0.8778 (mttt) cc_final: 0.8459 (mtmt) REVERT: F 146 ARG cc_start: 0.8532 (tmm-80) cc_final: 0.7981 (ttp-170) REVERT: F 157 MET cc_start: 0.7692 (ttp) cc_final: 0.7385 (ttp) REVERT: F 208 ASP cc_start: 0.6382 (t70) cc_final: 0.6000 (t0) REVERT: F 224 LEU cc_start: 0.8412 (tp) cc_final: 0.8202 (tp) REVERT: F 226 TYR cc_start: 0.8143 (m-80) cc_final: 0.7835 (m-10) REVERT: F 236 ASP cc_start: 0.7316 (p0) cc_final: 0.7042 (p0) REVERT: F 240 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7207 (mp10) REVERT: F 275 PHE cc_start: 0.8003 (m-80) cc_final: 0.7753 (m-80) REVERT: G 61 MET cc_start: 0.6805 (tpp) cc_final: 0.6400 (mmm) REVERT: K 118 MET cc_start: 0.6352 (tpp) cc_final: 0.6012 (tpp) REVERT: K 163 LYS cc_start: 0.7128 (mttt) cc_final: 0.6847 (mttt) REVERT: K 179 LYS cc_start: 0.7888 (mttt) cc_final: 0.7601 (mtmm) REVERT: K 181 TYR cc_start: 0.8311 (m-80) cc_final: 0.8073 (m-80) REVERT: K 201 GLU cc_start: 0.7226 (mt-10) cc_final: 0.7006 (mt-10) REVERT: K 209 GLU cc_start: 0.7573 (tp30) cc_final: 0.7101 (tp30) REVERT: K 213 LYS cc_start: 0.7925 (tptt) cc_final: 0.7513 (tptt) REVERT: K 245 GLU cc_start: 0.7539 (mp0) cc_final: 0.7337 (mp0) REVERT: K 272 LYS cc_start: 0.6369 (ttmm) cc_final: 0.5939 (tptt) outliers start: 97 outliers final: 42 residues processed: 867 average time/residue: 0.4016 time to fit residues: 508.8437 Evaluate side-chains 821 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 769 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 715 LYS Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 213 TRP Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 248 HIS Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 141 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 211 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 275 optimal weight: 5.9990 chunk 226 optimal weight: 1.9990 chunk 252 optimal weight: 0.0370 chunk 86 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 overall best weight: 1.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS ** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 GLN B 241 ASN ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 ASN B 649 ASN C 524 HIS ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 GLN E 275 HIS E 293 GLN E 332 GLN E 364 GLN F 148 ASN G 18 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 24132 Z= 0.377 Angle : 0.688 9.756 32831 Z= 0.360 Chirality : 0.047 0.216 3677 Planarity : 0.005 0.068 4022 Dihedral : 14.530 179.726 3615 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 5.15 % Allowed : 18.17 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.16), residues: 2776 helix: 1.20 (0.15), residues: 1337 sheet: -0.06 (0.27), residues: 375 loop : -1.27 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 511 HIS 0.023 0.002 HIS B 210 PHE 0.023 0.002 PHE D 215 TYR 0.034 0.002 TYR C 533 ARG 0.009 0.001 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 829 time to evaluate : 2.680 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: A 117 LYS cc_start: 0.7974 (tttt) cc_final: 0.7540 (ttpt) REVERT: A 131 LEU cc_start: 0.8235 (mp) cc_final: 0.7899 (mp) REVERT: A 148 VAL cc_start: 0.8742 (t) cc_final: 0.8533 (m) REVERT: A 150 ASP cc_start: 0.7085 (t0) cc_final: 0.6853 (t0) REVERT: A 157 LYS cc_start: 0.8225 (tppt) cc_final: 0.7960 (ttmm) REVERT: A 165 LYS cc_start: 0.8066 (mttm) cc_final: 0.7805 (mttp) REVERT: A 273 LYS cc_start: 0.8000 (ttmt) cc_final: 0.7733 (mtmt) REVERT: A 282 LYS cc_start: 0.8604 (tttt) cc_final: 0.8119 (ttmm) REVERT: A 296 ASP cc_start: 0.6164 (t0) cc_final: 0.5875 (t0) REVERT: A 309 ASP cc_start: 0.5935 (p0) cc_final: 0.5404 (p0) REVERT: A 316 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8066 (pp) REVERT: A 375 LYS cc_start: 0.8394 (ttpt) cc_final: 0.8060 (ttmm) REVERT: A 506 GLN cc_start: 0.8020 (tt0) cc_final: 0.7657 (tt0) REVERT: A 510 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.8203 (t) REVERT: A 525 ILE cc_start: 0.8494 (tp) cc_final: 0.8019 (pt) REVERT: A 658 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.6999 (p90) REVERT: B 1 MET cc_start: 0.6518 (ppp) cc_final: 0.5806 (ppp) REVERT: B 12 PHE cc_start: 0.7019 (t80) cc_final: 0.6552 (m-80) REVERT: B 53 LEU cc_start: 0.8265 (mt) cc_final: 0.7337 (mm) REVERT: B 57 MET cc_start: 0.7254 (mmt) cc_final: 0.6874 (mmt) REVERT: B 61 ARG cc_start: 0.6716 (tpm170) cc_final: 0.6395 (tpm170) REVERT: B 76 THR cc_start: 0.6848 (OUTLIER) cc_final: 0.6511 (p) REVERT: B 94 TYR cc_start: 0.6124 (t80) cc_final: 0.5917 (t80) REVERT: B 95 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6838 (mm-30) REVERT: B 176 ASN cc_start: 0.6225 (t0) cc_final: 0.5817 (t0) REVERT: B 178 ASP cc_start: 0.7004 (p0) cc_final: 0.6582 (p0) REVERT: B 238 ASN cc_start: 0.8035 (m-40) cc_final: 0.7782 (m110) REVERT: B 244 ILE cc_start: 0.8703 (tp) cc_final: 0.8394 (tp) REVERT: B 262 ASN cc_start: 0.7227 (p0) cc_final: 0.6958 (p0) REVERT: B 462 SER cc_start: 0.5815 (OUTLIER) cc_final: 0.5482 (m) REVERT: B 469 LYS cc_start: 0.7388 (ptpt) cc_final: 0.7170 (ptpp) REVERT: B 487 ARG cc_start: 0.6517 (ptt-90) cc_final: 0.6164 (ptt-90) REVERT: B 511 ARG cc_start: 0.7656 (mtp85) cc_final: 0.7411 (mtt180) REVERT: B 589 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7110 (tp30) REVERT: B 613 HIS cc_start: 0.8272 (OUTLIER) cc_final: 0.7690 (p90) REVERT: B 668 ILE cc_start: 0.8079 (mm) cc_final: 0.7589 (mt) REVERT: B 672 THR cc_start: 0.7727 (p) cc_final: 0.7418 (m) REVERT: B 682 LYS cc_start: 0.7931 (pttp) cc_final: 0.7672 (ttpp) REVERT: C 405 GLN cc_start: 0.7875 (pp30) cc_final: 0.6920 (pp30) REVERT: C 409 GLN cc_start: 0.7473 (mt0) cc_final: 0.7098 (mt0) REVERT: C 442 GLN cc_start: 0.3004 (OUTLIER) cc_final: 0.1922 (pt0) REVERT: C 529 LEU cc_start: 0.8966 (mt) cc_final: 0.8752 (mt) REVERT: C 530 GLN cc_start: 0.7056 (tp40) cc_final: 0.6380 (tp40) REVERT: C 545 MET cc_start: 0.5433 (mtt) cc_final: 0.5218 (mtt) REVERT: D 33 ARG cc_start: 0.7514 (mmm-85) cc_final: 0.7252 (mtp85) REVERT: D 77 LYS cc_start: 0.7798 (mttt) cc_final: 0.7561 (mttt) REVERT: D 120 ILE cc_start: 0.8381 (mt) cc_final: 0.8133 (mm) REVERT: D 177 GLN cc_start: 0.7711 (mt0) cc_final: 0.7322 (tm-30) REVERT: D 180 SER cc_start: 0.8632 (m) cc_final: 0.8212 (p) REVERT: D 181 GLN cc_start: 0.7918 (mm-40) cc_final: 0.7601 (mm-40) REVERT: D 241 SER cc_start: 0.8293 (p) cc_final: 0.8000 (t) REVERT: D 252 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6760 (mt-10) REVERT: D 261 PHE cc_start: 0.8631 (t80) cc_final: 0.8311 (t80) REVERT: D 275 LYS cc_start: 0.8275 (pttt) cc_final: 0.7932 (ptmt) REVERT: D 313 TYR cc_start: 0.8192 (m-80) cc_final: 0.7917 (m-80) REVERT: D 365 ILE cc_start: 0.8459 (mt) cc_final: 0.8199 (mm) REVERT: D 395 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6845 (tm-30) REVERT: D 397 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.7007 (mt-10) REVERT: D 402 ARG cc_start: 0.6326 (mpt180) cc_final: 0.5808 (mtt90) REVERT: D 407 VAL cc_start: 0.8395 (t) cc_final: 0.8156 (m) REVERT: E 37 ILE cc_start: 0.8481 (mm) cc_final: 0.8217 (mm) REVERT: E 38 LEU cc_start: 0.8044 (mt) cc_final: 0.7768 (mt) REVERT: E 40 LYS cc_start: 0.8161 (tppt) cc_final: 0.7943 (mmmm) REVERT: E 66 ASP cc_start: 0.7445 (t0) cc_final: 0.7156 (t0) REVERT: E 69 ARG cc_start: 0.7020 (ptt-90) cc_final: 0.6243 (ptt-90) REVERT: E 81 LEU cc_start: 0.8573 (tp) cc_final: 0.8301 (tp) REVERT: E 116 LYS cc_start: 0.7374 (tttm) cc_final: 0.7114 (tttp) REVERT: E 172 SER cc_start: 0.8268 (t) cc_final: 0.7824 (p) REVERT: E 366 VAL cc_start: 0.8213 (OUTLIER) cc_final: 0.7730 (m) REVERT: F 39 ASP cc_start: 0.6672 (m-30) cc_final: 0.6420 (m-30) REVERT: F 55 ASN cc_start: 0.8169 (m-40) cc_final: 0.7716 (m-40) REVERT: F 113 GLU cc_start: 0.7260 (tt0) cc_final: 0.7045 (tt0) REVERT: F 116 LYS cc_start: 0.8934 (mmmm) cc_final: 0.8340 (mtpp) REVERT: F 139 LYS cc_start: 0.8869 (mttt) cc_final: 0.8535 (mtmt) REVERT: F 208 ASP cc_start: 0.6575 (t70) cc_final: 0.6302 (t0) REVERT: F 240 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7446 (mt0) REVERT: G 16 MET cc_start: 0.7867 (mmm) cc_final: 0.7522 (mmm) REVERT: G 46 ILE cc_start: 0.6884 (OUTLIER) cc_final: 0.6653 (mp) REVERT: K 118 MET cc_start: 0.6433 (tpp) cc_final: 0.6144 (tpp) REVERT: K 151 LYS cc_start: 0.7867 (mttt) cc_final: 0.7626 (mttt) REVERT: K 164 PHE cc_start: 0.8252 (p90) cc_final: 0.7972 (p90) REVERT: K 201 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6748 (mt-10) REVERT: K 209 GLU cc_start: 0.7702 (tp30) cc_final: 0.7259 (tp30) REVERT: K 213 LYS cc_start: 0.7998 (tptt) cc_final: 0.7572 (tptt) REVERT: K 245 GLU cc_start: 0.7663 (mp0) cc_final: 0.7321 (mp0) REVERT: K 258 ARG cc_start: 0.6969 (ttp-170) cc_final: 0.6669 (ttp-170) REVERT: K 263 MET cc_start: 0.3772 (OUTLIER) cc_final: 0.3565 (ptt) REVERT: K 272 LYS cc_start: 0.6473 (ttmm) cc_final: 0.5952 (tptt) outliers start: 128 outliers final: 75 residues processed: 893 average time/residue: 0.3990 time to fit residues: 520.9938 Evaluate side-chains 884 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 797 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 497 GLN Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 715 LYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 213 TRP Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain E residue 12 GLU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 139 CYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 173 GLN Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain F residue 236 ASP Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 255 CYS Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 263 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 251 optimal weight: 0.8980 chunk 191 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 171 optimal weight: 0.7980 chunk 255 optimal weight: 0.5980 chunk 270 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 242 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 ASN A 683 GLN B 60 GLN B 210 HIS ** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN C 402 ASN ** C 524 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 HIS E 324 HIS E 332 GLN F 260 ASN F 277 ASN G 54 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24132 Z= 0.244 Angle : 0.643 10.467 32831 Z= 0.331 Chirality : 0.044 0.244 3677 Planarity : 0.004 0.058 4022 Dihedral : 14.501 179.947 3608 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.78 % Allowed : 19.94 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2776 helix: 1.22 (0.15), residues: 1345 sheet: -0.10 (0.27), residues: 375 loop : -1.27 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 539 HIS 0.016 0.001 HIS B 613 PHE 0.027 0.002 PHE B 403 TYR 0.047 0.002 TYR C 533 ARG 0.010 0.001 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 942 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 823 time to evaluate : 2.695 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: A 117 LYS cc_start: 0.7886 (tttt) cc_final: 0.7409 (ttpt) REVERT: A 131 LEU cc_start: 0.8235 (mp) cc_final: 0.7929 (mp) REVERT: A 148 VAL cc_start: 0.8638 (t) cc_final: 0.8413 (m) REVERT: A 150 ASP cc_start: 0.7155 (t0) cc_final: 0.6939 (t0) REVERT: A 157 LYS cc_start: 0.8210 (tppt) cc_final: 0.7938 (ttmm) REVERT: A 165 LYS cc_start: 0.7969 (mttm) cc_final: 0.7671 (mttp) REVERT: A 270 PHE cc_start: 0.8151 (p90) cc_final: 0.7951 (p90) REVERT: A 273 LYS cc_start: 0.7964 (ttmt) cc_final: 0.7674 (mtmt) REVERT: A 279 GLU cc_start: 0.7102 (mp0) cc_final: 0.6901 (mp0) REVERT: A 282 LYS cc_start: 0.8587 (tttt) cc_final: 0.8100 (ttmm) REVERT: A 296 ASP cc_start: 0.6272 (t0) cc_final: 0.5987 (t0) REVERT: A 309 ASP cc_start: 0.6243 (p0) cc_final: 0.5741 (p0) REVERT: A 375 LYS cc_start: 0.8314 (ttpt) cc_final: 0.7958 (ttmm) REVERT: A 506 GLN cc_start: 0.8062 (tt0) cc_final: 0.7617 (tt0) REVERT: A 510 VAL cc_start: 0.8285 (OUTLIER) cc_final: 0.8051 (t) REVERT: A 525 ILE cc_start: 0.8457 (tp) cc_final: 0.7922 (pt) REVERT: A 625 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.7140 (tt0) REVERT: A 632 SER cc_start: 0.7885 (t) cc_final: 0.7631 (t) REVERT: A 697 GLU cc_start: 0.6817 (tp30) cc_final: 0.6457 (tp30) REVERT: A 710 GLN cc_start: 0.6838 (pp30) cc_final: 0.6578 (pp30) REVERT: B 1 MET cc_start: 0.6345 (ppp) cc_final: 0.5730 (ppp) REVERT: B 12 PHE cc_start: 0.6958 (t80) cc_final: 0.6553 (m-80) REVERT: B 53 LEU cc_start: 0.8288 (mt) cc_final: 0.7233 (mm) REVERT: B 57 MET cc_start: 0.7064 (mmt) cc_final: 0.6822 (mmt) REVERT: B 63 TYR cc_start: 0.7873 (m-80) cc_final: 0.7566 (m-80) REVERT: B 80 ILE cc_start: 0.7943 (mt) cc_final: 0.7742 (mm) REVERT: B 175 TYR cc_start: 0.6909 (m-80) cc_final: 0.5662 (m-10) REVERT: B 176 ASN cc_start: 0.6199 (t0) cc_final: 0.5829 (t0) REVERT: B 178 ASP cc_start: 0.7065 (p0) cc_final: 0.6649 (p0) REVERT: B 238 ASN cc_start: 0.8007 (m-40) cc_final: 0.7769 (m110) REVERT: B 244 ILE cc_start: 0.8650 (tp) cc_final: 0.8331 (tp) REVERT: B 262 ASN cc_start: 0.7215 (p0) cc_final: 0.6941 (p0) REVERT: B 338 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6053 (pm20) REVERT: B 462 SER cc_start: 0.6040 (OUTLIER) cc_final: 0.5526 (m) REVERT: B 469 LYS cc_start: 0.7300 (ptpt) cc_final: 0.7032 (ptpp) REVERT: B 487 ARG cc_start: 0.6413 (ptt-90) cc_final: 0.5917 (ptt180) REVERT: B 511 ARG cc_start: 0.7598 (mtp85) cc_final: 0.7374 (mtt180) REVERT: B 516 VAL cc_start: 0.8305 (m) cc_final: 0.7939 (p) REVERT: B 586 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6482 (pp20) REVERT: B 589 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6927 (tp30) REVERT: B 613 HIS cc_start: 0.8065 (OUTLIER) cc_final: 0.7466 (p90) REVERT: B 668 ILE cc_start: 0.7963 (mm) cc_final: 0.7585 (mt) REVERT: B 672 THR cc_start: 0.7711 (p) cc_final: 0.7398 (m) REVERT: B 682 LYS cc_start: 0.7878 (pttp) cc_final: 0.7601 (ttpp) REVERT: B 711 ASP cc_start: 0.7253 (m-30) cc_final: 0.7040 (m-30) REVERT: C 405 GLN cc_start: 0.7799 (pp30) cc_final: 0.7055 (pp30) REVERT: C 409 GLN cc_start: 0.7397 (mt0) cc_final: 0.7104 (mt0) REVERT: C 475 PHE cc_start: 0.8474 (t80) cc_final: 0.7561 (t80) REVERT: D 33 ARG cc_start: 0.7447 (mmm-85) cc_final: 0.7243 (mtp85) REVERT: D 53 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8519 (mtmm) REVERT: D 77 LYS cc_start: 0.7754 (mttt) cc_final: 0.7550 (mttt) REVERT: D 120 ILE cc_start: 0.8272 (mt) cc_final: 0.8028 (mm) REVERT: D 177 GLN cc_start: 0.7635 (mt0) cc_final: 0.7355 (tm-30) REVERT: D 180 SER cc_start: 0.8631 (m) cc_final: 0.8243 (p) REVERT: D 181 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7647 (mm-40) REVERT: D 216 MET cc_start: 0.8062 (tpp) cc_final: 0.7741 (mmp) REVERT: D 230 LEU cc_start: 0.8472 (tp) cc_final: 0.8186 (tt) REVERT: D 241 SER cc_start: 0.8216 (p) cc_final: 0.8016 (p) REVERT: D 261 PHE cc_start: 0.8644 (t80) cc_final: 0.8431 (t80) REVERT: D 275 LYS cc_start: 0.8422 (pttt) cc_final: 0.8068 (ptpt) REVERT: D 313 TYR cc_start: 0.8102 (m-80) cc_final: 0.7883 (m-80) REVERT: D 365 ILE cc_start: 0.8447 (mt) cc_final: 0.8183 (mm) REVERT: D 395 GLU cc_start: 0.7133 (tm-30) cc_final: 0.6799 (tm-30) REVERT: D 402 ARG cc_start: 0.6204 (mpt180) cc_final: 0.5644 (mtt90) REVERT: D 407 VAL cc_start: 0.8583 (t) cc_final: 0.8354 (m) REVERT: E 37 ILE cc_start: 0.8514 (mm) cc_final: 0.8238 (mm) REVERT: E 38 LEU cc_start: 0.8034 (mt) cc_final: 0.7745 (mt) REVERT: E 40 LYS cc_start: 0.8140 (tppt) cc_final: 0.7907 (mmmm) REVERT: E 66 ASP cc_start: 0.7404 (t0) cc_final: 0.7135 (t0) REVERT: E 81 LEU cc_start: 0.8593 (tp) cc_final: 0.8313 (tp) REVERT: E 172 SER cc_start: 0.8206 (t) cc_final: 0.7810 (p) REVERT: E 250 ILE cc_start: 0.7943 (mt) cc_final: 0.7614 (mm) REVERT: E 366 VAL cc_start: 0.8113 (OUTLIER) cc_final: 0.7666 (m) REVERT: F 36 LYS cc_start: 0.8303 (mmmt) cc_final: 0.8056 (mmmm) REVERT: F 39 ASP cc_start: 0.6670 (m-30) cc_final: 0.6363 (m-30) REVERT: F 55 ASN cc_start: 0.8189 (m-40) cc_final: 0.7738 (m-40) REVERT: F 113 GLU cc_start: 0.7223 (tt0) cc_final: 0.6982 (tt0) REVERT: F 116 LYS cc_start: 0.9055 (mmmm) cc_final: 0.8426 (mtpp) REVERT: F 139 LYS cc_start: 0.8847 (mttt) cc_final: 0.8510 (mtmt) REVERT: F 146 ARG cc_start: 0.8521 (tmm-80) cc_final: 0.8100 (ttt180) REVERT: F 208 ASP cc_start: 0.6595 (t70) cc_final: 0.6288 (t70) REVERT: F 240 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7403 (mt0) REVERT: G 16 MET cc_start: 0.7820 (mmm) cc_final: 0.7424 (mmm) REVERT: G 23 LEU cc_start: 0.8639 (mt) cc_final: 0.8310 (mp) REVERT: G 46 ILE cc_start: 0.6727 (OUTLIER) cc_final: 0.6481 (mp) REVERT: K 118 MET cc_start: 0.6468 (tpp) cc_final: 0.6164 (tpp) REVERT: K 209 GLU cc_start: 0.7663 (tp30) cc_final: 0.7213 (tp30) REVERT: K 213 LYS cc_start: 0.7987 (tptt) cc_final: 0.7589 (tptt) REVERT: K 245 GLU cc_start: 0.7635 (mp0) cc_final: 0.7260 (mp0) REVERT: K 258 ARG cc_start: 0.6977 (ttp-170) cc_final: 0.6679 (ttp-170) REVERT: K 272 LYS cc_start: 0.6418 (ttmm) cc_final: 0.5996 (tptt) outliers start: 119 outliers final: 82 residues processed: 876 average time/residue: 0.4349 time to fit residues: 565.8704 Evaluate side-chains 890 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 798 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 715 LYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 213 TRP Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 139 CYS Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 372 ASP Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 173 GLN Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain F residue 248 HIS Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 227 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 225 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 201 optimal weight: 0.6980 chunk 111 optimal weight: 0.5980 chunk 230 optimal weight: 0.9980 chunk 187 optimal weight: 0.0070 chunk 0 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 242 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 ASN A 683 GLN B 210 HIS ** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS C 524 HIS ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 HIS E 256 GLN E 275 HIS E 324 HIS E 332 GLN F 108 ASN F 205 GLN G 54 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24132 Z= 0.232 Angle : 0.647 9.569 32831 Z= 0.334 Chirality : 0.044 0.222 3677 Planarity : 0.004 0.064 4022 Dihedral : 14.488 179.882 3603 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 5.15 % Allowed : 21.27 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.16), residues: 2776 helix: 1.18 (0.15), residues: 1350 sheet: -0.18 (0.27), residues: 372 loop : -1.28 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 539 HIS 0.015 0.001 HIS B 613 PHE 0.028 0.002 PHE D 162 TYR 0.044 0.002 TYR C 533 ARG 0.012 0.001 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 942 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 814 time to evaluate : 2.611 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: A 60 ASP cc_start: 0.7468 (p0) cc_final: 0.7245 (p0) REVERT: A 117 LYS cc_start: 0.7858 (tttt) cc_final: 0.7523 (ttpt) REVERT: A 150 ASP cc_start: 0.7071 (t0) cc_final: 0.6857 (t0) REVERT: A 157 LYS cc_start: 0.8229 (tppt) cc_final: 0.7968 (ttmm) REVERT: A 165 LYS cc_start: 0.7962 (mttm) cc_final: 0.7665 (mttp) REVERT: A 270 PHE cc_start: 0.8197 (p90) cc_final: 0.7866 (p90) REVERT: A 271 GLU cc_start: 0.6643 (pp20) cc_final: 0.4724 (tm-30) REVERT: A 273 LYS cc_start: 0.7966 (ttmt) cc_final: 0.7607 (mtmt) REVERT: A 282 LYS cc_start: 0.8608 (tttt) cc_final: 0.8116 (ttmm) REVERT: A 296 ASP cc_start: 0.6365 (t0) cc_final: 0.6074 (t0) REVERT: A 309 ASP cc_start: 0.6280 (p0) cc_final: 0.5654 (p0) REVERT: A 506 GLN cc_start: 0.8020 (tt0) cc_final: 0.7746 (tt0) REVERT: A 510 VAL cc_start: 0.8283 (OUTLIER) cc_final: 0.8070 (t) REVERT: A 525 ILE cc_start: 0.8434 (tp) cc_final: 0.7865 (pt) REVERT: A 625 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.7131 (tt0) REVERT: A 632 SER cc_start: 0.7850 (t) cc_final: 0.7599 (t) REVERT: A 697 GLU cc_start: 0.6868 (tp30) cc_final: 0.6503 (tp30) REVERT: A 710 GLN cc_start: 0.6853 (pp30) cc_final: 0.6638 (pp30) REVERT: A 712 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8214 (tt) REVERT: B 12 PHE cc_start: 0.6931 (t80) cc_final: 0.6555 (m-80) REVERT: B 53 LEU cc_start: 0.8292 (mt) cc_final: 0.7238 (mm) REVERT: B 57 MET cc_start: 0.7178 (mmt) cc_final: 0.6931 (mmt) REVERT: B 63 TYR cc_start: 0.7935 (m-80) cc_final: 0.7677 (m-80) REVERT: B 95 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6935 (mm-30) REVERT: B 175 TYR cc_start: 0.6831 (m-80) cc_final: 0.5610 (m-10) REVERT: B 176 ASN cc_start: 0.6330 (t0) cc_final: 0.5931 (t0) REVERT: B 178 ASP cc_start: 0.7146 (p0) cc_final: 0.6770 (p0) REVERT: B 238 ASN cc_start: 0.8014 (m-40) cc_final: 0.7777 (m110) REVERT: B 244 ILE cc_start: 0.8601 (tp) cc_final: 0.8290 (tp) REVERT: B 262 ASN cc_start: 0.7165 (p0) cc_final: 0.6925 (p0) REVERT: B 337 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7132 (mm) REVERT: B 338 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.6135 (pm20) REVERT: B 462 SER cc_start: 0.6059 (OUTLIER) cc_final: 0.5409 (m) REVERT: B 487 ARG cc_start: 0.6166 (ptt-90) cc_final: 0.5695 (ptt180) REVERT: B 507 LYS cc_start: 0.8026 (mtmt) cc_final: 0.7820 (mtmm) REVERT: B 511 ARG cc_start: 0.7730 (mtp85) cc_final: 0.7377 (mtt180) REVERT: B 516 VAL cc_start: 0.8230 (m) cc_final: 0.7957 (p) REVERT: B 586 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.6495 (pp20) REVERT: B 589 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6909 (tp30) REVERT: B 613 HIS cc_start: 0.8056 (OUTLIER) cc_final: 0.7424 (p90) REVERT: B 634 LYS cc_start: 0.7895 (mttt) cc_final: 0.7510 (mptt) REVERT: B 668 ILE cc_start: 0.7948 (mm) cc_final: 0.7567 (mt) REVERT: B 672 THR cc_start: 0.7688 (p) cc_final: 0.7423 (m) REVERT: B 682 LYS cc_start: 0.7876 (pttp) cc_final: 0.7595 (ttpp) REVERT: B 711 ASP cc_start: 0.7269 (m-30) cc_final: 0.7018 (m-30) REVERT: C 405 GLN cc_start: 0.7765 (pp30) cc_final: 0.7029 (pp30) REVERT: C 409 GLN cc_start: 0.7398 (mt0) cc_final: 0.7110 (mt0) REVERT: C 493 MET cc_start: 0.6438 (mmm) cc_final: 0.6070 (mmm) REVERT: C 524 HIS cc_start: 0.7493 (t-170) cc_final: 0.7179 (t70) REVERT: D 23 LEU cc_start: 0.8408 (mm) cc_final: 0.8073 (mt) REVERT: D 42 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8352 (tp) REVERT: D 53 LYS cc_start: 0.8889 (mtmm) cc_final: 0.8562 (mtmm) REVERT: D 98 THR cc_start: 0.8693 (m) cc_final: 0.8405 (t) REVERT: D 162 PHE cc_start: 0.7445 (t80) cc_final: 0.7166 (t80) REVERT: D 177 GLN cc_start: 0.7662 (mt0) cc_final: 0.7281 (tm-30) REVERT: D 180 SER cc_start: 0.8551 (m) cc_final: 0.8155 (p) REVERT: D 181 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7734 (mm-40) REVERT: D 216 MET cc_start: 0.8063 (tpp) cc_final: 0.7793 (mmp) REVERT: D 218 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7461 (tt0) REVERT: D 219 TYR cc_start: 0.8178 (t80) cc_final: 0.7960 (t80) REVERT: D 261 PHE cc_start: 0.8664 (t80) cc_final: 0.8391 (t80) REVERT: D 275 LYS cc_start: 0.8416 (pttt) cc_final: 0.8018 (ptpt) REVERT: D 281 TYR cc_start: 0.8264 (p90) cc_final: 0.7850 (p90) REVERT: D 313 TYR cc_start: 0.8092 (m-80) cc_final: 0.7844 (m-80) REVERT: D 395 GLU cc_start: 0.7154 (tm-30) cc_final: 0.6801 (tm-30) REVERT: D 402 ARG cc_start: 0.6190 (mpt180) cc_final: 0.5588 (mtt90) REVERT: D 407 VAL cc_start: 0.8557 (t) cc_final: 0.8326 (m) REVERT: D 426 ARG cc_start: 0.6793 (ptp-110) cc_final: 0.6570 (ptp-110) REVERT: E 37 ILE cc_start: 0.8519 (mm) cc_final: 0.8230 (mm) REVERT: E 38 LEU cc_start: 0.8067 (mt) cc_final: 0.7739 (mt) REVERT: E 40 LYS cc_start: 0.8138 (tppt) cc_final: 0.7936 (mmmm) REVERT: E 81 LEU cc_start: 0.8647 (tp) cc_final: 0.8375 (tp) REVERT: E 172 SER cc_start: 0.8213 (t) cc_final: 0.7802 (p) REVERT: E 250 ILE cc_start: 0.7881 (mt) cc_final: 0.7589 (mm) REVERT: E 366 VAL cc_start: 0.8179 (OUTLIER) cc_final: 0.7765 (m) REVERT: F 39 ASP cc_start: 0.6648 (m-30) cc_final: 0.6345 (m-30) REVERT: F 55 ASN cc_start: 0.8192 (m-40) cc_final: 0.7737 (m-40) REVERT: F 113 GLU cc_start: 0.7214 (tt0) cc_final: 0.6974 (tt0) REVERT: F 116 LYS cc_start: 0.9069 (mmmm) cc_final: 0.8353 (mtpp) REVERT: F 139 LYS cc_start: 0.8845 (mttt) cc_final: 0.8490 (mtpp) REVERT: F 146 ARG cc_start: 0.8531 (tmm-80) cc_final: 0.8069 (ttt180) REVERT: F 208 ASP cc_start: 0.6698 (t70) cc_final: 0.6367 (t70) REVERT: G 16 MET cc_start: 0.7762 (mmm) cc_final: 0.7410 (mmm) REVERT: G 46 ILE cc_start: 0.6706 (OUTLIER) cc_final: 0.6479 (mt) REVERT: K 118 MET cc_start: 0.6513 (tpp) cc_final: 0.6211 (tpp) REVERT: K 139 ILE cc_start: 0.8174 (mm) cc_final: 0.7610 (tp) REVERT: K 164 PHE cc_start: 0.8257 (p90) cc_final: 0.7957 (p90) REVERT: K 201 GLU cc_start: 0.6599 (tp30) cc_final: 0.6302 (tp30) REVERT: K 209 GLU cc_start: 0.7667 (tp30) cc_final: 0.7183 (tp30) REVERT: K 213 LYS cc_start: 0.7999 (tptt) cc_final: 0.7573 (tptt) REVERT: K 245 GLU cc_start: 0.7602 (mp0) cc_final: 0.7214 (mp0) REVERT: K 258 ARG cc_start: 0.6987 (ttp-170) cc_final: 0.6687 (ttp-170) REVERT: K 263 MET cc_start: 0.3554 (ptt) cc_final: 0.3347 (ptt) REVERT: K 272 LYS cc_start: 0.6547 (ttmm) cc_final: 0.6157 (tptp) outliers start: 128 outliers final: 86 residues processed: 877 average time/residue: 0.4077 time to fit residues: 522.3079 Evaluate side-chains 886 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 788 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 715 LYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 506 CYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 213 TRP Chi-restraints excluded: chain D residue 218 GLN Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 139 CYS Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 256 GLN Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 372 ASP Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 173 GLN Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain F residue 248 HIS Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 227 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 91 optimal weight: 6.9990 chunk 243 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 270 optimal weight: 0.7980 chunk 224 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 ASN ** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN B 210 HIS ** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN E 127 HIS E 275 HIS E 324 HIS E 332 GLN F 148 ASN G 54 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24132 Z= 0.274 Angle : 0.667 14.547 32831 Z= 0.345 Chirality : 0.045 0.237 3677 Planarity : 0.005 0.062 4022 Dihedral : 14.457 179.721 3600 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.91 % Allowed : 21.95 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.16), residues: 2776 helix: 1.06 (0.14), residues: 1349 sheet: -0.23 (0.27), residues: 371 loop : -1.33 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 539 HIS 0.016 0.001 HIS B 613 PHE 0.032 0.002 PHE B 403 TYR 0.045 0.002 TYR C 533 ARG 0.011 0.001 ARG E 113 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 802 time to evaluate : 2.591 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: A 60 ASP cc_start: 0.7435 (p0) cc_final: 0.7178 (p0) REVERT: A 117 LYS cc_start: 0.7926 (tttt) cc_final: 0.7518 (ttpt) REVERT: A 157 LYS cc_start: 0.8250 (tppt) cc_final: 0.7971 (ttmm) REVERT: A 165 LYS cc_start: 0.8011 (mttm) cc_final: 0.7720 (mttp) REVERT: A 270 PHE cc_start: 0.8207 (p90) cc_final: 0.7838 (p90) REVERT: A 271 GLU cc_start: 0.6820 (pp20) cc_final: 0.5180 (tm-30) REVERT: A 273 LYS cc_start: 0.7954 (ttmt) cc_final: 0.7621 (mttt) REVERT: A 282 LYS cc_start: 0.8614 (tttt) cc_final: 0.8125 (ttmm) REVERT: A 296 ASP cc_start: 0.6217 (t0) cc_final: 0.5963 (t0) REVERT: A 309 ASP cc_start: 0.6351 (p0) cc_final: 0.5744 (p0) REVERT: A 375 LYS cc_start: 0.8330 (ttpt) cc_final: 0.8002 (ttmm) REVERT: A 506 GLN cc_start: 0.8027 (tt0) cc_final: 0.7559 (tt0) REVERT: A 510 VAL cc_start: 0.8424 (OUTLIER) cc_final: 0.8182 (t) REVERT: A 525 ILE cc_start: 0.8438 (tp) cc_final: 0.7836 (pt) REVERT: A 625 GLN cc_start: 0.7453 (pt0) cc_final: 0.6833 (tt0) REVERT: A 632 SER cc_start: 0.7901 (t) cc_final: 0.7671 (t) REVERT: A 697 GLU cc_start: 0.6908 (tp30) cc_final: 0.6549 (tp30) REVERT: A 710 GLN cc_start: 0.7066 (pp30) cc_final: 0.6644 (pp30) REVERT: A 712 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8394 (tt) REVERT: B 12 PHE cc_start: 0.6938 (t80) cc_final: 0.6560 (m-80) REVERT: B 48 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8512 (ttmt) REVERT: B 53 LEU cc_start: 0.8303 (mt) cc_final: 0.7299 (mm) REVERT: B 57 MET cc_start: 0.7080 (mmt) cc_final: 0.6817 (mmt) REVERT: B 175 TYR cc_start: 0.6992 (m-80) cc_final: 0.5823 (m-10) REVERT: B 176 ASN cc_start: 0.6291 (t0) cc_final: 0.6087 (t0) REVERT: B 238 ASN cc_start: 0.8039 (m-40) cc_final: 0.7780 (m110) REVERT: B 244 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8319 (tp) REVERT: B 262 ASN cc_start: 0.7247 (p0) cc_final: 0.7020 (p0) REVERT: B 338 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.6186 (pm20) REVERT: B 352 GLU cc_start: 0.7724 (mp0) cc_final: 0.6636 (pm20) REVERT: B 462 SER cc_start: 0.6020 (OUTLIER) cc_final: 0.5654 (m) REVERT: B 469 LYS cc_start: 0.7369 (ptpp) cc_final: 0.7133 (ptpp) REVERT: B 487 ARG cc_start: 0.6372 (ptt-90) cc_final: 0.6090 (ptt180) REVERT: B 511 ARG cc_start: 0.7693 (mtp85) cc_final: 0.7376 (mtt180) REVERT: B 516 VAL cc_start: 0.8316 (m) cc_final: 0.8008 (p) REVERT: B 589 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6957 (tp30) REVERT: B 613 HIS cc_start: 0.8086 (OUTLIER) cc_final: 0.7596 (p90) REVERT: B 634 LYS cc_start: 0.7710 (mttt) cc_final: 0.7484 (mmtt) REVERT: B 668 ILE cc_start: 0.7937 (mm) cc_final: 0.7629 (mt) REVERT: B 672 THR cc_start: 0.7686 (p) cc_final: 0.7436 (m) REVERT: B 682 LYS cc_start: 0.7889 (pttp) cc_final: 0.7628 (ttpp) REVERT: B 711 ASP cc_start: 0.7229 (m-30) cc_final: 0.6963 (m-30) REVERT: C 405 GLN cc_start: 0.7820 (pp30) cc_final: 0.7069 (pp30) REVERT: C 409 GLN cc_start: 0.7456 (mt0) cc_final: 0.7099 (mt0) REVERT: C 412 GLU cc_start: 0.7010 (tt0) cc_final: 0.6742 (tt0) REVERT: C 475 PHE cc_start: 0.8076 (t80) cc_final: 0.7663 (t80) REVERT: C 479 PHE cc_start: 0.6717 (m-80) cc_final: 0.6434 (m-80) REVERT: C 493 MET cc_start: 0.6400 (mmm) cc_final: 0.6087 (mmm) REVERT: D 23 LEU cc_start: 0.8433 (mm) cc_final: 0.8114 (mt) REVERT: D 42 LEU cc_start: 0.8566 (tt) cc_final: 0.8348 (tp) REVERT: D 53 LYS cc_start: 0.8895 (mtmm) cc_final: 0.8489 (mtmm) REVERT: D 77 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7437 (mmtt) REVERT: D 98 THR cc_start: 0.8710 (m) cc_final: 0.8433 (t) REVERT: D 120 ILE cc_start: 0.8375 (mt) cc_final: 0.8051 (mm) REVERT: D 162 PHE cc_start: 0.7472 (t80) cc_final: 0.7176 (t80) REVERT: D 177 GLN cc_start: 0.7648 (mt0) cc_final: 0.7375 (tm-30) REVERT: D 180 SER cc_start: 0.8669 (m) cc_final: 0.8281 (p) REVERT: D 181 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7845 (mm-40) REVERT: D 216 MET cc_start: 0.8039 (tpp) cc_final: 0.7766 (mmp) REVERT: D 219 TYR cc_start: 0.8140 (t80) cc_final: 0.7937 (t80) REVERT: D 261 PHE cc_start: 0.8698 (t80) cc_final: 0.8422 (t80) REVERT: D 275 LYS cc_start: 0.8427 (pttt) cc_final: 0.8053 (ptpt) REVERT: D 281 TYR cc_start: 0.8292 (p90) cc_final: 0.7889 (p90) REVERT: D 313 TYR cc_start: 0.8115 (m-80) cc_final: 0.7858 (m-80) REVERT: D 365 ILE cc_start: 0.8320 (mt) cc_final: 0.8093 (mm) REVERT: D 395 GLU cc_start: 0.7145 (tm-30) cc_final: 0.6786 (tm-30) REVERT: D 402 ARG cc_start: 0.6247 (mpt180) cc_final: 0.5639 (mtt90) REVERT: E 37 ILE cc_start: 0.8517 (mm) cc_final: 0.8224 (mm) REVERT: E 38 LEU cc_start: 0.8105 (mt) cc_final: 0.7771 (mt) REVERT: E 40 LYS cc_start: 0.8195 (tppt) cc_final: 0.7957 (mmmm) REVERT: E 81 LEU cc_start: 0.8589 (tp) cc_final: 0.8310 (tp) REVERT: E 172 SER cc_start: 0.8147 (t) cc_final: 0.7778 (p) REVERT: E 230 GLU cc_start: 0.7175 (tp30) cc_final: 0.6838 (tp30) REVERT: E 250 ILE cc_start: 0.7944 (mt) cc_final: 0.7657 (mm) REVERT: F 39 ASP cc_start: 0.6704 (m-30) cc_final: 0.6414 (m-30) REVERT: F 55 ASN cc_start: 0.8192 (m-40) cc_final: 0.7731 (m-40) REVERT: F 116 LYS cc_start: 0.9087 (mmmm) cc_final: 0.8345 (mtpp) REVERT: F 139 LYS cc_start: 0.8854 (mttt) cc_final: 0.8504 (mtpp) REVERT: F 146 ARG cc_start: 0.8507 (tmm-80) cc_final: 0.8058 (ttt180) REVERT: F 208 ASP cc_start: 0.6730 (t70) cc_final: 0.6412 (t70) REVERT: G 5 LEU cc_start: 0.8497 (mm) cc_final: 0.8218 (mm) REVERT: G 16 MET cc_start: 0.7735 (mmm) cc_final: 0.7368 (mmm) REVERT: G 46 ILE cc_start: 0.6872 (OUTLIER) cc_final: 0.6575 (mt) REVERT: K 118 MET cc_start: 0.6520 (tpp) cc_final: 0.6234 (tpp) REVERT: K 151 LYS cc_start: 0.7824 (mttt) cc_final: 0.7550 (mtmt) REVERT: K 163 LYS cc_start: 0.7208 (mttt) cc_final: 0.6956 (mttt) REVERT: K 164 PHE cc_start: 0.8280 (p90) cc_final: 0.8035 (p90) REVERT: K 188 LYS cc_start: 0.8049 (tttt) cc_final: 0.7800 (tmtt) REVERT: K 201 GLU cc_start: 0.6773 (tp30) cc_final: 0.6405 (tp30) REVERT: K 209 GLU cc_start: 0.7712 (tp30) cc_final: 0.7208 (tp30) REVERT: K 213 LYS cc_start: 0.8053 (tptt) cc_final: 0.7623 (tptt) REVERT: K 245 GLU cc_start: 0.7631 (mp0) cc_final: 0.7242 (mp0) REVERT: K 258 ARG cc_start: 0.7009 (ttp-170) cc_final: 0.6711 (ttp-170) REVERT: K 263 MET cc_start: 0.3776 (ptt) cc_final: 0.3524 (ptt) outliers start: 122 outliers final: 86 residues processed: 864 average time/residue: 0.3998 time to fit residues: 505.6291 Evaluate side-chains 882 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 787 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 715 LYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 506 CYS Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 213 TRP Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 139 CYS Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 372 ASP Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 173 GLN Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain F residue 248 HIS Chi-restraints excluded: chain F residue 255 CYS Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 261 optimal weight: 0.0770 chunk 30 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 197 optimal weight: 0.8980 chunk 153 optimal weight: 0.5980 chunk 228 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 269 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN A 497 GLN ** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 HIS ** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS C 524 HIS ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 GLN E 275 HIS E 293 GLN E 324 HIS E 332 GLN G 54 GLN K 136 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24132 Z= 0.241 Angle : 0.672 12.494 32831 Z= 0.347 Chirality : 0.044 0.236 3677 Planarity : 0.004 0.064 4022 Dihedral : 14.400 179.705 3596 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 5.07 % Allowed : 22.88 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.16), residues: 2776 helix: 1.03 (0.14), residues: 1349 sheet: -0.26 (0.27), residues: 371 loop : -1.32 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 539 HIS 0.015 0.001 HIS B 613 PHE 0.027 0.001 PHE B 403 TYR 0.046 0.002 TYR C 533 ARG 0.012 0.001 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 805 time to evaluate : 2.978 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: A 60 ASP cc_start: 0.7277 (p0) cc_final: 0.7044 (p0) REVERT: A 64 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7230 (mp10) REVERT: A 148 VAL cc_start: 0.8658 (p) cc_final: 0.8276 (m) REVERT: A 157 LYS cc_start: 0.8220 (tppt) cc_final: 0.7944 (ttmm) REVERT: A 165 LYS cc_start: 0.7974 (mttm) cc_final: 0.7698 (mttp) REVERT: A 270 PHE cc_start: 0.8213 (p90) cc_final: 0.7892 (p90) REVERT: A 271 GLU cc_start: 0.6788 (pp20) cc_final: 0.5068 (tm-30) REVERT: A 273 LYS cc_start: 0.7927 (ttmt) cc_final: 0.7708 (mtpt) REVERT: A 282 LYS cc_start: 0.8600 (tttt) cc_final: 0.8126 (ttmm) REVERT: A 296 ASP cc_start: 0.6289 (t0) cc_final: 0.5964 (t0) REVERT: A 309 ASP cc_start: 0.6378 (p0) cc_final: 0.5806 (p0) REVERT: A 375 LYS cc_start: 0.8276 (ttpt) cc_final: 0.7937 (ttmm) REVERT: A 427 MET cc_start: 0.7448 (tpp) cc_final: 0.7216 (tpp) REVERT: A 457 ILE cc_start: 0.8615 (tt) cc_final: 0.8302 (mm) REVERT: A 506 GLN cc_start: 0.8016 (tt0) cc_final: 0.7478 (tt0) REVERT: A 510 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.8165 (t) REVERT: A 517 GLU cc_start: 0.7097 (mp0) cc_final: 0.6892 (mm-30) REVERT: A 625 GLN cc_start: 0.7419 (pt0) cc_final: 0.6796 (tt0) REVERT: A 632 SER cc_start: 0.7865 (t) cc_final: 0.7613 (t) REVERT: A 697 GLU cc_start: 0.6919 (tp30) cc_final: 0.6567 (tp30) REVERT: A 710 GLN cc_start: 0.6963 (pp30) cc_final: 0.6537 (pp30) REVERT: B 12 PHE cc_start: 0.6956 (t80) cc_final: 0.6656 (m-80) REVERT: B 25 MET cc_start: 0.6221 (mmm) cc_final: 0.5907 (mmm) REVERT: B 48 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8499 (ttmt) REVERT: B 53 LEU cc_start: 0.8399 (mt) cc_final: 0.7362 (mm) REVERT: B 57 MET cc_start: 0.7094 (mmt) cc_final: 0.6863 (mmt) REVERT: B 92 ASN cc_start: 0.7733 (m-40) cc_final: 0.7256 (m-40) REVERT: B 95 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6842 (mm-30) REVERT: B 175 TYR cc_start: 0.6900 (m-80) cc_final: 0.5705 (m-10) REVERT: B 178 ASP cc_start: 0.7186 (p0) cc_final: 0.6769 (p0) REVERT: B 200 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7348 (pp) REVERT: B 238 ASN cc_start: 0.8007 (m-40) cc_final: 0.7779 (m110) REVERT: B 244 ILE cc_start: 0.8619 (tp) cc_final: 0.8283 (tp) REVERT: B 262 ASN cc_start: 0.7168 (p0) cc_final: 0.6951 (p0) REVERT: B 338 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.6183 (pm20) REVERT: B 352 GLU cc_start: 0.7684 (mp0) cc_final: 0.6540 (pm20) REVERT: B 462 SER cc_start: 0.6181 (OUTLIER) cc_final: 0.5710 (m) REVERT: B 469 LYS cc_start: 0.7296 (ptpp) cc_final: 0.7013 (ttpp) REVERT: B 487 ARG cc_start: 0.6168 (ptt-90) cc_final: 0.5813 (ptt180) REVERT: B 511 ARG cc_start: 0.7651 (mtp85) cc_final: 0.7332 (mtt180) REVERT: B 516 VAL cc_start: 0.8248 (m) cc_final: 0.7967 (p) REVERT: B 589 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6958 (tp30) REVERT: B 613 HIS cc_start: 0.8006 (OUTLIER) cc_final: 0.7571 (p90) REVERT: B 668 ILE cc_start: 0.7959 (mm) cc_final: 0.7614 (mt) REVERT: B 672 THR cc_start: 0.7692 (p) cc_final: 0.7455 (m) REVERT: B 682 LYS cc_start: 0.7888 (pttp) cc_final: 0.7621 (ttpp) REVERT: C 405 GLN cc_start: 0.7779 (pp30) cc_final: 0.6988 (pp30) REVERT: C 409 GLN cc_start: 0.7421 (mt0) cc_final: 0.7089 (mt0) REVERT: C 412 GLU cc_start: 0.6985 (tt0) cc_final: 0.6753 (tt0) REVERT: C 479 PHE cc_start: 0.6827 (m-80) cc_final: 0.6530 (m-80) REVERT: C 542 ARG cc_start: 0.7795 (tmm-80) cc_final: 0.7569 (tmm-80) REVERT: D 19 LEU cc_start: 0.7967 (tp) cc_final: 0.7746 (tp) REVERT: D 23 LEU cc_start: 0.8408 (mm) cc_final: 0.8038 (mt) REVERT: D 42 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8308 (tp) REVERT: D 53 LYS cc_start: 0.8845 (mtmm) cc_final: 0.8631 (mtmm) REVERT: D 77 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7417 (mmtt) REVERT: D 98 THR cc_start: 0.8733 (m) cc_final: 0.8465 (t) REVERT: D 120 ILE cc_start: 0.8377 (mt) cc_final: 0.8046 (mm) REVERT: D 162 PHE cc_start: 0.7462 (t80) cc_final: 0.7179 (t80) REVERT: D 177 GLN cc_start: 0.7527 (mt0) cc_final: 0.6950 (tm-30) REVERT: D 180 SER cc_start: 0.8605 (m) cc_final: 0.8202 (p) REVERT: D 215 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7758 (t80) REVERT: D 216 MET cc_start: 0.7982 (tpp) cc_final: 0.7668 (mmp) REVERT: D 252 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6943 (mt-10) REVERT: D 261 PHE cc_start: 0.8686 (t80) cc_final: 0.8341 (t80) REVERT: D 275 LYS cc_start: 0.8405 (pttt) cc_final: 0.8068 (ptpt) REVERT: D 281 TYR cc_start: 0.8265 (p90) cc_final: 0.7996 (p90) REVERT: D 313 TYR cc_start: 0.8110 (m-80) cc_final: 0.7865 (m-80) REVERT: D 395 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6740 (tm-30) REVERT: D 402 ARG cc_start: 0.6176 (mpt180) cc_final: 0.5689 (mtt90) REVERT: E 37 ILE cc_start: 0.8517 (mm) cc_final: 0.8221 (mm) REVERT: E 38 LEU cc_start: 0.8110 (mt) cc_final: 0.7779 (mt) REVERT: E 40 LYS cc_start: 0.8184 (tppt) cc_final: 0.7960 (mmmm) REVERT: E 81 LEU cc_start: 0.8636 (tp) cc_final: 0.8387 (tp) REVERT: E 157 LYS cc_start: 0.7943 (tmmt) cc_final: 0.7652 (ptmm) REVERT: E 172 SER cc_start: 0.8137 (t) cc_final: 0.7768 (p) REVERT: E 213 ARG cc_start: 0.7547 (tmm-80) cc_final: 0.7339 (ttp80) REVERT: E 230 GLU cc_start: 0.7137 (tp30) cc_final: 0.6797 (tp30) REVERT: E 250 ILE cc_start: 0.7935 (mt) cc_final: 0.7676 (mm) REVERT: F 36 LYS cc_start: 0.8276 (mmmm) cc_final: 0.8066 (mmmt) REVERT: F 39 ASP cc_start: 0.6676 (m-30) cc_final: 0.6395 (m-30) REVERT: F 55 ASN cc_start: 0.8170 (m-40) cc_final: 0.7710 (m-40) REVERT: F 116 LYS cc_start: 0.9005 (mmmm) cc_final: 0.8311 (mtpp) REVERT: F 139 LYS cc_start: 0.8848 (mttt) cc_final: 0.8503 (mtpp) REVERT: F 146 ARG cc_start: 0.8536 (tmm-80) cc_final: 0.8085 (ttt180) REVERT: F 157 MET cc_start: 0.7806 (ttt) cc_final: 0.7593 (ttt) REVERT: F 208 ASP cc_start: 0.6757 (t70) cc_final: 0.6426 (t70) REVERT: G 16 MET cc_start: 0.7689 (mmm) cc_final: 0.7388 (mmm) REVERT: G 46 ILE cc_start: 0.6852 (OUTLIER) cc_final: 0.6517 (pt) REVERT: K 118 MET cc_start: 0.6461 (tpp) cc_final: 0.6184 (tpp) REVERT: K 151 LYS cc_start: 0.7774 (mttt) cc_final: 0.7453 (mtmt) REVERT: K 163 LYS cc_start: 0.7172 (mttt) cc_final: 0.6901 (mttt) REVERT: K 164 PHE cc_start: 0.8282 (p90) cc_final: 0.8071 (p90) REVERT: K 188 LYS cc_start: 0.8125 (tttt) cc_final: 0.7866 (tmtt) REVERT: K 201 GLU cc_start: 0.6783 (tp30) cc_final: 0.6439 (tp30) REVERT: K 209 GLU cc_start: 0.7629 (tp30) cc_final: 0.7118 (tp30) REVERT: K 213 LYS cc_start: 0.8049 (tptt) cc_final: 0.7599 (tptt) REVERT: K 245 GLU cc_start: 0.7606 (mp0) cc_final: 0.7202 (mp0) REVERT: K 258 ARG cc_start: 0.6955 (ttp-170) cc_final: 0.6680 (ttp-170) REVERT: K 263 MET cc_start: 0.3634 (ptt) cc_final: 0.3329 (ptt) outliers start: 126 outliers final: 90 residues processed: 866 average time/residue: 0.4063 time to fit residues: 517.8761 Evaluate side-chains 892 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 791 time to evaluate : 2.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 723 GLN Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 506 CYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 213 TRP Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain E residue 12 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 139 CYS Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 173 GLN Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain F residue 248 HIS Chi-restraints excluded: chain F residue 255 CYS Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 227 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 166 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 161 optimal weight: 0.0470 chunk 81 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 171 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 212 optimal weight: 3.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN ** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 HIS ** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 GLN C 474 HIS ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 HIS E 324 HIS E 332 GLN ** F 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24132 Z= 0.242 Angle : 0.691 11.846 32831 Z= 0.355 Chirality : 0.045 0.241 3677 Planarity : 0.004 0.062 4022 Dihedral : 14.406 179.735 3596 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.42 % Allowed : 24.25 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.16), residues: 2776 helix: 1.00 (0.14), residues: 1348 sheet: -0.25 (0.27), residues: 355 loop : -1.31 (0.18), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 342 HIS 0.015 0.001 HIS B 613 PHE 0.019 0.001 PHE A 270 TYR 0.046 0.002 TYR C 533 ARG 0.009 0.001 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 796 time to evaluate : 2.757 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: A 148 VAL cc_start: 0.8721 (p) cc_final: 0.8364 (m) REVERT: A 157 LYS cc_start: 0.8224 (tppt) cc_final: 0.7949 (ttmm) REVERT: A 165 LYS cc_start: 0.7965 (mttm) cc_final: 0.7705 (mttp) REVERT: A 271 GLU cc_start: 0.6796 (pp20) cc_final: 0.5052 (tm-30) REVERT: A 282 LYS cc_start: 0.8601 (tttt) cc_final: 0.8181 (ttmm) REVERT: A 285 ILE cc_start: 0.8572 (pt) cc_final: 0.8236 (pt) REVERT: A 296 ASP cc_start: 0.6306 (t0) cc_final: 0.5933 (t0) REVERT: A 309 ASP cc_start: 0.6361 (p0) cc_final: 0.5857 (p0) REVERT: A 375 LYS cc_start: 0.8229 (ttpt) cc_final: 0.7946 (ttmm) REVERT: A 427 MET cc_start: 0.7512 (tpp) cc_final: 0.7255 (tpp) REVERT: A 457 ILE cc_start: 0.8599 (tt) cc_final: 0.8271 (mm) REVERT: A 506 GLN cc_start: 0.8002 (tt0) cc_final: 0.7576 (tt0) REVERT: A 510 VAL cc_start: 0.8382 (OUTLIER) cc_final: 0.8164 (t) REVERT: A 525 ILE cc_start: 0.8475 (tp) cc_final: 0.7871 (pt) REVERT: A 588 GLU cc_start: 0.6683 (tp30) cc_final: 0.6446 (tp30) REVERT: A 625 GLN cc_start: 0.7416 (pt0) cc_final: 0.6781 (tt0) REVERT: A 632 SER cc_start: 0.7860 (t) cc_final: 0.7613 (t) REVERT: A 697 GLU cc_start: 0.6942 (tp30) cc_final: 0.6613 (tp30) REVERT: A 710 GLN cc_start: 0.6938 (pp30) cc_final: 0.6373 (pp30) REVERT: A 712 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8302 (tt) REVERT: B 1 MET cc_start: 0.6256 (ppp) cc_final: 0.5951 (ppp) REVERT: B 12 PHE cc_start: 0.7005 (t80) cc_final: 0.6672 (m-80) REVERT: B 25 MET cc_start: 0.5955 (mmm) cc_final: 0.5601 (mmm) REVERT: B 48 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8548 (ttmt) REVERT: B 53 LEU cc_start: 0.8399 (mt) cc_final: 0.7311 (mm) REVERT: B 57 MET cc_start: 0.7094 (mmt) cc_final: 0.6868 (mmt) REVERT: B 92 ASN cc_start: 0.7745 (m-40) cc_final: 0.7281 (m-40) REVERT: B 95 GLU cc_start: 0.7086 (mm-30) cc_final: 0.6872 (mm-30) REVERT: B 200 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7351 (pp) REVERT: B 238 ASN cc_start: 0.8006 (m-40) cc_final: 0.7783 (m110) REVERT: B 244 ILE cc_start: 0.8638 (tp) cc_final: 0.8310 (tp) REVERT: B 262 ASN cc_start: 0.7150 (p0) cc_final: 0.6939 (p0) REVERT: B 352 GLU cc_start: 0.7687 (mp0) cc_final: 0.6422 (pm20) REVERT: B 363 GLN cc_start: 0.7293 (tm-30) cc_final: 0.7068 (pp30) REVERT: B 462 SER cc_start: 0.6235 (OUTLIER) cc_final: 0.5640 (m) REVERT: B 469 LYS cc_start: 0.7275 (ptpp) cc_final: 0.7019 (ttpp) REVERT: B 487 ARG cc_start: 0.6268 (ptt-90) cc_final: 0.6062 (ptt180) REVERT: B 511 ARG cc_start: 0.7605 (mtp85) cc_final: 0.7319 (mtt180) REVERT: B 516 VAL cc_start: 0.8236 (m) cc_final: 0.7971 (p) REVERT: B 589 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6950 (tp30) REVERT: B 613 HIS cc_start: 0.7949 (OUTLIER) cc_final: 0.7525 (p90) REVERT: B 634 LYS cc_start: 0.7574 (mttp) cc_final: 0.7314 (mmtt) REVERT: B 668 ILE cc_start: 0.7987 (mm) cc_final: 0.7627 (mt) REVERT: B 672 THR cc_start: 0.7682 (p) cc_final: 0.7420 (m) REVERT: B 682 LYS cc_start: 0.7887 (pttp) cc_final: 0.7626 (ttpp) REVERT: C 405 GLN cc_start: 0.7825 (pp30) cc_final: 0.7059 (pp30) REVERT: C 409 GLN cc_start: 0.7438 (mt0) cc_final: 0.7125 (mt0) REVERT: C 412 GLU cc_start: 0.7023 (tt0) cc_final: 0.6807 (tt0) REVERT: C 542 ARG cc_start: 0.7837 (tmm-80) cc_final: 0.7627 (ttp80) REVERT: D 23 LEU cc_start: 0.8368 (mm) cc_final: 0.8034 (mt) REVERT: D 42 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8323 (tp) REVERT: D 53 LYS cc_start: 0.8838 (mtmm) cc_final: 0.8300 (mtmm) REVERT: D 77 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7396 (mmtt) REVERT: D 98 THR cc_start: 0.8736 (m) cc_final: 0.8470 (t) REVERT: D 120 ILE cc_start: 0.8382 (mt) cc_final: 0.8048 (mm) REVERT: D 162 PHE cc_start: 0.7472 (t80) cc_final: 0.7256 (t80) REVERT: D 180 SER cc_start: 0.8644 (m) cc_final: 0.8409 (p) REVERT: D 215 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7774 (t80) REVERT: D 216 MET cc_start: 0.7944 (tpp) cc_final: 0.7641 (mmp) REVERT: D 247 LYS cc_start: 0.7601 (tttm) cc_final: 0.7318 (tttm) REVERT: D 252 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6935 (mt-10) REVERT: D 275 LYS cc_start: 0.8487 (pttt) cc_final: 0.8107 (pttp) REVERT: D 277 LYS cc_start: 0.8521 (mttt) cc_final: 0.8245 (mttt) REVERT: D 281 TYR cc_start: 0.8278 (p90) cc_final: 0.7980 (p90) REVERT: D 313 TYR cc_start: 0.8123 (m-80) cc_final: 0.7878 (m-80) REVERT: D 334 MET cc_start: 0.8023 (mmm) cc_final: 0.7700 (mmt) REVERT: D 395 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6739 (tm-30) REVERT: D 402 ARG cc_start: 0.6145 (mpt180) cc_final: 0.5685 (mtt90) REVERT: E 37 ILE cc_start: 0.8520 (mm) cc_final: 0.8221 (mm) REVERT: E 38 LEU cc_start: 0.8083 (mt) cc_final: 0.7776 (mt) REVERT: E 40 LYS cc_start: 0.8182 (tppt) cc_final: 0.7959 (mmmm) REVERT: E 81 LEU cc_start: 0.8653 (tp) cc_final: 0.8380 (tp) REVERT: E 90 TYR cc_start: 0.6993 (t80) cc_final: 0.6579 (t80) REVERT: E 172 SER cc_start: 0.8131 (t) cc_final: 0.7759 (p) REVERT: E 230 GLU cc_start: 0.7116 (tp30) cc_final: 0.6758 (tp30) REVERT: E 250 ILE cc_start: 0.7941 (mt) cc_final: 0.7682 (mm) REVERT: F 36 LYS cc_start: 0.8303 (mmmm) cc_final: 0.8066 (mmmt) REVERT: F 39 ASP cc_start: 0.6689 (m-30) cc_final: 0.6405 (m-30) REVERT: F 55 ASN cc_start: 0.8158 (m-40) cc_final: 0.7717 (m-40) REVERT: F 116 LYS cc_start: 0.9159 (mmmm) cc_final: 0.8732 (mtpp) REVERT: F 139 LYS cc_start: 0.8835 (mttt) cc_final: 0.8478 (mtpp) REVERT: F 146 ARG cc_start: 0.8533 (tmm-80) cc_final: 0.8042 (ttt180) REVERT: F 157 MET cc_start: 0.7795 (ttt) cc_final: 0.7586 (ttt) REVERT: F 208 ASP cc_start: 0.6719 (t70) cc_final: 0.6405 (t70) REVERT: F 239 SER cc_start: 0.7927 (m) cc_final: 0.7651 (p) REVERT: G 16 MET cc_start: 0.7640 (mmm) cc_final: 0.7338 (mmm) REVERT: K 118 MET cc_start: 0.6424 (tpp) cc_final: 0.6166 (tpp) REVERT: K 139 ILE cc_start: 0.8207 (mm) cc_final: 0.7660 (tp) REVERT: K 151 LYS cc_start: 0.7752 (mttt) cc_final: 0.7435 (mtmt) REVERT: K 163 LYS cc_start: 0.7152 (mttt) cc_final: 0.6911 (mttt) REVERT: K 164 PHE cc_start: 0.8293 (p90) cc_final: 0.8084 (p90) REVERT: K 188 LYS cc_start: 0.8130 (tttt) cc_final: 0.7872 (tmtt) REVERT: K 201 GLU cc_start: 0.6800 (tp30) cc_final: 0.6412 (tp30) REVERT: K 209 GLU cc_start: 0.7635 (tp30) cc_final: 0.7129 (tp30) REVERT: K 213 LYS cc_start: 0.8046 (tptt) cc_final: 0.7634 (tptt) REVERT: K 245 GLU cc_start: 0.7583 (mp0) cc_final: 0.7182 (mp0) REVERT: K 258 ARG cc_start: 0.6988 (ttp-170) cc_final: 0.6690 (ttp-170) REVERT: K 263 MET cc_start: 0.3688 (OUTLIER) cc_final: 0.3326 (ptt) outliers start: 110 outliers final: 85 residues processed: 847 average time/residue: 0.4137 time to fit residues: 513.6139 Evaluate side-chains 883 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 788 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 723 GLN Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 506 CYS Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 213 TRP Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain E residue 12 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 139 CYS Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain F residue 248 HIS Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 263 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 245 optimal weight: 0.7980 chunk 258 optimal weight: 0.9980 chunk 235 optimal weight: 0.9990 chunk 251 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 197 optimal weight: 0.5980 chunk 77 optimal weight: 0.0970 chunk 227 optimal weight: 0.0570 chunk 237 optimal weight: 0.9980 chunk 250 optimal weight: 0.7980 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 HIS ** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 HIS E 340 ASN ** F 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 54 GLN K 120 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24132 Z= 0.218 Angle : 0.693 11.646 32831 Z= 0.355 Chirality : 0.044 0.239 3677 Planarity : 0.004 0.064 4022 Dihedral : 14.369 179.991 3593 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.90 % Allowed : 25.09 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.16), residues: 2776 helix: 0.99 (0.14), residues: 1346 sheet: -0.15 (0.28), residues: 342 loop : -1.27 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 539 HIS 0.014 0.001 HIS B 613 PHE 0.027 0.001 PHE A 270 TYR 0.047 0.002 TYR C 533 ARG 0.009 0.001 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 799 time to evaluate : 2.578 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: A 148 VAL cc_start: 0.8716 (p) cc_final: 0.8353 (m) REVERT: A 157 LYS cc_start: 0.8203 (tppt) cc_final: 0.7919 (ttmm) REVERT: A 165 LYS cc_start: 0.7930 (mttm) cc_final: 0.7672 (mttp) REVERT: A 282 LYS cc_start: 0.8576 (tttt) cc_final: 0.8165 (ttmm) REVERT: A 285 ILE cc_start: 0.8563 (pt) cc_final: 0.8230 (pt) REVERT: A 296 ASP cc_start: 0.6308 (t0) cc_final: 0.5948 (t0) REVERT: A 309 ASP cc_start: 0.6360 (p0) cc_final: 0.5864 (p0) REVERT: A 375 LYS cc_start: 0.8226 (ttpt) cc_final: 0.7910 (ttmm) REVERT: A 427 MET cc_start: 0.7532 (tpp) cc_final: 0.7279 (tpp) REVERT: A 457 ILE cc_start: 0.8562 (tt) cc_final: 0.8335 (mm) REVERT: A 506 GLN cc_start: 0.8001 (tt0) cc_final: 0.7790 (tt0) REVERT: A 510 VAL cc_start: 0.8264 (OUTLIER) cc_final: 0.8055 (t) REVERT: A 525 ILE cc_start: 0.8464 (tp) cc_final: 0.7899 (pt) REVERT: A 588 GLU cc_start: 0.6727 (tp30) cc_final: 0.6381 (tp30) REVERT: A 625 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.6782 (tt0) REVERT: A 632 SER cc_start: 0.7808 (t) cc_final: 0.7579 (t) REVERT: A 697 GLU cc_start: 0.6944 (tp30) cc_final: 0.6623 (tp30) REVERT: A 712 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8313 (tt) REVERT: B 1 MET cc_start: 0.6350 (ppp) cc_final: 0.6071 (ppp) REVERT: B 12 PHE cc_start: 0.7057 (t80) cc_final: 0.6717 (m-80) REVERT: B 53 LEU cc_start: 0.8356 (mt) cc_final: 0.7306 (mm) REVERT: B 95 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6862 (mm-30) REVERT: B 200 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7290 (pp) REVERT: B 238 ASN cc_start: 0.8007 (m-40) cc_final: 0.7698 (m110) REVERT: B 244 ILE cc_start: 0.8634 (tp) cc_final: 0.8292 (tp) REVERT: B 262 ASN cc_start: 0.7137 (p0) cc_final: 0.6857 (p0) REVERT: B 350 VAL cc_start: 0.7156 (m) cc_final: 0.6919 (m) REVERT: B 462 SER cc_start: 0.6041 (OUTLIER) cc_final: 0.5497 (m) REVERT: B 469 LYS cc_start: 0.7218 (ptpp) cc_final: 0.6979 (ttpp) REVERT: B 511 ARG cc_start: 0.7591 (mtp85) cc_final: 0.7291 (mtt180) REVERT: B 516 VAL cc_start: 0.8215 (m) cc_final: 0.7932 (p) REVERT: B 589 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6935 (tp30) REVERT: B 613 HIS cc_start: 0.7830 (OUTLIER) cc_final: 0.7384 (p90) REVERT: B 668 ILE cc_start: 0.7938 (mm) cc_final: 0.7599 (mt) REVERT: B 672 THR cc_start: 0.7798 (p) cc_final: 0.7578 (m) REVERT: B 682 LYS cc_start: 0.7875 (pttp) cc_final: 0.7622 (ttpp) REVERT: C 405 GLN cc_start: 0.7796 (pp30) cc_final: 0.7000 (pp30) REVERT: C 409 GLN cc_start: 0.7429 (mt0) cc_final: 0.7094 (mt0) REVERT: C 412 GLU cc_start: 0.7029 (tt0) cc_final: 0.6803 (tt0) REVERT: C 475 PHE cc_start: 0.8163 (t80) cc_final: 0.7599 (t80) REVERT: C 542 ARG cc_start: 0.7861 (tmm-80) cc_final: 0.7661 (ttp80) REVERT: D 23 LEU cc_start: 0.8365 (mm) cc_final: 0.8014 (mt) REVERT: D 42 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8151 (tp) REVERT: D 53 LYS cc_start: 0.8761 (mtmm) cc_final: 0.8267 (mtmm) REVERT: D 77 LYS cc_start: 0.7668 (mttt) cc_final: 0.7381 (mmtt) REVERT: D 98 THR cc_start: 0.8719 (m) cc_final: 0.8456 (t) REVERT: D 120 ILE cc_start: 0.8356 (mt) cc_final: 0.8038 (mm) REVERT: D 162 PHE cc_start: 0.7547 (t80) cc_final: 0.7334 (t80) REVERT: D 177 GLN cc_start: 0.7520 (mt0) cc_final: 0.6955 (tm-30) REVERT: D 180 SER cc_start: 0.8583 (m) cc_final: 0.8333 (p) REVERT: D 215 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7770 (t80) REVERT: D 216 MET cc_start: 0.7903 (tpp) cc_final: 0.7660 (mmp) REVERT: D 218 GLN cc_start: 0.7593 (mt0) cc_final: 0.7306 (mt0) REVERT: D 242 PHE cc_start: 0.7992 (m-10) cc_final: 0.7725 (m-10) REVERT: D 252 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6892 (mt-10) REVERT: D 261 PHE cc_start: 0.8647 (t80) cc_final: 0.8369 (t80) REVERT: D 266 ARG cc_start: 0.8307 (ttt-90) cc_final: 0.8042 (ttm-80) REVERT: D 281 TYR cc_start: 0.8297 (p90) cc_final: 0.8089 (p90) REVERT: D 313 TYR cc_start: 0.8107 (m-80) cc_final: 0.7901 (m-80) REVERT: D 395 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6731 (tm-30) REVERT: D 402 ARG cc_start: 0.6099 (mpt180) cc_final: 0.5634 (mtt90) REVERT: D 426 ARG cc_start: 0.6873 (ptp-110) cc_final: 0.6634 (ptp-110) REVERT: E 37 ILE cc_start: 0.8551 (mm) cc_final: 0.8223 (mm) REVERT: E 38 LEU cc_start: 0.8089 (mt) cc_final: 0.7474 (mp) REVERT: E 40 LYS cc_start: 0.8178 (tppt) cc_final: 0.7949 (mmmm) REVERT: E 81 LEU cc_start: 0.8621 (tp) cc_final: 0.8375 (tp) REVERT: E 90 TYR cc_start: 0.6999 (t80) cc_final: 0.6572 (t80) REVERT: E 172 SER cc_start: 0.8165 (t) cc_final: 0.7825 (p) REVERT: E 230 GLU cc_start: 0.7081 (tp30) cc_final: 0.6683 (tp30) REVERT: E 250 ILE cc_start: 0.7930 (mt) cc_final: 0.7679 (mm) REVERT: E 353 LYS cc_start: 0.8098 (mttt) cc_final: 0.7753 (mttt) REVERT: F 36 LYS cc_start: 0.8278 (mmmm) cc_final: 0.8040 (mmmt) REVERT: F 39 ASP cc_start: 0.6629 (m-30) cc_final: 0.6338 (m-30) REVERT: F 55 ASN cc_start: 0.8163 (m-40) cc_final: 0.7864 (m-40) REVERT: F 116 LYS cc_start: 0.8990 (mmmm) cc_final: 0.8633 (mtpp) REVERT: F 139 LYS cc_start: 0.8819 (mttt) cc_final: 0.8468 (mtpp) REVERT: F 146 ARG cc_start: 0.8525 (tmm-80) cc_final: 0.8026 (ttt180) REVERT: F 157 MET cc_start: 0.7787 (ttt) cc_final: 0.7575 (ttt) REVERT: F 208 ASP cc_start: 0.6755 (t70) cc_final: 0.6395 (t70) REVERT: F 239 SER cc_start: 0.7899 (m) cc_final: 0.7627 (p) REVERT: G 16 MET cc_start: 0.7667 (mmm) cc_final: 0.7351 (mmm) REVERT: K 118 MET cc_start: 0.6350 (tpp) cc_final: 0.6026 (tpp) REVERT: K 139 ILE cc_start: 0.8246 (mm) cc_final: 0.7722 (tp) REVERT: K 151 LYS cc_start: 0.7748 (mttt) cc_final: 0.7448 (mtmt) REVERT: K 163 LYS cc_start: 0.7102 (mttt) cc_final: 0.6866 (mttt) REVERT: K 164 PHE cc_start: 0.8292 (p90) cc_final: 0.8088 (p90) REVERT: K 188 LYS cc_start: 0.8118 (tttt) cc_final: 0.7861 (tmtt) REVERT: K 201 GLU cc_start: 0.6815 (tp30) cc_final: 0.6438 (tp30) REVERT: K 209 GLU cc_start: 0.7624 (tp30) cc_final: 0.7097 (tp30) REVERT: K 213 LYS cc_start: 0.8047 (tptt) cc_final: 0.7508 (tptt) REVERT: K 245 GLU cc_start: 0.7546 (mp0) cc_final: 0.7134 (mp0) REVERT: K 258 ARG cc_start: 0.6950 (ttp-170) cc_final: 0.6657 (ttp-170) REVERT: K 263 MET cc_start: 0.3658 (OUTLIER) cc_final: 0.3267 (ptt) outliers start: 97 outliers final: 74 residues processed: 843 average time/residue: 0.4093 time to fit residues: 503.1326 Evaluate side-chains 863 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 780 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 723 GLN Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 506 CYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 213 TRP Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain E residue 12 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 139 CYS Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 173 GLN Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain F residue 248 HIS Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 263 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 165 optimal weight: 0.9980 chunk 265 optimal weight: 3.9990 chunk 162 optimal weight: 0.0670 chunk 126 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 278 optimal weight: 1.9990 chunk 256 optimal weight: 0.0170 chunk 222 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 HIS ** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 GLN A 710 GLN ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 GLN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS E 127 HIS E 147 ASN E 324 HIS E 332 GLN F 108 ASN ** F 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.4919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24132 Z= 0.234 Angle : 0.730 20.282 32831 Z= 0.370 Chirality : 0.044 0.239 3677 Planarity : 0.004 0.062 4022 Dihedral : 14.361 179.776 3592 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.90 % Allowed : 25.37 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.16), residues: 2776 helix: 0.93 (0.14), residues: 1345 sheet: -0.17 (0.28), residues: 342 loop : -1.26 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 342 HIS 0.015 0.001 HIS B 613 PHE 0.034 0.001 PHE A 270 TYR 0.048 0.002 TYR C 533 ARG 0.011 0.001 ARG A 325 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 793 time to evaluate : 2.584 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: A 148 VAL cc_start: 0.8716 (p) cc_final: 0.8368 (m) REVERT: A 157 LYS cc_start: 0.8208 (tppt) cc_final: 0.7939 (ttmm) REVERT: A 165 LYS cc_start: 0.7936 (mttm) cc_final: 0.7674 (mttp) REVERT: A 282 LYS cc_start: 0.8577 (tttt) cc_final: 0.8173 (ttmm) REVERT: A 285 ILE cc_start: 0.8556 (pt) cc_final: 0.8246 (pt) REVERT: A 309 ASP cc_start: 0.6397 (p0) cc_final: 0.5913 (p0) REVERT: A 321 GLU cc_start: 0.7238 (mm-30) cc_final: 0.7010 (mm-30) REVERT: A 375 LYS cc_start: 0.8220 (ttpt) cc_final: 0.7848 (ttmm) REVERT: A 427 MET cc_start: 0.7538 (tpp) cc_final: 0.7281 (tpp) REVERT: A 442 GLU cc_start: 0.6547 (mp0) cc_final: 0.6319 (mp0) REVERT: A 457 ILE cc_start: 0.8567 (tt) cc_final: 0.8342 (mm) REVERT: A 506 GLN cc_start: 0.8011 (tt0) cc_final: 0.7785 (tt0) REVERT: A 510 VAL cc_start: 0.8282 (OUTLIER) cc_final: 0.8069 (t) REVERT: A 525 ILE cc_start: 0.8519 (tp) cc_final: 0.7922 (pt) REVERT: A 588 GLU cc_start: 0.6747 (tp30) cc_final: 0.6354 (tp30) REVERT: A 625 GLN cc_start: 0.7410 (pt0) cc_final: 0.6774 (tt0) REVERT: A 632 SER cc_start: 0.7831 (t) cc_final: 0.7585 (t) REVERT: A 697 GLU cc_start: 0.6970 (tp30) cc_final: 0.6644 (tp30) REVERT: A 712 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8404 (tt) REVERT: B 1 MET cc_start: 0.6318 (ppp) cc_final: 0.5996 (ppp) REVERT: B 12 PHE cc_start: 0.7060 (t80) cc_final: 0.6753 (m-80) REVERT: B 20 GLU cc_start: 0.5845 (mp0) cc_final: 0.5429 (mp0) REVERT: B 25 MET cc_start: 0.5446 (mmm) cc_final: 0.5217 (mmp) REVERT: B 53 LEU cc_start: 0.8398 (mt) cc_final: 0.8161 (mm) REVERT: B 238 ASN cc_start: 0.8003 (m-40) cc_final: 0.7720 (m110) REVERT: B 244 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8289 (tp) REVERT: B 363 GLN cc_start: 0.7223 (pp30) cc_final: 0.6742 (pp30) REVERT: B 403 PHE cc_start: 0.7384 (t80) cc_final: 0.7140 (t80) REVERT: B 462 SER cc_start: 0.6141 (OUTLIER) cc_final: 0.5735 (m) REVERT: B 469 LYS cc_start: 0.7222 (ptpp) cc_final: 0.6988 (ttpp) REVERT: B 511 ARG cc_start: 0.7578 (mtp85) cc_final: 0.7281 (mtt180) REVERT: B 516 VAL cc_start: 0.8212 (m) cc_final: 0.7932 (p) REVERT: B 589 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6955 (mm-30) REVERT: B 613 HIS cc_start: 0.7875 (OUTLIER) cc_final: 0.7322 (p90) REVERT: B 668 ILE cc_start: 0.7961 (mm) cc_final: 0.7613 (mt) REVERT: B 672 THR cc_start: 0.7809 (p) cc_final: 0.7575 (m) REVERT: B 682 LYS cc_start: 0.7874 (pttp) cc_final: 0.7621 (ttpp) REVERT: C 405 GLN cc_start: 0.7901 (pp30) cc_final: 0.6936 (pp30) REVERT: C 409 GLN cc_start: 0.7450 (mt0) cc_final: 0.7094 (mt0) REVERT: C 412 GLU cc_start: 0.7047 (tt0) cc_final: 0.6823 (tt0) REVERT: C 424 SER cc_start: 0.8401 (p) cc_final: 0.8115 (t) REVERT: D 23 LEU cc_start: 0.8343 (mm) cc_final: 0.7985 (mt) REVERT: D 42 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8150 (tp) REVERT: D 53 LYS cc_start: 0.8750 (mtmm) cc_final: 0.8446 (ttmt) REVERT: D 62 LEU cc_start: 0.8202 (mt) cc_final: 0.7665 (mm) REVERT: D 77 LYS cc_start: 0.7637 (mttt) cc_final: 0.7348 (mmtt) REVERT: D 98 THR cc_start: 0.8714 (m) cc_final: 0.8488 (t) REVERT: D 120 ILE cc_start: 0.8365 (mt) cc_final: 0.8051 (mm) REVERT: D 177 GLN cc_start: 0.7356 (mt0) cc_final: 0.6872 (tm-30) REVERT: D 180 SER cc_start: 0.8567 (m) cc_final: 0.8316 (p) REVERT: D 215 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.7731 (t80) REVERT: D 216 MET cc_start: 0.7891 (tpp) cc_final: 0.7654 (mmp) REVERT: D 242 PHE cc_start: 0.7996 (m-10) cc_final: 0.7733 (m-10) REVERT: D 252 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6874 (mt-10) REVERT: D 258 LEU cc_start: 0.8656 (tp) cc_final: 0.8446 (tp) REVERT: D 266 ARG cc_start: 0.8281 (ttt-90) cc_final: 0.8041 (ttm-80) REVERT: D 281 TYR cc_start: 0.8313 (p90) cc_final: 0.8030 (p90) REVERT: D 395 GLU cc_start: 0.7114 (tm-30) cc_final: 0.6727 (tm-30) REVERT: D 402 ARG cc_start: 0.6056 (mpt180) cc_final: 0.5545 (mtt90) REVERT: D 404 THR cc_start: 0.8199 (m) cc_final: 0.7919 (p) REVERT: D 426 ARG cc_start: 0.6904 (ptp-110) cc_final: 0.6651 (ptp-110) REVERT: E 37 ILE cc_start: 0.8550 (mm) cc_final: 0.8241 (mm) REVERT: E 81 LEU cc_start: 0.8620 (tp) cc_final: 0.8376 (tp) REVERT: E 172 SER cc_start: 0.8158 (t) cc_final: 0.7823 (p) REVERT: E 230 GLU cc_start: 0.7075 (tp30) cc_final: 0.6724 (tp30) REVERT: E 250 ILE cc_start: 0.7935 (mt) cc_final: 0.7692 (mm) REVERT: E 353 LYS cc_start: 0.8077 (mttt) cc_final: 0.7763 (mttt) REVERT: F 36 LYS cc_start: 0.8287 (mmmm) cc_final: 0.8048 (mmmt) REVERT: F 39 ASP cc_start: 0.6632 (m-30) cc_final: 0.6344 (m-30) REVERT: F 55 ASN cc_start: 0.8180 (m-40) cc_final: 0.7873 (m-40) REVERT: F 116 LYS cc_start: 0.9050 (mmmm) cc_final: 0.8657 (mtpp) REVERT: F 139 LYS cc_start: 0.8813 (mttt) cc_final: 0.8476 (mtpp) REVERT: F 146 ARG cc_start: 0.8518 (tmm-80) cc_final: 0.8038 (ttt180) REVERT: F 178 MET cc_start: 0.7731 (mmm) cc_final: 0.7471 (mmp) REVERT: F 208 ASP cc_start: 0.6744 (t70) cc_final: 0.6411 (t70) REVERT: F 239 SER cc_start: 0.7926 (m) cc_final: 0.7685 (p) REVERT: G 16 MET cc_start: 0.7688 (mmm) cc_final: 0.7390 (mmm) REVERT: G 52 VAL cc_start: 0.8409 (m) cc_final: 0.8160 (p) REVERT: K 118 MET cc_start: 0.6380 (tpp) cc_final: 0.6000 (tpp) REVERT: K 139 ILE cc_start: 0.8255 (mm) cc_final: 0.7740 (tp) REVERT: K 151 LYS cc_start: 0.7756 (mttt) cc_final: 0.7454 (mtmt) REVERT: K 163 LYS cc_start: 0.7104 (mttt) cc_final: 0.6852 (mttt) REVERT: K 164 PHE cc_start: 0.8282 (p90) cc_final: 0.7962 (p90) REVERT: K 188 LYS cc_start: 0.8128 (tttt) cc_final: 0.7873 (tmtt) REVERT: K 201 GLU cc_start: 0.6825 (tp30) cc_final: 0.6450 (tp30) REVERT: K 209 GLU cc_start: 0.7638 (tp30) cc_final: 0.7098 (tp30) REVERT: K 213 LYS cc_start: 0.8072 (tptt) cc_final: 0.7724 (tptt) REVERT: K 245 GLU cc_start: 0.7537 (mp0) cc_final: 0.7131 (mp0) REVERT: K 252 LEU cc_start: 0.7059 (mt) cc_final: 0.6685 (mt) REVERT: K 258 ARG cc_start: 0.6940 (ttp-170) cc_final: 0.6638 (ttp-170) REVERT: K 263 MET cc_start: 0.3992 (OUTLIER) cc_final: 0.3546 (ptt) outliers start: 97 outliers final: 81 residues processed: 835 average time/residue: 0.4052 time to fit residues: 493.4422 Evaluate side-chains 876 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 787 time to evaluate : 2.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 723 GLN Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 213 TRP Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain E residue 12 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 139 CYS Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 173 GLN Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain F residue 248 HIS Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 263 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 176 optimal weight: 0.5980 chunk 236 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 222 optimal weight: 0.6980 chunk 93 optimal weight: 8.9990 chunk 228 optimal weight: 0.5980 chunk 28 optimal weight: 0.0030 chunk 40 optimal weight: 0.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 GLN A 677 GLN ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS E 60 HIS E 147 ASN E 158 HIS E 324 HIS E 332 GLN E 356 HIS ** F 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.149650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.122039 restraints weight = 38538.798| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.55 r_work: 0.3432 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24132 Z= 0.218 Angle : 0.728 18.401 32831 Z= 0.369 Chirality : 0.044 0.228 3677 Planarity : 0.004 0.064 4022 Dihedral : 14.345 179.408 3592 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.98 % Allowed : 25.81 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.16), residues: 2776 helix: 0.91 (0.14), residues: 1347 sheet: -0.23 (0.28), residues: 352 loop : -1.21 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP C 539 HIS 0.014 0.001 HIS B 613 PHE 0.029 0.001 PHE D 272 TYR 0.047 0.001 TYR C 533 ARG 0.009 0.001 ARG B 518 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8409.41 seconds wall clock time: 148 minutes 13.85 seconds (8893.85 seconds total)