Starting phenix.real_space_refine on Fri Jun 20 07:09:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ebu_27998/06_2025/8ebu_27998.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ebu_27998/06_2025/8ebu_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/cci-nas-00/data/ceres_data/8ebu_27998/06_2025/8ebu_27998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ebu_27998/06_2025/8ebu_27998.map" model { file = "/net/cci-nas-00/data/ceres_data/8ebu_27998/06_2025/8ebu_27998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ebu_27998/06_2025/8ebu_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 13.54, per 1000 atoms: 0.58 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: 7.31 Conformation dependent library (CDL) restraints added in 3.0 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: 8.71 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: 9.86 Time building geometry restraints manager: 8.42 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: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.850 Check model and map are aligned: 0.150 Set scattering table: 0.220 Process input model: 73.560 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.360 ------------------------------------------------------------------------------- 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 24160 Z= 0.108 Angle : 0.507 10.807 32876 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 Details of bonding type rmsd hydrogen bonds : bond 0.17597 ( 1083) hydrogen bonds : angle 5.91180 ( 3076) metal coordination : bond 0.00265 ( 28) metal coordination : angle 3.37411 ( 45) covalent geometry : bond 0.00212 (24132) covalent geometry : angle 0.49162 (32831) *********************** 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 to be fit. rotamer outliers: 75 poor density : 926 time to evaluate : 2.624 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: 0.4218 time to fit residues: 597.9924 Evaluate side-chains 808 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 769 time to evaluate : 2.578 ------------------------------------------------------------------------------- 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: 1.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.155199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.126948 restraints weight = 39163.845| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.58 r_work: 0.3507 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 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 0.044 24160 Z= 0.152 Angle : 0.628 13.209 32876 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 Details of bonding type rmsd hydrogen bonds : bond 0.04101 ( 1083) hydrogen bonds : angle 4.58061 ( 3076) metal coordination : bond 0.00607 ( 28) metal coordination : angle 4.01929 ( 45) covalent geometry : bond 0.00334 (24132) covalent geometry : angle 0.61050 (32831) *********************** 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 to be fit. rotamer outliers: 97 poor density : 813 time to evaluate : 2.426 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 98 ASP cc_start: 0.7531 (m-30) cc_final: 0.7173 (m-30) REVERT: A 105 GLU cc_start: 0.8038 (pm20) cc_final: 0.7669 (pm20) REVERT: A 117 LYS cc_start: 0.8578 (tttt) cc_final: 0.7989 (ttpt) REVERT: A 131 LEU cc_start: 0.8150 (mp) cc_final: 0.7892 (mp) REVERT: A 157 LYS cc_start: 0.8355 (tppt) cc_final: 0.8068 (ttmm) REVERT: A 165 LYS cc_start: 0.8096 (mttm) cc_final: 0.7720 (mttp) REVERT: A 167 LYS cc_start: 0.7787 (ttmm) cc_final: 0.7579 (ttpp) REVERT: A 178 GLU cc_start: 0.6964 (tp30) cc_final: 0.6670 (tp30) REVERT: A 282 LYS cc_start: 0.8796 (tttt) cc_final: 0.8181 (ttmm) REVERT: A 296 ASP cc_start: 0.6537 (t0) cc_final: 0.6242 (t0) REVERT: A 298 ARG cc_start: 0.8163 (mmm160) cc_final: 0.7822 (tpp80) REVERT: A 309 ASP cc_start: 0.6594 (p0) cc_final: 0.6072 (p0) REVERT: A 316 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7831 (pp) REVERT: A 334 ARG cc_start: 0.7981 (ptp-170) cc_final: 0.7549 (ptp-170) REVERT: A 351 VAL cc_start: 0.8277 (t) cc_final: 0.8045 (p) REVERT: A 375 LYS cc_start: 0.8624 (ttpt) cc_final: 0.8304 (ttmm) REVERT: A 419 ARG cc_start: 0.7822 (ttm170) cc_final: 0.7530 (ttm110) REVERT: A 446 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.7994 (mm) REVERT: A 454 VAL cc_start: 0.8718 (t) cc_final: 0.8396 (p) REVERT: A 487 LYS cc_start: 0.8702 (ttmt) cc_final: 0.8494 (ttpp) REVERT: A 504 LYS cc_start: 0.8668 (tttt) cc_final: 0.8329 (tttp) REVERT: A 506 GLN cc_start: 0.8446 (tt0) cc_final: 0.8058 (tt0) REVERT: A 570 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6638 (pm20) REVERT: A 586 GLN cc_start: 0.8247 (tp40) cc_final: 0.7774 (tm-30) REVERT: A 625 GLN cc_start: 0.8081 (pt0) cc_final: 0.7268 (pt0) REVERT: A 636 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7533 (tp30) REVERT: A 658 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7590 (p90) REVERT: A 659 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.6768 (p90) REVERT: A 668 GLN cc_start: 0.8353 (mt0) cc_final: 0.8137 (mt0) REVERT: A 688 LYS cc_start: 0.8750 (ttmm) cc_final: 0.8383 (ttmt) REVERT: A 714 GLN cc_start: 0.7719 (mp10) cc_final: 0.7464 (mp10) REVERT: B 12 PHE cc_start: 0.7174 (t80) cc_final: 0.6555 (m-80) REVERT: B 27 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7271 (tm-30) REVERT: B 53 LEU cc_start: 0.8152 (mt) cc_final: 0.7429 (mm) REVERT: B 57 MET cc_start: 0.8286 (mmt) cc_final: 0.7743 (mmt) REVERT: B 61 ARG cc_start: 0.7267 (tpm170) cc_final: 0.6579 (tpm170) REVERT: B 94 TYR cc_start: 0.6740 (t80) cc_final: 0.6456 (t80) REVERT: B 133 LYS cc_start: 0.7545 (mttt) cc_final: 0.7309 (mttp) REVERT: B 176 ASN cc_start: 0.6125 (t0) cc_final: 0.5764 (t0) REVERT: B 203 ASN cc_start: 0.7782 (t0) cc_final: 0.7579 (t0) REVERT: B 235 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: B 237 HIS cc_start: 0.8392 (p-80) cc_final: 0.8075 (p90) REVERT: B 238 ASN cc_start: 0.8215 (m-40) cc_final: 0.7922 (m110) REVERT: B 244 ILE cc_start: 0.8057 (tp) cc_final: 0.7836 (tp) REVERT: B 259 CYS cc_start: 0.7146 (m) cc_final: 0.6941 (m) REVERT: B 262 ASN cc_start: 0.7632 (p0) cc_final: 0.7331 (p0) REVERT: B 341 LYS cc_start: 0.7878 (mtmm) cc_final: 0.7476 (mttt) REVERT: B 363 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7192 (mm-40) REVERT: B 397 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7416 (mm) REVERT: B 469 LYS cc_start: 0.8088 (ptpt) cc_final: 0.7749 (ptpp) REVERT: B 471 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7991 (pp) REVERT: B 487 ARG cc_start: 0.6543 (ptt-90) cc_final: 0.5709 (ptt180) REVERT: B 511 ARG cc_start: 0.7989 (mtp85) cc_final: 0.7640 (mtt180) REVERT: B 570 GLU cc_start: 0.7274 (tm-30) cc_final: 0.6916 (tm-30) REVERT: B 583 LYS cc_start: 0.8218 (ptpp) cc_final: 0.7931 (mtmm) REVERT: B 589 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7565 (tp30) REVERT: B 603 LYS cc_start: 0.7740 (ptmm) cc_final: 0.7355 (ptmm) REVERT: B 631 ARG cc_start: 0.7019 (mtp-110) cc_final: 0.6772 (mpp80) REVERT: B 634 LYS cc_start: 0.7297 (ptpp) cc_final: 0.7021 (mttm) REVERT: B 668 ILE cc_start: 0.8377 (mm) cc_final: 0.8086 (mt) REVERT: B 672 THR cc_start: 0.8146 (p) cc_final: 0.7713 (m) REVERT: B 681 ASP cc_start: 0.8408 (t0) cc_final: 0.7699 (t70) REVERT: B 682 LYS cc_start: 0.8585 (pttp) cc_final: 0.8152 (ttpp) REVERT: B 712 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6961 (mt-10) REVERT: B 724 MET cc_start: 0.8033 (mmm) cc_final: 0.7729 (mmm) REVERT: C 411 MET cc_start: 0.7512 (tpp) cc_final: 0.7297 (tpp) REVERT: C 441 MET cc_start: 0.5650 (mmm) cc_final: 0.5104 (mmt) REVERT: C 442 GLN cc_start: 0.2775 (OUTLIER) cc_final: 0.1923 (pt0) REVERT: C 473 ARG cc_start: 0.6954 (tmt170) cc_final: 0.6606 (tmt170) REVERT: C 474 HIS cc_start: 0.8114 (m-70) cc_final: 0.7653 (m-70) REVERT: C 524 HIS cc_start: 0.8038 (t-170) cc_final: 0.7777 (t70) REVERT: C 529 LEU cc_start: 0.8974 (mt) cc_final: 0.8196 (mt) REVERT: C 545 MET cc_start: 0.6123 (mtt) cc_final: 0.5676 (mtt) REVERT: D 53 LYS cc_start: 0.9035 (mtmt) cc_final: 0.8519 (mtmm) REVERT: D 57 MET cc_start: 0.8512 (mmm) cc_final: 0.8308 (mmm) REVERT: D 76 LYS cc_start: 0.7158 (mttm) cc_final: 0.6903 (mttm) REVERT: D 77 LYS cc_start: 0.8100 (mttt) cc_final: 0.7788 (mttt) REVERT: D 89 LEU cc_start: 0.8600 (tp) cc_final: 0.8301 (tt) REVERT: D 113 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7643 (mp) REVERT: D 115 ARG cc_start: 0.8272 (ttt-90) cc_final: 0.7980 (ttt-90) REVERT: D 117 ASN cc_start: 0.7992 (m-40) cc_final: 0.7712 (m-40) REVERT: D 120 ILE cc_start: 0.8557 (mt) cc_final: 0.8229 (mm) REVERT: D 139 ASP cc_start: 0.6554 (t0) cc_final: 0.6059 (t0) REVERT: D 156 TRP cc_start: 0.8663 (t-100) cc_final: 0.8343 (t-100) REVERT: D 177 GLN cc_start: 0.8053 (mt0) cc_final: 0.7260 (tm-30) REVERT: D 180 SER cc_start: 0.8274 (m) cc_final: 0.7767 (p) REVERT: D 185 MET cc_start: 0.7765 (mtm) cc_final: 0.7419 (mpp) REVERT: D 204 LEU cc_start: 0.8476 (mt) cc_final: 0.8090 (mt) REVERT: D 216 MET cc_start: 0.8525 (tpp) cc_final: 0.8261 (mmp) REVERT: D 239 GLN cc_start: 0.8268 (tt0) cc_final: 0.8059 (tm-30) REVERT: D 243 SER cc_start: 0.8586 (m) cc_final: 0.8187 (m) REVERT: D 248 ASP cc_start: 0.7771 (p0) cc_final: 0.7552 (p0) REVERT: D 249 TYR cc_start: 0.8019 (m-80) cc_final: 0.7793 (m-80) REVERT: D 261 PHE cc_start: 0.8630 (t80) cc_final: 0.8279 (t80) REVERT: D 266 ARG cc_start: 0.8500 (ttt180) cc_final: 0.8293 (ttp-170) REVERT: D 282 TYR cc_start: 0.8063 (m-80) cc_final: 0.7526 (m-80) REVERT: D 313 TYR cc_start: 0.8662 (m-80) cc_final: 0.8311 (m-80) REVERT: D 365 ILE cc_start: 0.8580 (mt) cc_final: 0.8326 (mm) REVERT: D 395 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7497 (tm-30) REVERT: D 397 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7457 (mm-30) REVERT: D 402 ARG cc_start: 0.6536 (mpt180) cc_final: 0.6085 (mtt90) REVERT: D 407 VAL cc_start: 0.8462 (t) cc_final: 0.8143 (m) REVERT: D 438 LYS cc_start: 0.8294 (mttt) cc_final: 0.8074 (mttt) REVERT: D 450 ASP cc_start: 0.7342 (t0) cc_final: 0.6974 (t0) REVERT: E 17 ARG cc_start: 0.7883 (mpp80) cc_final: 0.7520 (mtt-85) REVERT: E 37 ILE cc_start: 0.8254 (mm) cc_final: 0.7960 (mm) REVERT: E 38 LEU cc_start: 0.7992 (mt) cc_final: 0.7659 (mt) REVERT: E 40 LYS cc_start: 0.8143 (tppt) cc_final: 0.7884 (mmmm) REVERT: E 66 ASP cc_start: 0.7890 (t0) cc_final: 0.7437 (t0) REVERT: E 157 LYS cc_start: 0.8516 (tttt) cc_final: 0.8233 (ttpp) REVERT: E 159 MET cc_start: 0.8377 (mmt) cc_final: 0.8034 (mmp) REVERT: E 172 SER cc_start: 0.8625 (t) cc_final: 0.8298 (p) REVERT: E 224 ASP cc_start: 0.7136 (p0) cc_final: 0.6750 (p0) REVERT: E 229 LYS cc_start: 0.8343 (tttt) cc_final: 0.8140 (tttt) REVERT: E 230 GLU cc_start: 0.7712 (tp30) cc_final: 0.7437 (tp30) REVERT: E 328 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7490 (tt) REVERT: E 329 ASP cc_start: 0.7642 (p0) cc_final: 0.7346 (p0) REVERT: E 332 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7796 (pt0) REVERT: E 336 LEU cc_start: 0.8305 (tp) cc_final: 0.8087 (tt) REVERT: E 366 VAL cc_start: 0.8164 (OUTLIER) cc_final: 0.7753 (m) REVERT: F 36 LYS cc_start: 0.8447 (mmmm) cc_final: 0.8218 (mmmt) REVERT: F 39 ASP cc_start: 0.7383 (m-30) cc_final: 0.7002 (m-30) REVERT: F 55 ASN cc_start: 0.8391 (m-40) cc_final: 0.7876 (m-40) REVERT: F 106 SER cc_start: 0.8340 (m) cc_final: 0.8132 (t) REVERT: F 116 LYS cc_start: 0.8819 (mmmm) cc_final: 0.8477 (mtpp) REVERT: F 139 LYS cc_start: 0.8838 (mttt) cc_final: 0.8591 (mtmt) REVERT: F 146 ARG cc_start: 0.8680 (tmm-80) cc_final: 0.8307 (ttp-170) REVERT: F 186 LYS cc_start: 0.8507 (tttt) cc_final: 0.8299 (ttmm) REVERT: F 199 ASP cc_start: 0.7943 (m-30) cc_final: 0.7645 (m-30) REVERT: F 204 GLN cc_start: 0.8706 (mt0) cc_final: 0.8448 (mt0) REVERT: F 208 ASP cc_start: 0.7559 (t70) cc_final: 0.7112 (t0) REVERT: F 217 VAL cc_start: 0.8813 (t) cc_final: 0.8600 (p) REVERT: F 224 LEU cc_start: 0.8646 (tp) cc_final: 0.8443 (tp) REVERT: F 226 TYR cc_start: 0.8710 (m-80) cc_final: 0.8420 (m-10) REVERT: F 236 ASP cc_start: 0.8106 (p0) cc_final: 0.7772 (p0) REVERT: F 240 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7457 (mp10) REVERT: G 61 MET cc_start: 0.7590 (tpp) cc_final: 0.7173 (mmm) REVERT: K 118 MET cc_start: 0.6996 (tpp) cc_final: 0.6587 (tpp) REVERT: K 163 LYS cc_start: 0.7507 (mttt) cc_final: 0.7162 (mttt) REVERT: K 179 LYS cc_start: 0.7955 (mttt) cc_final: 0.7619 (mtmm) REVERT: K 181 TYR cc_start: 0.8459 (m-80) cc_final: 0.8191 (m-80) REVERT: K 209 GLU cc_start: 0.8230 (tp30) cc_final: 0.7618 (tp30) REVERT: K 213 LYS cc_start: 0.8295 (tptt) cc_final: 0.7629 (tptt) REVERT: K 245 GLU cc_start: 0.8048 (mp0) cc_final: 0.7721 (mp0) REVERT: K 272 LYS cc_start: 0.6462 (ttmm) cc_final: 0.5976 (tptt) outliers start: 97 outliers final: 42 residues processed: 867 average time/residue: 0.4120 time to fit residues: 523.6115 Evaluate side-chains 827 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 769 time to evaluate : 2.578 ------------------------------------------------------------------------------- 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 636 GLU 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 235 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 471 LEU Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 712 GLU 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 332 GLN 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 85 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 225 optimal weight: 0.9980 chunk 150 optimal weight: 0.0970 chunk 69 optimal weight: 0.7980 chunk 127 optimal weight: 50.0000 chunk 239 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 551 HIS ** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 GLN A 683 GLN B 60 GLN B 210 HIS B 241 ASN ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 ASN B 649 ASN C 474 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 G 18 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.151419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.123618 restraints weight = 39002.248| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.50 r_work: 0.3431 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24160 Z= 0.194 Angle : 0.643 16.386 32876 Z= 0.324 Chirality : 0.045 0.206 3677 Planarity : 0.004 0.064 4022 Dihedral : 14.440 179.694 3623 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.70 % Allowed : 18.25 % Favored : 77.04 % 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: 0.35 (0.16), residues: 2776 helix: 1.38 (0.15), residues: 1342 sheet: 0.06 (0.26), residues: 377 loop : -1.20 (0.18), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 511 HIS 0.019 0.001 HIS B 210 PHE 0.022 0.002 PHE F 278 TYR 0.034 0.002 TYR C 533 ARG 0.012 0.001 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.04110 ( 1083) hydrogen bonds : angle 4.44649 ( 3076) metal coordination : bond 0.00651 ( 28) metal coordination : angle 4.30321 ( 45) covalent geometry : bond 0.00417 (24132) covalent geometry : angle 0.62309 (32831) *********************** 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 927 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 810 time to evaluate : 2.359 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 60 ASP cc_start: 0.8018 (p0) cc_final: 0.7608 (p0) REVERT: A 98 ASP cc_start: 0.7572 (m-30) cc_final: 0.7018 (m-30) REVERT: A 105 GLU cc_start: 0.8108 (pm20) cc_final: 0.7713 (pm20) REVERT: A 117 LYS cc_start: 0.8545 (tttt) cc_final: 0.7880 (ttpt) REVERT: A 131 LEU cc_start: 0.8266 (mp) cc_final: 0.8053 (mp) REVERT: A 150 ASP cc_start: 0.7844 (t0) cc_final: 0.7543 (t0) REVERT: A 153 MET cc_start: 0.7479 (mmm) cc_final: 0.7224 (mmm) REVERT: A 157 LYS cc_start: 0.8531 (tppt) cc_final: 0.8242 (ttmm) REVERT: A 165 LYS cc_start: 0.8292 (mttm) cc_final: 0.7910 (mttp) REVERT: A 191 ASP cc_start: 0.7744 (t0) cc_final: 0.7382 (t0) REVERT: A 273 LYS cc_start: 0.8355 (ttmt) cc_final: 0.7941 (mtmt) REVERT: A 279 GLU cc_start: 0.7691 (mp0) cc_final: 0.7470 (mp0) REVERT: A 282 LYS cc_start: 0.8731 (tttt) cc_final: 0.8219 (ttmm) REVERT: A 296 ASP cc_start: 0.6643 (t0) cc_final: 0.6161 (t0) REVERT: A 298 ARG cc_start: 0.8154 (mmm160) cc_final: 0.7876 (tpp80) REVERT: A 309 ASP cc_start: 0.6564 (p0) cc_final: 0.6028 (p0) REVERT: A 316 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7900 (pp) REVERT: A 334 ARG cc_start: 0.8086 (ptp-170) cc_final: 0.7627 (ptp-170) REVERT: A 351 VAL cc_start: 0.8314 (t) cc_final: 0.8105 (p) REVERT: A 360 ARG cc_start: 0.8021 (mtp180) cc_final: 0.7782 (mtp85) REVERT: A 373 GLN cc_start: 0.8260 (tp40) cc_final: 0.8038 (tp40) REVERT: A 375 LYS cc_start: 0.8700 (ttpt) cc_final: 0.8323 (ttmm) REVERT: A 391 ARG cc_start: 0.8189 (mtm-85) cc_final: 0.7983 (mtm110) REVERT: A 434 GLU cc_start: 0.8084 (pm20) cc_final: 0.7738 (pm20) REVERT: A 446 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8259 (mm) REVERT: A 454 VAL cc_start: 0.8721 (t) cc_final: 0.8501 (p) REVERT: A 504 LYS cc_start: 0.8687 (tttt) cc_final: 0.8388 (tttt) REVERT: A 506 GLN cc_start: 0.8556 (tt0) cc_final: 0.8229 (tt0) REVERT: A 510 VAL cc_start: 0.8137 (OUTLIER) cc_final: 0.7776 (t) REVERT: A 525 ILE cc_start: 0.8562 (tp) cc_final: 0.8016 (pt) REVERT: A 586 GLN cc_start: 0.8208 (tp40) cc_final: 0.7725 (tm-30) REVERT: A 621 ASN cc_start: 0.8235 (m110) cc_final: 0.7981 (m-40) REVERT: A 625 GLN cc_start: 0.8044 (pt0) cc_final: 0.7415 (pt0) REVERT: A 636 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7742 (tp30) REVERT: A 658 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.7367 (p90) REVERT: A 688 LYS cc_start: 0.8759 (ttmm) cc_final: 0.8341 (ttmt) REVERT: A 710 GLN cc_start: 0.7564 (pt0) cc_final: 0.7264 (pp30) REVERT: A 712 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8008 (tt) REVERT: B 1 MET cc_start: 0.6634 (ppp) cc_final: 0.6144 (ppp) REVERT: B 12 PHE cc_start: 0.7297 (t80) cc_final: 0.6722 (m-80) REVERT: B 27 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7300 (tm-30) REVERT: B 53 LEU cc_start: 0.8341 (mt) cc_final: 0.7443 (mm) REVERT: B 57 MET cc_start: 0.8319 (mmt) cc_final: 0.7725 (mmt) REVERT: B 59 TYR cc_start: 0.8197 (t80) cc_final: 0.7989 (t80) REVERT: B 63 TYR cc_start: 0.7946 (m-80) cc_final: 0.7522 (m-80) REVERT: B 76 THR cc_start: 0.6968 (OUTLIER) cc_final: 0.6612 (p) REVERT: B 94 TYR cc_start: 0.6888 (t80) cc_final: 0.6549 (t80) REVERT: B 95 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7062 (mm-30) REVERT: B 133 LYS cc_start: 0.7584 (mttt) cc_final: 0.7326 (mttp) REVERT: B 176 ASN cc_start: 0.6300 (t0) cc_final: 0.5742 (t0) REVERT: B 178 ASP cc_start: 0.7192 (p0) cc_final: 0.6765 (p0) REVERT: B 235 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: B 238 ASN cc_start: 0.8261 (m-40) cc_final: 0.7972 (m110) REVERT: B 244 ILE cc_start: 0.8389 (tp) cc_final: 0.8098 (tp) REVERT: B 259 CYS cc_start: 0.7088 (m) cc_final: 0.6880 (m) REVERT: B 262 ASN cc_start: 0.7664 (p0) cc_final: 0.7395 (p0) REVERT: B 397 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7361 (mm) REVERT: B 439 ASP cc_start: 0.7636 (t0) cc_final: 0.7435 (t0) REVERT: B 469 LYS cc_start: 0.8191 (ptpt) cc_final: 0.7939 (ptpp) REVERT: B 471 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8014 (pp) REVERT: B 487 ARG cc_start: 0.6887 (ptt-90) cc_final: 0.5943 (ptt180) REVERT: B 511 ARG cc_start: 0.7876 (mtp85) cc_final: 0.7600 (mtt180) REVERT: B 518 ARG cc_start: 0.8409 (mtp85) cc_final: 0.7899 (mtp-110) REVERT: B 545 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8431 (ttp) REVERT: B 583 LYS cc_start: 0.8152 (ptpp) cc_final: 0.7857 (mttt) REVERT: B 589 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7724 (tp30) REVERT: B 613 HIS cc_start: 0.8313 (OUTLIER) cc_final: 0.7826 (p90) REVERT: B 634 LYS cc_start: 0.7567 (ptpp) cc_final: 0.7237 (mttt) REVERT: B 638 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7923 (tm-30) REVERT: B 644 PHE cc_start: 0.8816 (m-80) cc_final: 0.8578 (m-80) REVERT: B 668 ILE cc_start: 0.8514 (mm) cc_final: 0.8067 (mt) REVERT: B 672 THR cc_start: 0.8104 (p) cc_final: 0.7715 (m) REVERT: B 681 ASP cc_start: 0.8475 (t0) cc_final: 0.7685 (t70) REVERT: B 682 LYS cc_start: 0.8579 (pttp) cc_final: 0.8176 (ttpp) REVERT: B 712 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7218 (mt-10) REVERT: C 402 ASN cc_start: 0.7422 (m-40) cc_final: 0.7078 (m-40) REVERT: C 405 GLN cc_start: 0.7813 (pp30) cc_final: 0.6671 (pp30) REVERT: C 409 GLN cc_start: 0.7638 (mt0) cc_final: 0.7304 (mt0) REVERT: C 411 MET cc_start: 0.7739 (tpp) cc_final: 0.7402 (tpp) REVERT: C 441 MET cc_start: 0.5941 (mmm) cc_final: 0.5410 (tpp) REVERT: C 442 GLN cc_start: 0.2947 (OUTLIER) cc_final: 0.1712 (pt0) REVERT: C 473 ARG cc_start: 0.7124 (tmt170) cc_final: 0.6713 (tmt170) REVERT: C 474 HIS cc_start: 0.8120 (m90) cc_final: 0.7699 (m-70) REVERT: C 524 HIS cc_start: 0.8227 (t-170) cc_final: 0.7767 (t-90) REVERT: C 529 LEU cc_start: 0.9118 (mt) cc_final: 0.8874 (mt) REVERT: C 545 MET cc_start: 0.6002 (mtt) cc_final: 0.5596 (mtt) REVERT: D 77 LYS cc_start: 0.8162 (mttt) cc_final: 0.7839 (mttt) REVERT: D 113 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7672 (mp) REVERT: D 117 ASN cc_start: 0.7913 (m-40) cc_final: 0.7634 (m-40) REVERT: D 120 ILE cc_start: 0.8601 (mt) cc_final: 0.8302 (mm) REVERT: D 154 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7103 (mt-10) REVERT: D 177 GLN cc_start: 0.8054 (mt0) cc_final: 0.7355 (tm-30) REVERT: D 180 SER cc_start: 0.8584 (m) cc_final: 0.8150 (p) REVERT: D 204 LEU cc_start: 0.8632 (mt) cc_final: 0.8295 (mt) REVERT: D 229 ASP cc_start: 0.7495 (t0) cc_final: 0.7161 (t70) REVERT: D 241 SER cc_start: 0.8549 (p) cc_final: 0.8337 (p) REVERT: D 243 SER cc_start: 0.8869 (m) cc_final: 0.8468 (p) REVERT: D 252 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7317 (mt-10) REVERT: D 261 PHE cc_start: 0.8775 (t80) cc_final: 0.8396 (t80) REVERT: D 275 LYS cc_start: 0.8269 (pttt) cc_final: 0.7967 (ptmt) REVERT: D 313 TYR cc_start: 0.8588 (m-80) cc_final: 0.8233 (m-80) REVERT: D 365 ILE cc_start: 0.8621 (mt) cc_final: 0.8377 (mm) REVERT: D 395 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7517 (tm-30) REVERT: D 402 ARG cc_start: 0.6787 (mpt180) cc_final: 0.6393 (mtt90) REVERT: D 407 VAL cc_start: 0.8435 (t) cc_final: 0.8165 (m) REVERT: D 438 LYS cc_start: 0.8422 (mttt) cc_final: 0.8186 (mttt) REVERT: D 450 ASP cc_start: 0.7378 (t0) cc_final: 0.7010 (t0) REVERT: E 37 ILE cc_start: 0.8308 (mm) cc_final: 0.8011 (mm) REVERT: E 38 LEU cc_start: 0.8012 (mt) cc_final: 0.7665 (mt) REVERT: E 40 LYS cc_start: 0.8200 (tppt) cc_final: 0.7925 (mmmm) REVERT: E 66 ASP cc_start: 0.7869 (t0) cc_final: 0.7332 (t0) REVERT: E 81 LEU cc_start: 0.8371 (tp) cc_final: 0.8097 (tp) REVERT: E 94 GLU cc_start: 0.8091 (tp30) cc_final: 0.7806 (tp30) REVERT: E 157 LYS cc_start: 0.8525 (tttt) cc_final: 0.8323 (ttpp) REVERT: E 159 MET cc_start: 0.8461 (mmt) cc_final: 0.8121 (mmp) REVERT: E 172 SER cc_start: 0.8719 (t) cc_final: 0.8371 (p) REVERT: E 224 ASP cc_start: 0.7229 (p0) cc_final: 0.6893 (p0) REVERT: E 229 LYS cc_start: 0.8264 (tttt) cc_final: 0.8027 (tttt) REVERT: E 230 GLU cc_start: 0.7733 (tp30) cc_final: 0.7520 (tp30) REVERT: E 233 THR cc_start: 0.7864 (m) cc_final: 0.7658 (p) REVERT: E 328 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7598 (tt) REVERT: E 329 ASP cc_start: 0.7754 (p0) cc_final: 0.7549 (p0) REVERT: E 336 LEU cc_start: 0.8313 (tp) cc_final: 0.8108 (tt) REVERT: E 366 VAL cc_start: 0.8250 (OUTLIER) cc_final: 0.7810 (m) REVERT: F 55 ASN cc_start: 0.8444 (m-40) cc_final: 0.7889 (m-40) REVERT: F 106 SER cc_start: 0.8425 (m) cc_final: 0.8200 (t) REVERT: F 113 GLU cc_start: 0.7994 (tt0) cc_final: 0.7721 (tt0) REVERT: F 116 LYS cc_start: 0.8889 (mmmm) cc_final: 0.8119 (mtpp) REVERT: F 139 LYS cc_start: 0.8874 (mttt) cc_final: 0.8632 (mtmt) REVERT: F 146 ARG cc_start: 0.8640 (tmm-80) cc_final: 0.8360 (ttt-90) REVERT: F 186 LYS cc_start: 0.8548 (tttt) cc_final: 0.8314 (ttmm) REVERT: F 199 ASP cc_start: 0.8026 (m-30) cc_final: 0.7812 (m-30) REVERT: F 208 ASP cc_start: 0.7644 (t70) cc_final: 0.7238 (t0) REVERT: F 217 VAL cc_start: 0.8818 (t) cc_final: 0.8611 (p) REVERT: F 240 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7633 (mt0) REVERT: G 16 MET cc_start: 0.8923 (mmm) cc_final: 0.8554 (mmp) REVERT: G 46 ILE cc_start: 0.6612 (OUTLIER) cc_final: 0.6391 (mp) REVERT: K 118 MET cc_start: 0.7077 (tpp) cc_final: 0.6687 (tpp) REVERT: K 141 LYS cc_start: 0.8502 (tttt) cc_final: 0.8268 (tttp) REVERT: K 151 LYS cc_start: 0.7700 (mttt) cc_final: 0.7382 (mttt) REVERT: K 163 LYS cc_start: 0.7481 (mttt) cc_final: 0.7154 (mttt) REVERT: K 164 PHE cc_start: 0.8495 (p90) cc_final: 0.8126 (p90) REVERT: K 179 LYS cc_start: 0.7993 (mttt) cc_final: 0.7706 (mtmm) REVERT: K 209 GLU cc_start: 0.8340 (tp30) cc_final: 0.7761 (tp30) REVERT: K 213 LYS cc_start: 0.8350 (tptt) cc_final: 0.7686 (tptt) REVERT: K 245 GLU cc_start: 0.8136 (mp0) cc_final: 0.7588 (mp0) REVERT: K 258 ARG cc_start: 0.7526 (ttp-170) cc_final: 0.6915 (ttp-170) REVERT: K 272 LYS cc_start: 0.6444 (ttmm) cc_final: 0.5895 (tptt) outliers start: 117 outliers final: 67 residues processed: 869 average time/residue: 0.3943 time to fit residues: 503.5321 Evaluate side-chains 873 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 788 time to evaluate : 2.417 ------------------------------------------------------------------------------- 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 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 446 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 629 HIS Chi-restraints excluded: chain A residue 636 GLU 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 28 LEU 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 235 GLU 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 471 LEU Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 545 MET 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 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 205 LEU 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 322 GLU Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain E residue 12 GLU 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 328 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 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 177 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 271 optimal weight: 8.9990 chunk 165 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 163 optimal weight: 0.6980 chunk 127 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 HIS E 332 GLN F 108 ASN F 260 ASN G 54 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.148037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.120196 restraints weight = 38988.782| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.48 r_work: 0.3374 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 24160 Z= 0.245 Angle : 0.701 20.938 32876 Z= 0.351 Chirality : 0.047 0.250 3677 Planarity : 0.005 0.058 4022 Dihedral : 14.610 179.960 3617 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 5.11 % Allowed : 18.82 % Favored : 76.08 % 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: 1.14 (0.15), residues: 1345 sheet: -0.22 (0.26), residues: 375 loop : -1.27 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 511 HIS 0.017 0.001 HIS B 613 PHE 0.027 0.002 PHE B 403 TYR 0.045 0.002 TYR C 533 ARG 0.012 0.001 ARG K 227 Details of bonding type rmsd hydrogen bonds : bond 0.04443 ( 1083) hydrogen bonds : angle 4.47520 ( 3076) metal coordination : bond 0.00868 ( 28) metal coordination : angle 5.21034 ( 45) covalent geometry : bond 0.00535 (24132) covalent geometry : angle 0.67443 (32831) *********************** 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 957 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 830 time to evaluate : 2.663 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 60 ASP cc_start: 0.7833 (p0) cc_final: 0.7601 (p0) REVERT: A 87 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7642 (mt-10) REVERT: A 98 ASP cc_start: 0.7639 (m-30) cc_final: 0.7059 (m-30) REVERT: A 105 GLU cc_start: 0.7980 (pm20) cc_final: 0.7631 (pm20) REVERT: A 117 LYS cc_start: 0.8554 (tttt) cc_final: 0.7784 (ttpt) REVERT: A 131 LEU cc_start: 0.8360 (mp) cc_final: 0.8063 (mp) REVERT: A 148 VAL cc_start: 0.9008 (p) cc_final: 0.8610 (m) REVERT: A 150 ASP cc_start: 0.7812 (t0) cc_final: 0.7520 (t0) REVERT: A 153 MET cc_start: 0.7436 (mmm) cc_final: 0.7066 (mmm) REVERT: A 157 LYS cc_start: 0.8538 (tppt) cc_final: 0.8248 (ttmm) REVERT: A 165 LYS cc_start: 0.8393 (mttm) cc_final: 0.8032 (mttp) REVERT: A 191 ASP cc_start: 0.7900 (t0) cc_final: 0.7648 (t0) REVERT: A 273 LYS cc_start: 0.8338 (ttmt) cc_final: 0.7989 (mtmt) REVERT: A 279 GLU cc_start: 0.7757 (mp0) cc_final: 0.7429 (mp0) REVERT: A 282 LYS cc_start: 0.8777 (tttt) cc_final: 0.8239 (ttmm) REVERT: A 296 ASP cc_start: 0.6783 (t0) cc_final: 0.6332 (t0) REVERT: A 298 ARG cc_start: 0.8193 (mmm160) cc_final: 0.7980 (tpp80) REVERT: A 309 ASP cc_start: 0.6883 (p0) cc_final: 0.6366 (p0) REVERT: A 316 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7941 (pp) REVERT: A 351 VAL cc_start: 0.8379 (t) cc_final: 0.8162 (p) REVERT: A 375 LYS cc_start: 0.8712 (ttpt) cc_final: 0.8295 (ttmm) REVERT: A 425 ARG cc_start: 0.7859 (tpp-160) cc_final: 0.7603 (tpp-160) REVERT: A 434 GLU cc_start: 0.8101 (pm20) cc_final: 0.7811 (pm20) REVERT: A 510 VAL cc_start: 0.8429 (OUTLIER) cc_final: 0.8081 (t) REVERT: A 525 ILE cc_start: 0.8557 (tp) cc_final: 0.7918 (pt) REVERT: A 586 GLN cc_start: 0.8245 (tp40) cc_final: 0.7746 (tm-30) REVERT: A 621 ASN cc_start: 0.8259 (m110) cc_final: 0.8003 (m-40) REVERT: A 625 GLN cc_start: 0.8068 (pt0) cc_final: 0.7225 (pt0) REVERT: A 697 GLU cc_start: 0.7308 (tp30) cc_final: 0.7060 (tp30) REVERT: A 710 GLN cc_start: 0.7687 (pt0) cc_final: 0.7316 (pp30) REVERT: A 712 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8172 (tt) REVERT: B 1 MET cc_start: 0.6576 (ppp) cc_final: 0.5850 (ppp) REVERT: B 12 PHE cc_start: 0.7365 (t80) cc_final: 0.6788 (m-80) REVERT: B 25 MET cc_start: 0.7384 (mmm) cc_final: 0.7157 (mmm) REVERT: B 27 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7242 (tm-30) REVERT: B 28 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7508 (tt) REVERT: B 41 GLU cc_start: 0.7698 (tt0) cc_final: 0.7381 (tt0) REVERT: B 53 LEU cc_start: 0.8539 (mt) cc_final: 0.7643 (mm) REVERT: B 57 MET cc_start: 0.8356 (mmt) cc_final: 0.7890 (mmt) REVERT: B 63 TYR cc_start: 0.8108 (m-80) cc_final: 0.7768 (m-80) REVERT: B 80 ILE cc_start: 0.8526 (mt) cc_final: 0.8303 (mm) REVERT: B 83 VAL cc_start: 0.8284 (m) cc_final: 0.8050 (p) REVERT: B 94 TYR cc_start: 0.7019 (t80) cc_final: 0.6784 (t80) REVERT: B 133 LYS cc_start: 0.7477 (mttt) cc_final: 0.7246 (mtmt) REVERT: B 176 ASN cc_start: 0.6418 (t0) cc_final: 0.5873 (t0) REVERT: B 178 ASP cc_start: 0.7321 (p0) cc_final: 0.6878 (p0) REVERT: B 235 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: B 238 ASN cc_start: 0.8322 (m-40) cc_final: 0.8044 (m110) REVERT: B 244 ILE cc_start: 0.8513 (tp) cc_final: 0.8232 (tp) REVERT: B 259 CYS cc_start: 0.7154 (m) cc_final: 0.6932 (m) REVERT: B 262 ASN cc_start: 0.7715 (p0) cc_final: 0.7439 (p0) REVERT: B 338 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6887 (pm20) REVERT: B 341 LYS cc_start: 0.8096 (mttt) cc_final: 0.7830 (mptt) REVERT: B 352 GLU cc_start: 0.8140 (mp0) cc_final: 0.7044 (pm20) REVERT: B 397 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7391 (mm) REVERT: B 403 PHE cc_start: 0.8150 (t80) cc_final: 0.7732 (t80) REVERT: B 438 MET cc_start: 0.8130 (mtm) cc_final: 0.7884 (mtm) REVERT: B 439 ASP cc_start: 0.7602 (t0) cc_final: 0.7342 (t0) REVERT: B 471 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7926 (pp) REVERT: B 487 ARG cc_start: 0.7039 (ptt-90) cc_final: 0.6182 (ptt180) REVERT: B 511 ARG cc_start: 0.7869 (mtp85) cc_final: 0.7639 (mtt180) REVERT: B 516 VAL cc_start: 0.8498 (m) cc_final: 0.8097 (p) REVERT: B 518 ARG cc_start: 0.8493 (mtp85) cc_final: 0.8292 (mtp-110) REVERT: B 583 LYS cc_start: 0.8168 (ptpp) cc_final: 0.7937 (mtmm) REVERT: B 586 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7323 (pp20) REVERT: B 589 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7872 (tp30) REVERT: B 613 HIS cc_start: 0.8291 (OUTLIER) cc_final: 0.7682 (p90) REVERT: B 631 ARG cc_start: 0.7268 (mtp-110) cc_final: 0.6903 (mpp80) REVERT: B 634 LYS cc_start: 0.7690 (ptpp) cc_final: 0.7385 (mttt) REVERT: B 638 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7977 (tm-30) REVERT: B 668 ILE cc_start: 0.8460 (mm) cc_final: 0.7972 (mt) REVERT: B 672 THR cc_start: 0.8081 (p) cc_final: 0.7672 (m) REVERT: B 682 LYS cc_start: 0.8566 (pttp) cc_final: 0.8268 (ttpp) REVERT: B 712 GLU cc_start: 0.7613 (mt-10) cc_final: 0.6852 (mp0) REVERT: B 724 MET cc_start: 0.8109 (mmm) cc_final: 0.7862 (mmm) REVERT: C 402 ASN cc_start: 0.7707 (m-40) cc_final: 0.7470 (m-40) REVERT: C 405 GLN cc_start: 0.7958 (pp30) cc_final: 0.7269 (pp30) REVERT: C 409 GLN cc_start: 0.7780 (mt0) cc_final: 0.7482 (mt0) REVERT: C 411 MET cc_start: 0.7848 (tpp) cc_final: 0.7595 (tpp) REVERT: C 473 ARG cc_start: 0.7271 (tmt170) cc_final: 0.6767 (tmt170) REVERT: C 474 HIS cc_start: 0.8205 (m90) cc_final: 0.7684 (m-70) REVERT: C 524 HIS cc_start: 0.8189 (t-170) cc_final: 0.7555 (t-90) REVERT: C 545 MET cc_start: 0.6014 (mtt) cc_final: 0.5610 (mtt) REVERT: D 33 ARG cc_start: 0.8128 (mmm-85) cc_final: 0.7829 (mtp85) REVERT: D 53 LYS cc_start: 0.8980 (mtmt) cc_final: 0.8472 (mtmm) REVERT: D 77 LYS cc_start: 0.8241 (mttt) cc_final: 0.7937 (mttt) REVERT: D 117 ASN cc_start: 0.7920 (m-40) cc_final: 0.7582 (m-40) REVERT: D 120 ILE cc_start: 0.8641 (mt) cc_final: 0.8302 (mm) REVERT: D 123 LEU cc_start: 0.8579 (mt) cc_final: 0.8257 (mp) REVERT: D 154 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7196 (mt-10) REVERT: D 180 SER cc_start: 0.8691 (m) cc_final: 0.8292 (p) REVERT: D 204 LEU cc_start: 0.8752 (mt) cc_final: 0.8471 (mt) REVERT: D 215 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.8319 (t80) REVERT: D 216 MET cc_start: 0.8685 (tpp) cc_final: 0.8410 (mmp) REVERT: D 229 ASP cc_start: 0.7776 (t0) cc_final: 0.7450 (t0) REVERT: D 231 VAL cc_start: 0.8712 (t) cc_final: 0.8422 (m) REVERT: D 241 SER cc_start: 0.8656 (p) cc_final: 0.8344 (t) REVERT: D 243 SER cc_start: 0.8805 (m) cc_final: 0.8577 (p) REVERT: D 261 PHE cc_start: 0.8822 (t80) cc_final: 0.8479 (t80) REVERT: D 275 LYS cc_start: 0.8502 (pttt) cc_final: 0.8162 (ptpt) REVERT: D 313 TYR cc_start: 0.8608 (m-80) cc_final: 0.8218 (m-80) REVERT: D 357 SER cc_start: 0.8320 (m) cc_final: 0.8030 (p) REVERT: D 365 ILE cc_start: 0.8638 (mt) cc_final: 0.8381 (mm) REVERT: D 395 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7449 (tm-30) REVERT: D 397 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7839 (mt-10) REVERT: D 398 ARG cc_start: 0.7578 (ttt180) cc_final: 0.7287 (ttt180) REVERT: D 402 ARG cc_start: 0.6835 (mpt180) cc_final: 0.6356 (mtt90) REVERT: D 407 VAL cc_start: 0.8606 (t) cc_final: 0.8377 (m) REVERT: D 450 ASP cc_start: 0.7489 (t0) cc_final: 0.7124 (t0) REVERT: E 17 ARG cc_start: 0.8153 (mpp80) cc_final: 0.7750 (mtp85) REVERT: E 37 ILE cc_start: 0.8443 (mm) cc_final: 0.8146 (mm) REVERT: E 38 LEU cc_start: 0.8073 (mt) cc_final: 0.7716 (mt) REVERT: E 40 LYS cc_start: 0.8244 (tppt) cc_final: 0.7986 (mmmm) REVERT: E 66 ASP cc_start: 0.7878 (t0) cc_final: 0.7435 (t0) REVERT: E 69 ARG cc_start: 0.7664 (ptt-90) cc_final: 0.7456 (ptt-90) REVERT: E 81 LEU cc_start: 0.8452 (tp) cc_final: 0.8232 (tp) REVERT: E 94 GLU cc_start: 0.8085 (tp30) cc_final: 0.7838 (tp30) REVERT: E 119 GLU cc_start: 0.7686 (tp30) cc_final: 0.7276 (tp30) REVERT: E 157 LYS cc_start: 0.8578 (tttt) cc_final: 0.8304 (tttt) REVERT: E 159 MET cc_start: 0.8529 (mmt) cc_final: 0.8238 (mmp) REVERT: E 172 SER cc_start: 0.8692 (t) cc_final: 0.8220 (p) REVERT: E 224 ASP cc_start: 0.7279 (p0) cc_final: 0.6929 (p0) REVERT: E 229 LYS cc_start: 0.8305 (tttt) cc_final: 0.8034 (tttt) REVERT: E 230 GLU cc_start: 0.7848 (tp30) cc_final: 0.7388 (tp30) REVERT: E 233 THR cc_start: 0.7990 (m) cc_final: 0.7762 (p) REVERT: E 250 ILE cc_start: 0.8290 (mt) cc_final: 0.8054 (mm) REVERT: E 328 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7814 (tt) REVERT: E 329 ASP cc_start: 0.7973 (p0) cc_final: 0.7760 (p0) REVERT: E 336 LEU cc_start: 0.8344 (tp) cc_final: 0.8081 (tt) REVERT: E 352 LEU cc_start: 0.8033 (mt) cc_final: 0.7705 (mp) REVERT: F 55 ASN cc_start: 0.8272 (m-40) cc_final: 0.7767 (m-40) REVERT: F 106 SER cc_start: 0.8456 (m) cc_final: 0.8186 (t) REVERT: F 113 GLU cc_start: 0.8030 (tt0) cc_final: 0.7763 (tt0) REVERT: F 116 LYS cc_start: 0.8849 (mmmm) cc_final: 0.8130 (mtpp) REVERT: F 139 LYS cc_start: 0.8881 (mttt) cc_final: 0.8645 (mtmt) REVERT: F 146 ARG cc_start: 0.8672 (tmm-80) cc_final: 0.8383 (ttp-170) REVERT: F 186 LYS cc_start: 0.8584 (tttt) cc_final: 0.8310 (ttmm) REVERT: F 197 ASP cc_start: 0.8192 (t0) cc_final: 0.7992 (t0) REVERT: F 208 ASP cc_start: 0.7777 (t70) cc_final: 0.7386 (t70) REVERT: F 217 VAL cc_start: 0.8819 (t) cc_final: 0.8588 (p) REVERT: F 240 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7757 (mt0) REVERT: G 16 MET cc_start: 0.8904 (mmm) cc_final: 0.8605 (mmm) REVERT: G 46 ILE cc_start: 0.7058 (OUTLIER) cc_final: 0.6727 (mp) REVERT: K 118 MET cc_start: 0.7274 (tpp) cc_final: 0.6886 (tpp) REVERT: K 135 LYS cc_start: 0.8767 (tttt) cc_final: 0.8451 (tttt) REVERT: K 151 LYS cc_start: 0.7785 (mttt) cc_final: 0.7471 (mttt) REVERT: K 209 GLU cc_start: 0.8336 (tp30) cc_final: 0.7759 (tp30) REVERT: K 213 LYS cc_start: 0.8397 (tptt) cc_final: 0.7706 (tptt) REVERT: K 245 GLU cc_start: 0.8212 (mp0) cc_final: 0.7616 (mp0) REVERT: K 250 GLU cc_start: 0.7008 (tp30) cc_final: 0.6767 (tp30) REVERT: K 258 ARG cc_start: 0.7604 (ttp-170) cc_final: 0.7003 (ttp-170) REVERT: K 263 MET cc_start: 0.4657 (OUTLIER) cc_final: 0.4319 (ptt) REVERT: K 272 LYS cc_start: 0.6498 (ttmm) cc_final: 0.6082 (tptp) outliers start: 127 outliers final: 88 residues processed: 890 average time/residue: 0.4040 time to fit residues: 529.5805 Evaluate side-chains 910 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 806 time to evaluate : 2.469 ------------------------------------------------------------------------------- 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 145 LYS 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 316 LEU Chi-restraints excluded: chain A residue 446 ILE 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 571 TYR 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 715 LYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 28 LEU 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 235 GLU 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 471 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 545 MET 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 663 CYS Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 678 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 446 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 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 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 9 LYS Chi-restraints excluded: chain E residue 12 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 139 CYS Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 333 GLU 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 236 ASP 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 249 VAL 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 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 184 LEU Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 263 MET Chi-restraints excluded: chain K residue 271 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 64 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 199 optimal weight: 0.0470 chunk 65 optimal weight: 0.7980 chunk 162 optimal weight: 0.6980 chunk 279 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 262 optimal weight: 0.4980 chunk 49 optimal weight: 0.4980 chunk 225 optimal weight: 1.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 683 GLN B 60 GLN ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 GLN E 275 HIS E 293 GLN E 324 HIS E 332 GLN F 205 GLN F 277 ASN G 54 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.149955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.122606 restraints weight = 38883.769| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.50 r_work: 0.3408 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24160 Z= 0.140 Angle : 0.643 17.457 32876 Z= 0.321 Chirality : 0.043 0.216 3677 Planarity : 0.004 0.062 4022 Dihedral : 14.480 179.932 3609 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.78 % Allowed : 21.11 % Favored : 74.11 % 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: 0.17 (0.16), residues: 2776 helix: 1.23 (0.15), residues: 1348 sheet: -0.12 (0.26), residues: 381 loop : -1.24 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 539 HIS 0.015 0.001 HIS B 613 PHE 0.028 0.001 PHE D 162 TYR 0.043 0.001 TYR C 533 ARG 0.011 0.001 ARG A 325 Details of bonding type rmsd hydrogen bonds : bond 0.03654 ( 1083) hydrogen bonds : angle 4.29428 ( 3076) metal coordination : bond 0.00503 ( 28) metal coordination : angle 4.59574 ( 45) covalent geometry : bond 0.00308 (24132) covalent geometry : angle 0.62091 (32831) *********************** 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 936 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 817 time to evaluate : 2.620 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: A 60 ASP cc_start: 0.7717 (p0) cc_final: 0.7482 (p0) REVERT: A 98 ASP cc_start: 0.7623 (m-30) cc_final: 0.7090 (m-30) REVERT: A 105 GLU cc_start: 0.7968 (pm20) cc_final: 0.7583 (pm20) REVERT: A 117 LYS cc_start: 0.8458 (tttt) cc_final: 0.7686 (ttpt) REVERT: A 131 LEU cc_start: 0.8356 (mp) cc_final: 0.8054 (mp) REVERT: A 148 VAL cc_start: 0.9012 (p) cc_final: 0.8673 (m) REVERT: A 150 ASP cc_start: 0.7824 (t0) cc_final: 0.7496 (t0) REVERT: A 153 MET cc_start: 0.7488 (mmm) cc_final: 0.7092 (mmm) REVERT: A 155 PHE cc_start: 0.8111 (t80) cc_final: 0.7768 (t80) REVERT: A 157 LYS cc_start: 0.8521 (tppt) cc_final: 0.8213 (ttmm) REVERT: A 165 LYS cc_start: 0.8330 (mttm) cc_final: 0.7911 (mttp) REVERT: A 178 GLU cc_start: 0.7278 (tp30) cc_final: 0.6928 (tp30) REVERT: A 271 GLU cc_start: 0.6981 (pp20) cc_final: 0.5110 (tm-30) REVERT: A 273 LYS cc_start: 0.8351 (ttmt) cc_final: 0.7976 (mtmt) REVERT: A 279 GLU cc_start: 0.7693 (mp0) cc_final: 0.7385 (mp0) REVERT: A 282 LYS cc_start: 0.8747 (tttt) cc_final: 0.8183 (ttmm) REVERT: A 296 ASP cc_start: 0.6854 (t0) cc_final: 0.6379 (t0) REVERT: A 298 ARG cc_start: 0.8187 (mmm160) cc_final: 0.7917 (tpp80) REVERT: A 309 ASP cc_start: 0.7064 (p0) cc_final: 0.6519 (p0) REVERT: A 316 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7868 (pp) REVERT: A 351 VAL cc_start: 0.8391 (t) cc_final: 0.8161 (p) REVERT: A 360 ARG cc_start: 0.8066 (mtp180) cc_final: 0.7845 (mtp85) REVERT: A 375 LYS cc_start: 0.8697 (ttpt) cc_final: 0.8467 (ttpt) REVERT: A 391 ARG cc_start: 0.8186 (mtm110) cc_final: 0.7940 (mtm110) REVERT: A 425 ARG cc_start: 0.7861 (tpp-160) cc_final: 0.7592 (tpp-160) REVERT: A 504 LYS cc_start: 0.8794 (tttt) cc_final: 0.8445 (tttp) REVERT: A 506 GLN cc_start: 0.8866 (tt0) cc_final: 0.8619 (tt0) REVERT: A 510 VAL cc_start: 0.8190 (OUTLIER) cc_final: 0.7846 (t) REVERT: A 525 ILE cc_start: 0.8508 (tp) cc_final: 0.7821 (pt) REVERT: A 586 GLN cc_start: 0.8238 (tp40) cc_final: 0.7762 (tm-30) REVERT: A 621 ASN cc_start: 0.8232 (m110) cc_final: 0.7971 (m-40) REVERT: A 625 GLN cc_start: 0.7770 (pt0) cc_final: 0.7288 (tt0) REVERT: A 636 GLU cc_start: 0.8031 (tp30) cc_final: 0.7807 (tp30) REVERT: A 697 GLU cc_start: 0.7212 (tp30) cc_final: 0.6925 (tp30) REVERT: A 710 GLN cc_start: 0.7645 (pt0) cc_final: 0.7365 (pp30) REVERT: A 712 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8001 (tt) REVERT: B 1 MET cc_start: 0.6534 (ppp) cc_final: 0.6285 (ppp) REVERT: B 12 PHE cc_start: 0.7300 (t80) cc_final: 0.6783 (m-80) REVERT: B 41 GLU cc_start: 0.7618 (tt0) cc_final: 0.7354 (tt0) REVERT: B 53 LEU cc_start: 0.8477 (mt) cc_final: 0.7609 (mm) REVERT: B 57 MET cc_start: 0.8405 (mmt) cc_final: 0.7939 (mmt) REVERT: B 63 TYR cc_start: 0.8156 (m-80) cc_final: 0.7887 (m-80) REVERT: B 76 THR cc_start: 0.6977 (OUTLIER) cc_final: 0.6745 (p) REVERT: B 83 VAL cc_start: 0.8249 (m) cc_final: 0.8017 (p) REVERT: B 133 LYS cc_start: 0.7459 (mttt) cc_final: 0.7234 (mtmt) REVERT: B 176 ASN cc_start: 0.6443 (t0) cc_final: 0.6078 (t0) REVERT: B 235 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: B 238 ASN cc_start: 0.8255 (m-40) cc_final: 0.8002 (m110) REVERT: B 244 ILE cc_start: 0.8450 (tp) cc_final: 0.8104 (tp) REVERT: B 259 CYS cc_start: 0.7082 (m) cc_final: 0.6861 (m) REVERT: B 262 ASN cc_start: 0.7711 (p0) cc_final: 0.7447 (p0) REVERT: B 338 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6617 (pm20) REVERT: B 341 LYS cc_start: 0.7997 (mttt) cc_final: 0.7772 (pttm) REVERT: B 386 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7321 (pp) REVERT: B 397 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7348 (mm) REVERT: B 403 PHE cc_start: 0.8059 (t80) cc_final: 0.7612 (t80) REVERT: B 439 ASP cc_start: 0.7579 (t0) cc_final: 0.7300 (t0) REVERT: B 471 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7867 (pp) REVERT: B 487 ARG cc_start: 0.6647 (ptt-90) cc_final: 0.5914 (ptt180) REVERT: B 507 LYS cc_start: 0.7949 (mtmt) cc_final: 0.7685 (mtmm) REVERT: B 511 ARG cc_start: 0.7916 (mtp85) cc_final: 0.7590 (mtt180) REVERT: B 516 VAL cc_start: 0.8451 (m) cc_final: 0.8100 (p) REVERT: B 545 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8481 (ttp) REVERT: B 583 LYS cc_start: 0.8174 (ptpp) cc_final: 0.7930 (mtmm) REVERT: B 586 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7297 (pp20) REVERT: B 589 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7715 (tp30) REVERT: B 613 HIS cc_start: 0.8059 (OUTLIER) cc_final: 0.7557 (p90) REVERT: B 631 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6815 (mpp80) REVERT: B 634 LYS cc_start: 0.7593 (ptpp) cc_final: 0.7365 (mttt) REVERT: B 638 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7929 (tm-30) REVERT: B 668 ILE cc_start: 0.8459 (mm) cc_final: 0.8102 (mt) REVERT: B 669 ARG cc_start: 0.6987 (mpt90) cc_final: 0.6765 (mpt180) REVERT: B 672 THR cc_start: 0.8021 (p) cc_final: 0.7667 (m) REVERT: B 681 ASP cc_start: 0.8468 (t0) cc_final: 0.7645 (t70) REVERT: B 682 LYS cc_start: 0.8548 (pttp) cc_final: 0.8186 (ttpp) REVERT: B 707 ASN cc_start: 0.8050 (t0) cc_final: 0.7391 (t0) REVERT: B 712 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7355 (mt-10) REVERT: C 405 GLN cc_start: 0.7832 (pp30) cc_final: 0.7095 (pp30) REVERT: C 409 GLN cc_start: 0.7757 (mt0) cc_final: 0.7434 (mt0) REVERT: C 411 MET cc_start: 0.7830 (tpp) cc_final: 0.7593 (tpp) REVERT: C 441 MET cc_start: 0.5903 (mmm) cc_final: 0.5448 (mmm) REVERT: C 473 ARG cc_start: 0.7124 (tmt170) cc_final: 0.6666 (tmt170) REVERT: C 474 HIS cc_start: 0.8125 (m90) cc_final: 0.7507 (m-70) REVERT: C 493 MET cc_start: 0.7204 (mmm) cc_final: 0.6916 (mmm) REVERT: C 524 HIS cc_start: 0.7993 (t-170) cc_final: 0.7361 (t-90) REVERT: C 528 MET cc_start: 0.8164 (mtm) cc_final: 0.7841 (mtt) REVERT: C 545 MET cc_start: 0.5694 (mtt) cc_final: 0.5308 (mtt) REVERT: D 23 LEU cc_start: 0.8579 (mt) cc_final: 0.8267 (mt) REVERT: D 33 ARG cc_start: 0.8116 (mmm-85) cc_final: 0.7876 (mtp85) REVERT: D 42 LEU cc_start: 0.8706 (tt) cc_final: 0.8492 (tp) REVERT: D 53 LYS cc_start: 0.8924 (mtmt) cc_final: 0.8641 (ttmt) REVERT: D 77 LYS cc_start: 0.8207 (mttt) cc_final: 0.7856 (mttt) REVERT: D 117 ASN cc_start: 0.7878 (m-40) cc_final: 0.7534 (m-40) REVERT: D 120 ILE cc_start: 0.8601 (mt) cc_final: 0.8267 (mm) REVERT: D 154 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7171 (mt-10) REVERT: D 177 GLN cc_start: 0.7874 (mt0) cc_final: 0.7331 (tm-30) REVERT: D 204 LEU cc_start: 0.8788 (mt) cc_final: 0.8530 (mt) REVERT: D 215 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.8207 (t80) REVERT: D 216 MET cc_start: 0.8632 (tpp) cc_final: 0.8368 (mmp) REVERT: D 229 ASP cc_start: 0.7568 (t0) cc_final: 0.7176 (t70) REVERT: D 230 LEU cc_start: 0.8627 (tp) cc_final: 0.8369 (tt) REVERT: D 261 PHE cc_start: 0.8764 (t80) cc_final: 0.8389 (t80) REVERT: D 275 LYS cc_start: 0.8500 (pttt) cc_final: 0.8221 (ptpt) REVERT: D 281 TYR cc_start: 0.8372 (p90) cc_final: 0.8005 (p90) REVERT: D 313 TYR cc_start: 0.8592 (m-80) cc_final: 0.8225 (m-80) REVERT: D 395 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7395 (tm-30) REVERT: D 397 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7736 (mt-10) REVERT: D 398 ARG cc_start: 0.7470 (ttt180) cc_final: 0.7257 (ttt180) REVERT: D 402 ARG cc_start: 0.6733 (mpt180) cc_final: 0.6296 (mtt180) REVERT: D 407 VAL cc_start: 0.8554 (t) cc_final: 0.8329 (m) REVERT: D 450 ASP cc_start: 0.7493 (t0) cc_final: 0.7141 (t0) REVERT: E 17 ARG cc_start: 0.8050 (mpp80) cc_final: 0.7677 (mtp85) REVERT: E 37 ILE cc_start: 0.8377 (mm) cc_final: 0.8080 (mm) REVERT: E 38 LEU cc_start: 0.8062 (mt) cc_final: 0.7671 (mt) REVERT: E 40 LYS cc_start: 0.8270 (tppt) cc_final: 0.7977 (mmmm) REVERT: E 66 ASP cc_start: 0.7827 (t0) cc_final: 0.7378 (t0) REVERT: E 81 LEU cc_start: 0.8443 (tp) cc_final: 0.8203 (tp) REVERT: E 94 GLU cc_start: 0.8060 (tp30) cc_final: 0.7815 (tp30) REVERT: E 113 ARG cc_start: 0.7855 (mtm110) cc_final: 0.7644 (mtm110) REVERT: E 118 THR cc_start: 0.8365 (m) cc_final: 0.8142 (p) REVERT: E 119 GLU cc_start: 0.7641 (tp30) cc_final: 0.7194 (tp30) REVERT: E 142 GLU cc_start: 0.7612 (mp0) cc_final: 0.7386 (mp0) REVERT: E 144 SER cc_start: 0.8368 (t) cc_final: 0.8139 (t) REVERT: E 157 LYS cc_start: 0.8577 (tttt) cc_final: 0.8301 (tttt) REVERT: E 159 MET cc_start: 0.8540 (mmt) cc_final: 0.8232 (mmp) REVERT: E 172 SER cc_start: 0.8604 (t) cc_final: 0.8232 (p) REVERT: E 204 GLU cc_start: 0.8225 (tt0) cc_final: 0.7895 (tt0) REVERT: E 224 ASP cc_start: 0.7222 (p0) cc_final: 0.6893 (p0) REVERT: E 229 LYS cc_start: 0.8220 (tttt) cc_final: 0.7901 (tttt) REVERT: E 230 GLU cc_start: 0.7666 (tp30) cc_final: 0.7445 (tp30) REVERT: E 233 THR cc_start: 0.7928 (m) cc_final: 0.7698 (p) REVERT: E 250 ILE cc_start: 0.8233 (mt) cc_final: 0.7987 (mm) REVERT: E 328 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7795 (tt) REVERT: E 336 LEU cc_start: 0.8295 (tp) cc_final: 0.8034 (tt) REVERT: F 55 ASN cc_start: 0.8224 (m-40) cc_final: 0.7691 (m-40) REVERT: F 56 LYS cc_start: 0.8505 (mtpp) cc_final: 0.8062 (mtpp) REVERT: F 106 SER cc_start: 0.8408 (m) cc_final: 0.8153 (t) REVERT: F 113 GLU cc_start: 0.7992 (tt0) cc_final: 0.7789 (tt0) REVERT: F 116 LYS cc_start: 0.8800 (mmmm) cc_final: 0.8132 (mtpp) REVERT: F 139 LYS cc_start: 0.8861 (mttt) cc_final: 0.8607 (mtpp) REVERT: F 146 ARG cc_start: 0.8675 (tmm-80) cc_final: 0.8271 (ttt180) REVERT: F 186 LYS cc_start: 0.8546 (tttt) cc_final: 0.8339 (ttmm) REVERT: F 189 ILE cc_start: 0.8573 (mt) cc_final: 0.8366 (mm) REVERT: F 197 ASP cc_start: 0.8136 (t0) cc_final: 0.7913 (t0) REVERT: F 208 ASP cc_start: 0.7768 (t70) cc_final: 0.7360 (t70) REVERT: F 217 VAL cc_start: 0.8775 (t) cc_final: 0.8562 (p) REVERT: G 16 MET cc_start: 0.8923 (mmm) cc_final: 0.8620 (mmm) REVERT: K 118 MET cc_start: 0.7184 (tpp) cc_final: 0.6819 (tpp) REVERT: K 135 LYS cc_start: 0.8727 (tttt) cc_final: 0.8431 (tttt) REVERT: K 139 ILE cc_start: 0.8220 (mm) cc_final: 0.7433 (tp) REVERT: K 151 LYS cc_start: 0.7738 (mttt) cc_final: 0.7463 (mttt) REVERT: K 164 PHE cc_start: 0.8473 (p90) cc_final: 0.8185 (p90) REVERT: K 201 GLU cc_start: 0.7293 (tp30) cc_final: 0.6979 (tp30) REVERT: K 209 GLU cc_start: 0.8349 (tp30) cc_final: 0.7702 (tp30) REVERT: K 213 LYS cc_start: 0.8377 (tptt) cc_final: 0.7682 (tptt) REVERT: K 245 GLU cc_start: 0.8189 (mp0) cc_final: 0.7552 (mp0) REVERT: K 250 GLU cc_start: 0.7091 (tp30) cc_final: 0.6769 (tp30) REVERT: K 258 ARG cc_start: 0.7573 (ttp-170) cc_final: 0.6977 (ttp-170) REVERT: K 263 MET cc_start: 0.4749 (OUTLIER) cc_final: 0.4385 (ptt) outliers start: 119 outliers final: 76 residues processed: 875 average time/residue: 0.4086 time to fit residues: 525.5118 Evaluate side-chains 889 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 796 time to evaluate : 2.593 ------------------------------------------------------------------------------- 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 285 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 446 ILE 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 552 GLU Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 629 HIS 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 28 LEU Chi-restraints excluded: chain B residue 76 THR 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 210 HIS Chi-restraints excluded: chain B residue 235 GLU 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 351 GLN 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 399 LEU Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 545 MET 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 631 ARG Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 678 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 446 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 485 PHE Chi-restraints excluded: chain C residue 506 CYS Chi-restraints excluded: chain D residue 48 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 174 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 353 GLN Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain E residue 256 GLN Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain E residue 372 ASP 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 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 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 263 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 28 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 268 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 117 optimal weight: 0.4980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 ASN ** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 GLN B 118 HIS ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 GLN C 402 ASN E 275 HIS E 324 HIS F 108 ASN G 54 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.148674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.120950 restraints weight = 38570.557| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.52 r_work: 0.3378 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24160 Z= 0.180 Angle : 0.668 18.934 32876 Z= 0.331 Chirality : 0.044 0.232 3677 Planarity : 0.004 0.060 4022 Dihedral : 14.432 179.684 3605 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.62 % Allowed : 21.67 % Favored : 73.70 % 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: 0.11 (0.16), residues: 2776 helix: 1.13 (0.15), residues: 1351 sheet: -0.16 (0.27), residues: 364 loop : -1.20 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 342 HIS 0.016 0.001 HIS B 613 PHE 0.025 0.002 PHE D 162 TYR 0.044 0.002 TYR C 533 ARG 0.011 0.001 ARG C 542 Details of bonding type rmsd hydrogen bonds : bond 0.03911 ( 1083) hydrogen bonds : angle 4.29488 ( 3076) metal coordination : bond 0.00604 ( 28) metal coordination : angle 5.06340 ( 45) covalent geometry : bond 0.00399 (24132) covalent geometry : angle 0.64127 (32831) *********************** 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 926 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 811 time to evaluate : 2.805 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 98 ASP cc_start: 0.7654 (m-30) cc_final: 0.7086 (m-30) REVERT: A 105 GLU cc_start: 0.7963 (pm20) cc_final: 0.7588 (pm20) REVERT: A 117 LYS cc_start: 0.8524 (tttt) cc_final: 0.7655 (ttpt) REVERT: A 131 LEU cc_start: 0.8346 (mp) cc_final: 0.8076 (mt) REVERT: A 148 VAL cc_start: 0.9035 (p) cc_final: 0.8733 (m) REVERT: A 150 ASP cc_start: 0.7851 (t0) cc_final: 0.7527 (t0) REVERT: A 153 MET cc_start: 0.7488 (mmm) cc_final: 0.7069 (mmm) REVERT: A 157 LYS cc_start: 0.8538 (tppt) cc_final: 0.8222 (ttmm) REVERT: A 165 LYS cc_start: 0.8389 (mttm) cc_final: 0.8004 (mttp) REVERT: A 183 ASP cc_start: 0.8650 (p0) cc_final: 0.8417 (p0) REVERT: A 271 GLU cc_start: 0.7105 (pp20) cc_final: 0.5157 (tm-30) REVERT: A 279 GLU cc_start: 0.7714 (mp0) cc_final: 0.7226 (mp0) REVERT: A 282 LYS cc_start: 0.8765 (tttt) cc_final: 0.8208 (ttmm) REVERT: A 289 TYR cc_start: 0.8275 (m-80) cc_final: 0.8043 (m-80) REVERT: A 298 ARG cc_start: 0.7998 (mmm160) cc_final: 0.7669 (tpp80) REVERT: A 309 ASP cc_start: 0.7083 (p0) cc_final: 0.6559 (p0) REVERT: A 316 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7829 (pp) REVERT: A 351 VAL cc_start: 0.8371 (t) cc_final: 0.8139 (p) REVERT: A 372 GLU cc_start: 0.7102 (mp0) cc_final: 0.6582 (mp0) REVERT: A 391 ARG cc_start: 0.8251 (mtm110) cc_final: 0.7940 (mtm110) REVERT: A 425 ARG cc_start: 0.7927 (tpp-160) cc_final: 0.7615 (tpp-160) REVERT: A 427 MET cc_start: 0.8346 (tpp) cc_final: 0.7972 (tpp) REVERT: A 457 ILE cc_start: 0.8871 (tt) cc_final: 0.8436 (mm) REVERT: A 495 GLU cc_start: 0.7716 (pt0) cc_final: 0.7440 (pp20) REVERT: A 504 LYS cc_start: 0.8875 (tttt) cc_final: 0.8508 (tttp) REVERT: A 506 GLN cc_start: 0.8832 (tt0) cc_final: 0.8551 (tt0) REVERT: A 510 VAL cc_start: 0.8354 (OUTLIER) cc_final: 0.7969 (t) REVERT: A 525 ILE cc_start: 0.8519 (tp) cc_final: 0.7808 (pt) REVERT: A 586 GLN cc_start: 0.8261 (tp40) cc_final: 0.7771 (tm-30) REVERT: A 621 ASN cc_start: 0.8240 (m110) cc_final: 0.8008 (m-40) REVERT: A 625 GLN cc_start: 0.7775 (pt0) cc_final: 0.7177 (tt0) REVERT: A 636 GLU cc_start: 0.8059 (tp30) cc_final: 0.7836 (tp30) REVERT: A 697 GLU cc_start: 0.7291 (tp30) cc_final: 0.6984 (tp30) REVERT: A 710 GLN cc_start: 0.7749 (pt0) cc_final: 0.7399 (pp30) REVERT: A 712 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8108 (tt) REVERT: B 1 MET cc_start: 0.6400 (ppp) cc_final: 0.6133 (ppp) REVERT: B 12 PHE cc_start: 0.7303 (t80) cc_final: 0.6773 (m-80) REVERT: B 40 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8444 (mm) REVERT: B 41 GLU cc_start: 0.7598 (tt0) cc_final: 0.7282 (tt0) REVERT: B 48 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8344 (ttmt) REVERT: B 53 LEU cc_start: 0.8617 (mt) cc_final: 0.7767 (mm) REVERT: B 57 MET cc_start: 0.8408 (mmt) cc_final: 0.7936 (mmt) REVERT: B 83 VAL cc_start: 0.8260 (m) cc_final: 0.8033 (p) REVERT: B 133 LYS cc_start: 0.7476 (mttt) cc_final: 0.7257 (mtmt) REVERT: B 235 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: B 237 HIS cc_start: 0.8467 (p-80) cc_final: 0.7885 (p90) REVERT: B 238 ASN cc_start: 0.8295 (m-40) cc_final: 0.7917 (m110) REVERT: B 244 ILE cc_start: 0.8464 (tp) cc_final: 0.8166 (tp) REVERT: B 259 CYS cc_start: 0.7084 (m) cc_final: 0.6852 (m) REVERT: B 262 ASN cc_start: 0.7658 (p0) cc_final: 0.7398 (p0) REVERT: B 338 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6942 (pm20) REVERT: B 384 HIS cc_start: 0.5423 (OUTLIER) cc_final: 0.5137 (p-80) REVERT: B 397 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7379 (mm) REVERT: B 438 MET cc_start: 0.8108 (mtm) cc_final: 0.7838 (mtm) REVERT: B 439 ASP cc_start: 0.7607 (t0) cc_final: 0.7299 (t70) REVERT: B 471 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7888 (pp) REVERT: B 487 ARG cc_start: 0.6576 (ptt-90) cc_final: 0.5775 (ptt180) REVERT: B 507 LYS cc_start: 0.7936 (mtmt) cc_final: 0.7683 (mtmm) REVERT: B 511 ARG cc_start: 0.7904 (mtp85) cc_final: 0.7586 (mtt180) REVERT: B 516 VAL cc_start: 0.8472 (m) cc_final: 0.8148 (p) REVERT: B 583 LYS cc_start: 0.8161 (ptpp) cc_final: 0.7943 (mtmm) REVERT: B 586 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7380 (pp20) REVERT: B 589 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7807 (tp30) REVERT: B 613 HIS cc_start: 0.8130 (OUTLIER) cc_final: 0.7676 (p90) REVERT: B 631 ARG cc_start: 0.7264 (mtp-110) cc_final: 0.6868 (mpp80) REVERT: B 638 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7928 (tm-30) REVERT: B 668 ILE cc_start: 0.8476 (mm) cc_final: 0.8109 (mt) REVERT: B 672 THR cc_start: 0.8001 (p) cc_final: 0.7654 (m) REVERT: B 681 ASP cc_start: 0.8466 (t0) cc_final: 0.7631 (t70) REVERT: B 682 LYS cc_start: 0.8558 (pttp) cc_final: 0.8202 (ttpp) REVERT: B 696 TRP cc_start: 0.8778 (p-90) cc_final: 0.8546 (p-90) REVERT: B 707 ASN cc_start: 0.8032 (t0) cc_final: 0.7350 (t0) REVERT: B 712 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7414 (mt-10) REVERT: C 402 ASN cc_start: 0.7542 (m110) cc_final: 0.7330 (m110) REVERT: C 405 GLN cc_start: 0.7902 (pp30) cc_final: 0.7188 (pp30) REVERT: C 409 GLN cc_start: 0.7819 (mt0) cc_final: 0.7473 (mt0) REVERT: C 441 MET cc_start: 0.5992 (mmm) cc_final: 0.5530 (mmm) REVERT: C 473 ARG cc_start: 0.7247 (tmt170) cc_final: 0.6736 (tmt170) REVERT: C 474 HIS cc_start: 0.8182 (m90) cc_final: 0.7805 (m-70) REVERT: C 524 HIS cc_start: 0.8067 (t-170) cc_final: 0.7604 (t-90) REVERT: C 545 MET cc_start: 0.5651 (mtt) cc_final: 0.5292 (mtt) REVERT: D 23 LEU cc_start: 0.8632 (mt) cc_final: 0.8310 (mt) REVERT: D 33 ARG cc_start: 0.8174 (mmm-85) cc_final: 0.7947 (mtp85) REVERT: D 42 LEU cc_start: 0.8721 (tt) cc_final: 0.8519 (tp) REVERT: D 53 LYS cc_start: 0.8985 (mtmt) cc_final: 0.8677 (ttmt) REVERT: D 77 LYS cc_start: 0.8249 (mttt) cc_final: 0.7923 (mttt) REVERT: D 117 ASN cc_start: 0.7963 (m-40) cc_final: 0.7616 (m-40) REVERT: D 120 ILE cc_start: 0.8620 (mt) cc_final: 0.8309 (mm) REVERT: D 154 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7334 (mt-10) REVERT: D 180 SER cc_start: 0.8641 (m) cc_final: 0.8262 (p) REVERT: D 204 LEU cc_start: 0.8810 (mt) cc_final: 0.8507 (mt) REVERT: D 215 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.8256 (t80) REVERT: D 216 MET cc_start: 0.8620 (tpp) cc_final: 0.8352 (mmp) REVERT: D 229 ASP cc_start: 0.7658 (t0) cc_final: 0.7308 (t0) REVERT: D 261 PHE cc_start: 0.8800 (t80) cc_final: 0.8431 (t80) REVERT: D 313 TYR cc_start: 0.8603 (m-80) cc_final: 0.8192 (m-80) REVERT: D 357 SER cc_start: 0.8343 (m) cc_final: 0.8064 (p) REVERT: D 395 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7382 (tm-30) REVERT: D 398 ARG cc_start: 0.7533 (ttt180) cc_final: 0.7251 (ttt180) REVERT: D 402 ARG cc_start: 0.6799 (mpt180) cc_final: 0.6358 (mtt180) REVERT: D 407 VAL cc_start: 0.8524 (t) cc_final: 0.8312 (m) REVERT: D 450 ASP cc_start: 0.7569 (t0) cc_final: 0.7198 (t0) REVERT: E 16 GLU cc_start: 0.7100 (pm20) cc_final: 0.6834 (pm20) REVERT: E 17 ARG cc_start: 0.8180 (mpp80) cc_final: 0.7735 (mtp85) REVERT: E 37 ILE cc_start: 0.8428 (mm) cc_final: 0.8123 (mm) REVERT: E 38 LEU cc_start: 0.8123 (mt) cc_final: 0.7734 (mt) REVERT: E 40 LYS cc_start: 0.8274 (tppt) cc_final: 0.7974 (mmmm) REVERT: E 66 ASP cc_start: 0.7870 (t0) cc_final: 0.7407 (t0) REVERT: E 69 ARG cc_start: 0.7648 (ptt-90) cc_final: 0.7418 (ptt-90) REVERT: E 81 LEU cc_start: 0.8443 (tp) cc_final: 0.8211 (tp) REVERT: E 94 GLU cc_start: 0.8047 (tp30) cc_final: 0.7801 (tp30) REVERT: E 118 THR cc_start: 0.8382 (m) cc_final: 0.8161 (p) REVERT: E 132 LYS cc_start: 0.8028 (mmtp) cc_final: 0.7812 (mmtp) REVERT: E 142 GLU cc_start: 0.7586 (mp0) cc_final: 0.6978 (mp0) REVERT: E 144 SER cc_start: 0.8413 (t) cc_final: 0.8175 (t) REVERT: E 157 LYS cc_start: 0.8590 (tttt) cc_final: 0.8290 (tttt) REVERT: E 159 MET cc_start: 0.8550 (mmt) cc_final: 0.8240 (mmp) REVERT: E 172 SER cc_start: 0.8603 (t) cc_final: 0.8214 (p) REVERT: E 190 LYS cc_start: 0.8869 (ttpp) cc_final: 0.8649 (ttpp) REVERT: E 204 GLU cc_start: 0.8245 (tt0) cc_final: 0.7909 (tt0) REVERT: E 229 LYS cc_start: 0.8228 (tttt) cc_final: 0.7899 (tttt) REVERT: E 230 GLU cc_start: 0.7751 (tp30) cc_final: 0.7482 (tp30) REVERT: E 233 THR cc_start: 0.7978 (m) cc_final: 0.7728 (p) REVERT: E 250 ILE cc_start: 0.8231 (mt) cc_final: 0.8016 (mm) REVERT: E 328 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7832 (tt) REVERT: E 336 LEU cc_start: 0.8310 (tp) cc_final: 0.8037 (tt) REVERT: E 338 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7631 (mm-30) REVERT: F 55 ASN cc_start: 0.8240 (m-40) cc_final: 0.7694 (m-40) REVERT: F 56 LYS cc_start: 0.8502 (mtpp) cc_final: 0.8045 (mtpp) REVERT: F 106 SER cc_start: 0.8430 (m) cc_final: 0.8175 (t) REVERT: F 113 GLU cc_start: 0.8040 (tt0) cc_final: 0.7793 (tt0) REVERT: F 116 LYS cc_start: 0.8800 (mmmm) cc_final: 0.8500 (mtpp) REVERT: F 117 ASP cc_start: 0.8153 (t0) cc_final: 0.7907 (t0) REVERT: F 139 LYS cc_start: 0.8844 (mttt) cc_final: 0.8606 (mtpp) REVERT: F 146 ARG cc_start: 0.8649 (tmm-80) cc_final: 0.8296 (ttt180) REVERT: F 148 ASN cc_start: 0.8503 (m-40) cc_final: 0.8267 (m-40) REVERT: F 186 LYS cc_start: 0.8478 (tttt) cc_final: 0.8201 (ttmm) REVERT: F 197 ASP cc_start: 0.8191 (t0) cc_final: 0.7963 (t0) REVERT: F 208 ASP cc_start: 0.7800 (t70) cc_final: 0.7393 (t70) REVERT: F 217 VAL cc_start: 0.8782 (t) cc_final: 0.8560 (p) REVERT: G 16 MET cc_start: 0.8945 (mmm) cc_final: 0.8631 (mmm) REVERT: G 46 ILE cc_start: 0.7036 (OUTLIER) cc_final: 0.6708 (mt) REVERT: K 118 MET cc_start: 0.7228 (tpp) cc_final: 0.6894 (tpp) REVERT: K 135 LYS cc_start: 0.8775 (tttt) cc_final: 0.8443 (tttt) REVERT: K 151 LYS cc_start: 0.7789 (mttt) cc_final: 0.7471 (mttt) REVERT: K 164 PHE cc_start: 0.8486 (p90) cc_final: 0.8205 (p90) REVERT: K 201 GLU cc_start: 0.7437 (tp30) cc_final: 0.7008 (tp30) REVERT: K 209 GLU cc_start: 0.8268 (tp30) cc_final: 0.7619 (tp30) REVERT: K 213 LYS cc_start: 0.8473 (tptt) cc_final: 0.7745 (tptt) REVERT: K 245 GLU cc_start: 0.8207 (mp0) cc_final: 0.7558 (mp0) REVERT: K 258 ARG cc_start: 0.7600 (ttp-170) cc_final: 0.7001 (ttp-170) REVERT: K 263 MET cc_start: 0.4722 (OUTLIER) cc_final: 0.4323 (ptt) outliers start: 115 outliers final: 76 residues processed: 874 average time/residue: 0.4165 time to fit residues: 533.9430 Evaluate side-chains 885 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 793 time to evaluate : 2.615 ------------------------------------------------------------------------------- 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 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 310 LEU Chi-restraints excluded: chain A residue 316 LEU 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 497 GLN 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 571 TYR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 688 LYS 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 28 LEU Chi-restraints excluded: chain B residue 40 LEU 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 235 GLU Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 471 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 545 MET Chi-restraints excluded: chain B residue 546 GLU 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 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 446 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 174 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 376 MET Chi-restraints excluded: chain E residue 12 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain E residue 372 ASP 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 109 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 274 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 153 optimal weight: 0.9990 chunk 173 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 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** B 649 ASN B 698 GLN E 256 GLN E 275 HIS E 324 HIS F 108 ASN G 54 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.147729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.119972 restraints weight = 38827.912| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.54 r_work: 0.3376 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24160 Z= 0.175 Angle : 0.685 19.658 32876 Z= 0.337 Chirality : 0.045 0.236 3677 Planarity : 0.004 0.064 4022 Dihedral : 14.441 179.510 3601 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.91 % Allowed : 22.16 % Favored : 72.94 % 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: 1350 sheet: -0.24 (0.27), residues: 358 loop : -1.20 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 539 HIS 0.016 0.001 HIS B 613 PHE 0.029 0.001 PHE D 162 TYR 0.045 0.002 TYR C 533 ARG 0.012 0.001 ARG C 542 Details of bonding type rmsd hydrogen bonds : bond 0.03850 ( 1083) hydrogen bonds : angle 4.28222 ( 3076) metal coordination : bond 0.00633 ( 28) metal coordination : angle 5.33752 ( 45) covalent geometry : bond 0.00389 (24132) covalent geometry : angle 0.65612 (32831) *********************** 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 935 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 813 time to evaluate : 2.478 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 87 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7284 (mt-10) REVERT: A 98 ASP cc_start: 0.7640 (m-30) cc_final: 0.7072 (m-30) REVERT: A 105 GLU cc_start: 0.7959 (pm20) cc_final: 0.7592 (pm20) REVERT: A 117 LYS cc_start: 0.8517 (tttt) cc_final: 0.7637 (ttpt) REVERT: A 148 VAL cc_start: 0.9046 (p) cc_final: 0.8829 (m) REVERT: A 150 ASP cc_start: 0.7882 (t0) cc_final: 0.7505 (t0) REVERT: A 153 MET cc_start: 0.7515 (mmm) cc_final: 0.7155 (mmm) REVERT: A 157 LYS cc_start: 0.8535 (tppt) cc_final: 0.8213 (ttmm) REVERT: A 165 LYS cc_start: 0.8391 (mttm) cc_final: 0.8004 (mttp) REVERT: A 271 GLU cc_start: 0.7048 (pp20) cc_final: 0.4865 (tm-30) REVERT: A 273 LYS cc_start: 0.8316 (mtmt) cc_final: 0.7774 (mttt) REVERT: A 279 GLU cc_start: 0.7685 (mp0) cc_final: 0.7187 (mp0) REVERT: A 282 LYS cc_start: 0.8785 (tttt) cc_final: 0.8289 (ttmm) REVERT: A 285 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8392 (pt) REVERT: A 289 TYR cc_start: 0.8272 (m-80) cc_final: 0.8070 (m-80) REVERT: A 298 ARG cc_start: 0.8051 (mmm160) cc_final: 0.7708 (tpp80) REVERT: A 309 ASP cc_start: 0.7156 (p0) cc_final: 0.6640 (p0) REVERT: A 316 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7823 (pp) REVERT: A 351 VAL cc_start: 0.8374 (t) cc_final: 0.8137 (p) REVERT: A 372 GLU cc_start: 0.7158 (mp0) cc_final: 0.6619 (mp0) REVERT: A 375 LYS cc_start: 0.8694 (ttpt) cc_final: 0.8344 (ttmm) REVERT: A 425 ARG cc_start: 0.7947 (tpp-160) cc_final: 0.7602 (tpp-160) REVERT: A 427 MET cc_start: 0.8424 (tpp) cc_final: 0.7979 (tpp) REVERT: A 457 ILE cc_start: 0.8876 (tt) cc_final: 0.8468 (mm) REVERT: A 510 VAL cc_start: 0.8372 (OUTLIER) cc_final: 0.7974 (t) REVERT: A 517 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7901 (mp0) REVERT: A 586 GLN cc_start: 0.8265 (tp40) cc_final: 0.7762 (tm-30) REVERT: A 619 GLU cc_start: 0.7387 (mp0) cc_final: 0.7044 (tp30) REVERT: A 621 ASN cc_start: 0.8244 (m110) cc_final: 0.8029 (m-40) REVERT: A 625 GLN cc_start: 0.7769 (pt0) cc_final: 0.7053 (tt0) REVERT: A 636 GLU cc_start: 0.8018 (tp30) cc_final: 0.7560 (tp30) REVERT: A 697 GLU cc_start: 0.7322 (tp30) cc_final: 0.7020 (tp30) REVERT: A 710 GLN cc_start: 0.7762 (pt0) cc_final: 0.7392 (pp30) REVERT: A 712 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8037 (tt) REVERT: B 1 MET cc_start: 0.6418 (ppp) cc_final: 0.5786 (ppp) REVERT: B 12 PHE cc_start: 0.7344 (t80) cc_final: 0.6868 (m-80) REVERT: B 27 GLU cc_start: 0.7542 (tm-30) cc_final: 0.7337 (tm-30) REVERT: B 40 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8433 (mm) REVERT: B 41 GLU cc_start: 0.7678 (tt0) cc_final: 0.7358 (tt0) REVERT: B 48 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8436 (ttmt) REVERT: B 53 LEU cc_start: 0.8644 (mt) cc_final: 0.7770 (mm) REVERT: B 57 MET cc_start: 0.8357 (mmt) cc_final: 0.7882 (mmt) REVERT: B 83 VAL cc_start: 0.8279 (m) cc_final: 0.8053 (p) REVERT: B 133 LYS cc_start: 0.7479 (mttt) cc_final: 0.7264 (mtmt) REVERT: B 235 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: B 237 HIS cc_start: 0.8441 (p-80) cc_final: 0.7808 (p90) REVERT: B 238 ASN cc_start: 0.8280 (m-40) cc_final: 0.7906 (m110) REVERT: B 244 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8155 (tp) REVERT: B 259 CYS cc_start: 0.7375 (m) cc_final: 0.7111 (m) REVERT: B 262 ASN cc_start: 0.7645 (p0) cc_final: 0.7389 (p0) REVERT: B 338 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7010 (pm20) REVERT: B 384 HIS cc_start: 0.5427 (OUTLIER) cc_final: 0.5146 (p-80) REVERT: B 397 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7373 (mm) REVERT: B 439 ASP cc_start: 0.7605 (t0) cc_final: 0.7282 (t0) REVERT: B 471 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7867 (pp) REVERT: B 487 ARG cc_start: 0.6614 (ptt-90) cc_final: 0.5695 (ptt180) REVERT: B 511 ARG cc_start: 0.7848 (mtp85) cc_final: 0.7546 (mtt180) REVERT: B 516 VAL cc_start: 0.8473 (m) cc_final: 0.8166 (p) REVERT: B 586 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7421 (pp20) REVERT: B 589 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7807 (tp30) REVERT: B 613 HIS cc_start: 0.8101 (OUTLIER) cc_final: 0.7723 (p90) REVERT: B 638 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7929 (tm-30) REVERT: B 668 ILE cc_start: 0.8448 (mm) cc_final: 0.8134 (mt) REVERT: B 672 THR cc_start: 0.7990 (p) cc_final: 0.7670 (m) REVERT: B 681 ASP cc_start: 0.8450 (t0) cc_final: 0.7603 (t70) REVERT: B 682 LYS cc_start: 0.8556 (pttp) cc_final: 0.8197 (ttpp) REVERT: B 696 TRP cc_start: 0.8746 (p-90) cc_final: 0.8462 (p-90) REVERT: B 707 ASN cc_start: 0.8104 (t0) cc_final: 0.7399 (t0) REVERT: B 712 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7422 (mt-10) REVERT: C 402 ASN cc_start: 0.7487 (m110) cc_final: 0.7278 (m110) REVERT: C 405 GLN cc_start: 0.7926 (pp30) cc_final: 0.7204 (pp30) REVERT: C 409 GLN cc_start: 0.7830 (mt0) cc_final: 0.7477 (mt0) REVERT: C 412 GLU cc_start: 0.7640 (tt0) cc_final: 0.7363 (tt0) REVERT: C 441 MET cc_start: 0.5994 (mmm) cc_final: 0.5574 (mmm) REVERT: C 473 ARG cc_start: 0.7127 (tmt170) cc_final: 0.6777 (tmt170) REVERT: C 474 HIS cc_start: 0.8151 (m90) cc_final: 0.7551 (m90) REVERT: C 524 HIS cc_start: 0.8005 (t-170) cc_final: 0.7705 (t-90) REVERT: C 545 MET cc_start: 0.5678 (mtt) cc_final: 0.5315 (mtt) REVERT: D 33 ARG cc_start: 0.8158 (mmm-85) cc_final: 0.7902 (mtp85) REVERT: D 42 LEU cc_start: 0.8728 (tt) cc_final: 0.8503 (tp) REVERT: D 53 LYS cc_start: 0.8976 (mtmt) cc_final: 0.8548 (ttmt) REVERT: D 56 VAL cc_start: 0.8906 (t) cc_final: 0.8704 (p) REVERT: D 77 LYS cc_start: 0.8245 (mttt) cc_final: 0.7905 (mttt) REVERT: D 117 ASN cc_start: 0.7988 (m-40) cc_final: 0.7638 (m-40) REVERT: D 120 ILE cc_start: 0.8661 (mt) cc_final: 0.8304 (mm) REVERT: D 154 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7363 (mt-10) REVERT: D 174 ASP cc_start: 0.7442 (OUTLIER) cc_final: 0.7158 (p0) REVERT: D 177 GLN cc_start: 0.7937 (mt0) cc_final: 0.7138 (tm-30) REVERT: D 180 SER cc_start: 0.8660 (m) cc_final: 0.8407 (p) REVERT: D 204 LEU cc_start: 0.8830 (mt) cc_final: 0.8511 (mt) REVERT: D 215 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.8219 (t80) REVERT: D 216 MET cc_start: 0.8553 (tpp) cc_final: 0.8303 (mmp) REVERT: D 261 PHE cc_start: 0.8802 (t80) cc_final: 0.8404 (t80) REVERT: D 288 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8298 (mm) REVERT: D 313 TYR cc_start: 0.8625 (m-80) cc_final: 0.8211 (m-80) REVERT: D 357 SER cc_start: 0.8358 (m) cc_final: 0.8109 (p) REVERT: D 395 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7394 (tm-30) REVERT: D 398 ARG cc_start: 0.7623 (ttt180) cc_final: 0.7295 (ttt180) REVERT: D 402 ARG cc_start: 0.6758 (mpt180) cc_final: 0.6308 (mtt180) REVERT: D 450 ASP cc_start: 0.7603 (t0) cc_final: 0.7248 (t0) REVERT: E 16 GLU cc_start: 0.7096 (pm20) cc_final: 0.6881 (pm20) REVERT: E 17 ARG cc_start: 0.8209 (mpp80) cc_final: 0.7821 (mtp85) REVERT: E 37 ILE cc_start: 0.8376 (mm) cc_final: 0.8062 (mm) REVERT: E 38 LEU cc_start: 0.8134 (mt) cc_final: 0.7738 (mt) REVERT: E 40 LYS cc_start: 0.8273 (tppt) cc_final: 0.7982 (mmmm) REVERT: E 66 ASP cc_start: 0.7865 (t0) cc_final: 0.7393 (t0) REVERT: E 69 ARG cc_start: 0.7696 (ptt-90) cc_final: 0.7361 (ptt-90) REVERT: E 81 LEU cc_start: 0.8444 (tp) cc_final: 0.8210 (tp) REVERT: E 94 GLU cc_start: 0.8064 (tp30) cc_final: 0.7832 (tp30) REVERT: E 142 GLU cc_start: 0.7635 (mp0) cc_final: 0.7101 (mp0) REVERT: E 144 SER cc_start: 0.8419 (t) cc_final: 0.8188 (t) REVERT: E 157 LYS cc_start: 0.8556 (tttt) cc_final: 0.8249 (tttt) REVERT: E 159 MET cc_start: 0.8559 (mmt) cc_final: 0.8248 (mmp) REVERT: E 172 SER cc_start: 0.8619 (t) cc_final: 0.8243 (p) REVERT: E 229 LYS cc_start: 0.8173 (tttt) cc_final: 0.7839 (tttt) REVERT: E 230 GLU cc_start: 0.7758 (tp30) cc_final: 0.7371 (tp30) REVERT: E 233 THR cc_start: 0.7975 (m) cc_final: 0.7729 (p) REVERT: E 250 ILE cc_start: 0.8261 (mt) cc_final: 0.8052 (mm) REVERT: E 328 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7851 (tt) REVERT: E 334 ILE cc_start: 0.8508 (mt) cc_final: 0.8287 (pt) REVERT: E 336 LEU cc_start: 0.8332 (tp) cc_final: 0.8072 (tt) REVERT: E 338 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7667 (mm-30) REVERT: F 55 ASN cc_start: 0.8219 (m-40) cc_final: 0.7661 (m-40) REVERT: F 106 SER cc_start: 0.8422 (m) cc_final: 0.8172 (t) REVERT: F 113 GLU cc_start: 0.8005 (tt0) cc_final: 0.7768 (tt0) REVERT: F 116 LYS cc_start: 0.8790 (mmmm) cc_final: 0.8512 (mtpp) REVERT: F 139 LYS cc_start: 0.8852 (mttt) cc_final: 0.8609 (mtpp) REVERT: F 146 ARG cc_start: 0.8659 (tmm-80) cc_final: 0.8302 (ttt180) REVERT: F 178 MET cc_start: 0.8084 (mmm) cc_final: 0.7876 (mmp) REVERT: F 197 ASP cc_start: 0.8176 (t0) cc_final: 0.7899 (t0) REVERT: F 208 ASP cc_start: 0.7824 (t70) cc_final: 0.7411 (t70) REVERT: F 217 VAL cc_start: 0.8777 (t) cc_final: 0.8560 (p) REVERT: F 239 SER cc_start: 0.8348 (m) cc_final: 0.7934 (p) REVERT: G 16 MET cc_start: 0.8936 (mmm) cc_final: 0.8561 (mmp) REVERT: G 46 ILE cc_start: 0.7060 (OUTLIER) cc_final: 0.6756 (pt) REVERT: K 118 MET cc_start: 0.7230 (tpp) cc_final: 0.6906 (tpp) REVERT: K 135 LYS cc_start: 0.8807 (tttt) cc_final: 0.8465 (tttt) REVERT: K 151 LYS cc_start: 0.7688 (mttt) cc_final: 0.7353 (mttt) REVERT: K 163 LYS cc_start: 0.7492 (mttt) cc_final: 0.7229 (mttt) REVERT: K 164 PHE cc_start: 0.8490 (p90) cc_final: 0.8222 (p90) REVERT: K 188 LYS cc_start: 0.8378 (tttt) cc_final: 0.7966 (tmtt) REVERT: K 201 GLU cc_start: 0.7509 (tp30) cc_final: 0.7057 (tp30) REVERT: K 209 GLU cc_start: 0.8287 (tp30) cc_final: 0.7651 (tp30) REVERT: K 213 LYS cc_start: 0.8462 (tptt) cc_final: 0.7757 (tptt) REVERT: K 245 GLU cc_start: 0.8208 (mp0) cc_final: 0.7564 (mp0) REVERT: K 258 ARG cc_start: 0.7557 (ttp-170) cc_final: 0.6970 (ttp-170) REVERT: K 263 MET cc_start: 0.5047 (OUTLIER) cc_final: 0.4533 (ptt) outliers start: 122 outliers final: 88 residues processed: 869 average time/residue: 0.4231 time to fit residues: 540.5884 Evaluate side-chains 898 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 790 time to evaluate : 2.637 ------------------------------------------------------------------------------- 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 285 ILE Chi-restraints excluded: chain A residue 316 LEU 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 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 570 GLU 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 688 LYS 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 28 LEU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 40 LEU 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 205 VAL Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 384 HIS 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 471 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 545 MET 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 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 446 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 127 LYS Chi-restraints excluded: chain D residue 174 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 288 ILE 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 E residue 33 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 139 CYS Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 333 GLU 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 158 LYS Chi-restraints excluded: chain F residue 173 GLN Chi-restraints excluded: chain F residue 213 LEU 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 184 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 131 optimal weight: 0.0970 chunk 57 optimal weight: 0.0770 chunk 214 optimal weight: 2.9990 chunk 1 optimal weight: 0.0270 chunk 192 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 201 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 181 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 overall best weight: 0.2994 ------------------------------------------------------------------------------- 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 92 ASN ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN E 324 HIS F 108 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.150111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.122696 restraints weight = 38303.264| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.54 r_work: 0.3435 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24160 Z= 0.128 Angle : 0.676 17.955 32876 Z= 0.333 Chirality : 0.043 0.228 3677 Planarity : 0.004 0.059 4022 Dihedral : 14.303 179.876 3601 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.30 % Allowed : 23.68 % Favored : 72.01 % 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: 0.11 (0.16), residues: 2776 helix: 1.13 (0.15), residues: 1352 sheet: -0.23 (0.27), residues: 371 loop : -1.18 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 539 HIS 0.014 0.001 HIS B 613 PHE 0.027 0.001 PHE D 162 TYR 0.042 0.001 TYR C 533 ARG 0.009 0.001 ARG C 542 Details of bonding type rmsd hydrogen bonds : bond 0.03433 ( 1083) hydrogen bonds : angle 4.22209 ( 3076) metal coordination : bond 0.00404 ( 28) metal coordination : angle 4.87191 ( 45) covalent geometry : bond 0.00289 (24132) covalent geometry : angle 0.65157 (32831) *********************** 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 914 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 807 time to evaluate : 2.881 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 73 SER cc_start: 0.7290 (m) cc_final: 0.6612 (p) REVERT: A 98 ASP cc_start: 0.7666 (m-30) cc_final: 0.7090 (m-30) REVERT: A 103 ILE cc_start: 0.8777 (pt) cc_final: 0.8501 (tp) REVERT: A 105 GLU cc_start: 0.7975 (pm20) cc_final: 0.7583 (pm20) REVERT: A 117 LYS cc_start: 0.8429 (tttt) cc_final: 0.7567 (ttpt) REVERT: A 148 VAL cc_start: 0.9003 (p) cc_final: 0.8789 (m) REVERT: A 150 ASP cc_start: 0.7857 (t0) cc_final: 0.7535 (t0) REVERT: A 153 MET cc_start: 0.7569 (mmm) cc_final: 0.7191 (mmm) REVERT: A 155 PHE cc_start: 0.8111 (t80) cc_final: 0.7752 (t80) REVERT: A 157 LYS cc_start: 0.8473 (tppt) cc_final: 0.8166 (ttmm) REVERT: A 165 LYS cc_start: 0.8338 (mttm) cc_final: 0.7933 (mttp) REVERT: A 271 GLU cc_start: 0.7074 (pp20) cc_final: 0.5038 (tm-30) REVERT: A 273 LYS cc_start: 0.8231 (mtmt) cc_final: 0.7609 (mttt) REVERT: A 279 GLU cc_start: 0.7726 (mp0) cc_final: 0.7190 (mp0) REVERT: A 282 LYS cc_start: 0.8757 (tttt) cc_final: 0.8244 (ttmm) REVERT: A 285 ILE cc_start: 0.8701 (pt) cc_final: 0.8390 (pt) REVERT: A 298 ARG cc_start: 0.8067 (mmm160) cc_final: 0.7708 (tpp80) REVERT: A 309 ASP cc_start: 0.7163 (p0) cc_final: 0.6666 (p0) REVERT: A 351 VAL cc_start: 0.8376 (t) cc_final: 0.8137 (p) REVERT: A 372 GLU cc_start: 0.7127 (mp0) cc_final: 0.6581 (mp0) REVERT: A 375 LYS cc_start: 0.8523 (ttpt) cc_final: 0.8145 (ttmm) REVERT: A 388 GLN cc_start: 0.8092 (mm110) cc_final: 0.7886 (mm-40) REVERT: A 391 ARG cc_start: 0.8165 (mtm180) cc_final: 0.7943 (mtm180) REVERT: A 425 ARG cc_start: 0.7924 (tpp-160) cc_final: 0.7572 (tpp-160) REVERT: A 427 MET cc_start: 0.8381 (tpp) cc_final: 0.7963 (tpp) REVERT: A 457 ILE cc_start: 0.8847 (tt) cc_final: 0.8435 (mm) REVERT: A 504 LYS cc_start: 0.8721 (tttt) cc_final: 0.8419 (tmtt) REVERT: A 506 GLN cc_start: 0.8788 (tt0) cc_final: 0.8476 (tt0) REVERT: A 510 VAL cc_start: 0.8187 (OUTLIER) cc_final: 0.7797 (t) REVERT: A 517 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7858 (mp0) REVERT: A 525 ILE cc_start: 0.8501 (tp) cc_final: 0.7872 (pt) REVERT: A 530 ARG cc_start: 0.7784 (ptm160) cc_final: 0.7584 (ptm160) REVERT: A 586 GLN cc_start: 0.8225 (tp40) cc_final: 0.7720 (tm-30) REVERT: A 594 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.7178 (tp-100) REVERT: A 619 GLU cc_start: 0.7327 (mp0) cc_final: 0.6992 (tp30) REVERT: A 621 ASN cc_start: 0.8237 (m110) cc_final: 0.7994 (m-40) REVERT: A 625 GLN cc_start: 0.7709 (pt0) cc_final: 0.7040 (tt0) REVERT: A 632 SER cc_start: 0.8320 (t) cc_final: 0.7929 (t) REVERT: A 636 GLU cc_start: 0.7971 (tp30) cc_final: 0.7548 (tp30) REVERT: A 697 GLU cc_start: 0.7295 (tp30) cc_final: 0.6984 (tp30) REVERT: A 710 GLN cc_start: 0.7731 (pt0) cc_final: 0.7389 (pp30) REVERT: A 712 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7964 (tt) REVERT: B 1 MET cc_start: 0.6284 (ppp) cc_final: 0.5127 (ppp) REVERT: B 12 PHE cc_start: 0.7326 (t80) cc_final: 0.6879 (m-80) REVERT: B 27 GLU cc_start: 0.7512 (tm-30) cc_final: 0.7269 (tm-30) REVERT: B 41 GLU cc_start: 0.7692 (tt0) cc_final: 0.7384 (tt0) REVERT: B 53 LEU cc_start: 0.8627 (mt) cc_final: 0.7667 (mm) REVERT: B 57 MET cc_start: 0.8406 (mmt) cc_final: 0.7888 (mmt) REVERT: B 83 VAL cc_start: 0.8238 (m) cc_final: 0.7994 (p) REVERT: B 133 LYS cc_start: 0.7498 (mttt) cc_final: 0.7244 (mttp) REVERT: B 200 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7565 (pp) REVERT: B 235 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: B 238 ASN cc_start: 0.8256 (m-40) cc_final: 0.7988 (m110) REVERT: B 244 ILE cc_start: 0.8422 (tp) cc_final: 0.8042 (tp) REVERT: B 259 CYS cc_start: 0.7385 (m) cc_final: 0.7137 (m) REVERT: B 262 ASN cc_start: 0.7656 (p0) cc_final: 0.7346 (p0) REVERT: B 338 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6899 (pm20) REVERT: B 384 HIS cc_start: 0.5337 (OUTLIER) cc_final: 0.5046 (p-80) REVERT: B 397 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7422 (mm) REVERT: B 403 PHE cc_start: 0.8068 (t80) cc_final: 0.7579 (t80) REVERT: B 439 ASP cc_start: 0.7550 (t0) cc_final: 0.7215 (t0) REVERT: B 471 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7870 (pp) REVERT: B 487 ARG cc_start: 0.6420 (ptt-90) cc_final: 0.5640 (ptt180) REVERT: B 511 ARG cc_start: 0.7786 (mtp85) cc_final: 0.7497 (mtt180) REVERT: B 516 VAL cc_start: 0.8417 (m) cc_final: 0.8108 (p) REVERT: B 583 LYS cc_start: 0.8361 (mtmm) cc_final: 0.8135 (mttt) REVERT: B 586 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7360 (pp20) REVERT: B 589 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7784 (tp30) REVERT: B 613 HIS cc_start: 0.7920 (OUTLIER) cc_final: 0.7479 (p90) REVERT: B 638 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7871 (tm-30) REVERT: B 668 ILE cc_start: 0.8490 (mm) cc_final: 0.8149 (mt) REVERT: B 672 THR cc_start: 0.7985 (p) cc_final: 0.7669 (m) REVERT: B 681 ASP cc_start: 0.8429 (t0) cc_final: 0.7590 (t70) REVERT: B 682 LYS cc_start: 0.8540 (pttp) cc_final: 0.8183 (ttpp) REVERT: B 707 ASN cc_start: 0.8085 (t0) cc_final: 0.7386 (t0) REVERT: C 398 GLN cc_start: 0.7719 (mt0) cc_final: 0.7222 (tm-30) REVERT: C 402 ASN cc_start: 0.7436 (m110) cc_final: 0.5739 (m110) REVERT: C 405 GLN cc_start: 0.7919 (pp30) cc_final: 0.7009 (pp30) REVERT: C 409 GLN cc_start: 0.7773 (mt0) cc_final: 0.7321 (mt0) REVERT: C 412 GLU cc_start: 0.7595 (tt0) cc_final: 0.7329 (tt0) REVERT: C 441 MET cc_start: 0.5913 (mmm) cc_final: 0.5491 (mmm) REVERT: C 473 ARG cc_start: 0.7178 (tmt170) cc_final: 0.6787 (tmt170) REVERT: C 474 HIS cc_start: 0.8088 (m90) cc_final: 0.7558 (m-70) REVERT: C 475 PHE cc_start: 0.8757 (t80) cc_final: 0.8131 (t80) REVERT: C 479 PHE cc_start: 0.7474 (m-80) cc_final: 0.6977 (m-80) REVERT: C 524 HIS cc_start: 0.7991 (t-170) cc_final: 0.7699 (t-90) REVERT: C 545 MET cc_start: 0.5655 (mtt) cc_final: 0.5280 (mtt) REVERT: D 33 ARG cc_start: 0.8123 (mmm-85) cc_final: 0.7888 (mtp85) REVERT: D 42 LEU cc_start: 0.8710 (tt) cc_final: 0.8500 (tp) REVERT: D 53 LYS cc_start: 0.8828 (mtmt) cc_final: 0.8434 (ttmt) REVERT: D 56 VAL cc_start: 0.8867 (t) cc_final: 0.8648 (p) REVERT: D 77 LYS cc_start: 0.8162 (mttt) cc_final: 0.7845 (mttt) REVERT: D 117 ASN cc_start: 0.7928 (m-40) cc_final: 0.7657 (m-40) REVERT: D 154 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7310 (mt-10) REVERT: D 177 GLN cc_start: 0.7862 (mt0) cc_final: 0.7089 (tm-30) REVERT: D 180 SER cc_start: 0.8592 (m) cc_final: 0.8334 (p) REVERT: D 204 LEU cc_start: 0.8771 (mt) cc_final: 0.8499 (mt) REVERT: D 215 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.8301 (t80) REVERT: D 216 MET cc_start: 0.8560 (tpp) cc_final: 0.8323 (mmp) REVERT: D 229 ASP cc_start: 0.7653 (t0) cc_final: 0.7448 (t70) REVERT: D 247 LYS cc_start: 0.8245 (tttt) cc_final: 0.7939 (tttm) REVERT: D 252 GLU cc_start: 0.7552 (mt-10) cc_final: 0.6944 (mt-10) REVERT: D 261 PHE cc_start: 0.8769 (t80) cc_final: 0.8359 (t80) REVERT: D 313 TYR cc_start: 0.8632 (m-80) cc_final: 0.8231 (m-80) REVERT: D 357 SER cc_start: 0.8324 (m) cc_final: 0.8064 (p) REVERT: D 395 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7378 (tm-30) REVERT: D 398 ARG cc_start: 0.7590 (ttt180) cc_final: 0.7380 (ttt180) REVERT: D 402 ARG cc_start: 0.6624 (mpt180) cc_final: 0.6239 (mtt180) REVERT: D 450 ASP cc_start: 0.7570 (t0) cc_final: 0.7197 (t0) REVERT: E 37 ILE cc_start: 0.8426 (mm) cc_final: 0.8093 (mm) REVERT: E 38 LEU cc_start: 0.8063 (mt) cc_final: 0.7384 (mp) REVERT: E 40 LYS cc_start: 0.8252 (tppt) cc_final: 0.7960 (mmmm) REVERT: E 66 ASP cc_start: 0.7856 (t0) cc_final: 0.7427 (t0) REVERT: E 81 LEU cc_start: 0.8546 (tp) cc_final: 0.8314 (tp) REVERT: E 90 TYR cc_start: 0.7835 (t80) cc_final: 0.7271 (t80) REVERT: E 94 GLU cc_start: 0.8154 (tp30) cc_final: 0.7896 (tp30) REVERT: E 157 LYS cc_start: 0.8503 (tttt) cc_final: 0.8192 (tttt) REVERT: E 159 MET cc_start: 0.8583 (mmt) cc_final: 0.8263 (mmp) REVERT: E 172 SER cc_start: 0.8620 (t) cc_final: 0.8245 (p) REVERT: E 190 LYS cc_start: 0.8845 (ttpp) cc_final: 0.8627 (ttpp) REVERT: E 229 LYS cc_start: 0.8235 (tttt) cc_final: 0.7946 (tttt) REVERT: E 230 GLU cc_start: 0.7636 (tp30) cc_final: 0.7072 (tp30) REVERT: E 233 THR cc_start: 0.7824 (m) cc_final: 0.7565 (p) REVERT: E 250 ILE cc_start: 0.8256 (mt) cc_final: 0.8049 (mm) REVERT: E 320 ARG cc_start: 0.8577 (ttm170) cc_final: 0.8339 (ttm-80) REVERT: E 328 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7868 (tt) REVERT: E 336 LEU cc_start: 0.8270 (tp) cc_final: 0.8004 (tt) REVERT: E 338 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7564 (mm-30) REVERT: F 55 ASN cc_start: 0.8103 (m-40) cc_final: 0.7594 (m-40) REVERT: F 106 SER cc_start: 0.8390 (m) cc_final: 0.8162 (t) REVERT: F 113 GLU cc_start: 0.8068 (tt0) cc_final: 0.7827 (tt0) REVERT: F 116 LYS cc_start: 0.8773 (mmmm) cc_final: 0.8501 (mtpp) REVERT: F 139 LYS cc_start: 0.8822 (mttt) cc_final: 0.8564 (mtpp) REVERT: F 178 MET cc_start: 0.7983 (mmm) cc_final: 0.7765 (mmp) REVERT: F 197 ASP cc_start: 0.8138 (t0) cc_final: 0.7830 (t0) REVERT: F 208 ASP cc_start: 0.7814 (t70) cc_final: 0.7379 (t70) REVERT: F 217 VAL cc_start: 0.8728 (t) cc_final: 0.8495 (p) REVERT: G 16 MET cc_start: 0.8843 (mmm) cc_final: 0.8501 (mmp) REVERT: G 27 ASN cc_start: 0.8266 (m-40) cc_final: 0.8005 (t0) REVERT: K 118 MET cc_start: 0.7157 (tpp) cc_final: 0.6832 (tpp) REVERT: K 135 LYS cc_start: 0.8791 (tttt) cc_final: 0.8457 (tttt) REVERT: K 139 ILE cc_start: 0.8287 (mm) cc_final: 0.7564 (tp) REVERT: K 151 LYS cc_start: 0.7678 (mttt) cc_final: 0.7313 (mttt) REVERT: K 163 LYS cc_start: 0.7465 (mttt) cc_final: 0.7210 (mttt) REVERT: K 164 PHE cc_start: 0.8463 (p90) cc_final: 0.8058 (p90) REVERT: K 188 LYS cc_start: 0.8317 (tttt) cc_final: 0.7916 (tmtt) REVERT: K 201 GLU cc_start: 0.7524 (tp30) cc_final: 0.7086 (tp30) REVERT: K 209 GLU cc_start: 0.8288 (tp30) cc_final: 0.7631 (tp30) REVERT: K 213 LYS cc_start: 0.8438 (tptt) cc_final: 0.7635 (tptt) REVERT: K 245 GLU cc_start: 0.8105 (mp0) cc_final: 0.7440 (mp0) REVERT: K 250 GLU cc_start: 0.7064 (tp30) cc_final: 0.6748 (tp30) REVERT: K 258 ARG cc_start: 0.7487 (ttp-170) cc_final: 0.6887 (ttp-170) REVERT: K 263 MET cc_start: 0.4904 (OUTLIER) cc_final: 0.4352 (ptt) outliers start: 107 outliers final: 70 residues processed: 860 average time/residue: 0.4138 time to fit residues: 523.9065 Evaluate side-chains 868 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 784 time to evaluate : 2.767 ------------------------------------------------------------------------------- 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 443 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 497 GLN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 629 HIS 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 28 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 210 HIS Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 384 HIS 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 471 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 490 LEU 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 B residue 702 THR 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 446 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 127 LYS 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 E residue 12 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 139 CYS Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain E residue 372 ASP Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 152 LYS Chi-restraints excluded: chain F residue 173 GLN Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 248 HIS 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 184 LEU 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 231 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 129 optimal weight: 0.0970 chunk 35 optimal weight: 3.9990 chunk 254 optimal weight: 0.9990 chunk 71 optimal weight: 0.0020 chunk 187 optimal weight: 0.0030 chunk 83 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 260 optimal weight: 0.9980 overall best weight: 0.3796 ------------------------------------------------------------------------------- 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 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 HIS E 332 GLN E 356 HIS ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.150207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.122790 restraints weight = 38362.252| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.52 r_work: 0.3439 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24160 Z= 0.133 Angle : 0.689 18.917 32876 Z= 0.337 Chirality : 0.043 0.229 3677 Planarity : 0.004 0.063 4022 Dihedral : 14.272 179.624 3595 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.78 % Allowed : 24.37 % Favored : 71.85 % 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: 1.09 (0.14), residues: 1351 sheet: -0.19 (0.27), residues: 370 loop : -1.18 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 539 HIS 0.014 0.001 HIS B 613 PHE 0.031 0.001 PHE A 270 TYR 0.051 0.002 TYR A 295 ARG 0.008 0.001 ARG B 518 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 1083) hydrogen bonds : angle 4.21175 ( 3076) metal coordination : bond 0.00428 ( 28) metal coordination : angle 4.85748 ( 45) covalent geometry : bond 0.00302 (24132) covalent geometry : angle 0.66563 (32831) *********************** 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 888 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 794 time to evaluate : 2.633 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 98 ASP cc_start: 0.7672 (m-30) cc_final: 0.7109 (m-30) REVERT: A 103 ILE cc_start: 0.8784 (pt) cc_final: 0.8514 (tp) REVERT: A 105 GLU cc_start: 0.7999 (pm20) cc_final: 0.7621 (pm20) REVERT: A 117 LYS cc_start: 0.8435 (tttt) cc_final: 0.7593 (ttpt) REVERT: A 150 ASP cc_start: 0.7829 (t0) cc_final: 0.7501 (t0) REVERT: A 153 MET cc_start: 0.7573 (mmm) cc_final: 0.7363 (mmm) REVERT: A 155 PHE cc_start: 0.8104 (t80) cc_final: 0.7751 (t80) REVERT: A 157 LYS cc_start: 0.8474 (tppt) cc_final: 0.8157 (ttmm) REVERT: A 165 LYS cc_start: 0.8278 (mttm) cc_final: 0.7924 (mttp) REVERT: A 273 LYS cc_start: 0.8241 (mtmt) cc_final: 0.7696 (mttt) REVERT: A 279 GLU cc_start: 0.7710 (mp0) cc_final: 0.7373 (mp0) REVERT: A 282 LYS cc_start: 0.8739 (tttt) cc_final: 0.8234 (ttmm) REVERT: A 285 ILE cc_start: 0.8716 (pt) cc_final: 0.8410 (pt) REVERT: A 298 ARG cc_start: 0.8024 (mmm160) cc_final: 0.7570 (tpp80) REVERT: A 309 ASP cc_start: 0.7165 (p0) cc_final: 0.6670 (p0) REVERT: A 351 VAL cc_start: 0.8398 (t) cc_final: 0.8155 (p) REVERT: A 372 GLU cc_start: 0.7119 (mp0) cc_final: 0.6608 (mp0) REVERT: A 375 LYS cc_start: 0.8531 (ttpt) cc_final: 0.8324 (ttmm) REVERT: A 388 GLN cc_start: 0.8091 (mm110) cc_final: 0.7762 (mm-40) REVERT: A 425 ARG cc_start: 0.7908 (tpp-160) cc_final: 0.7551 (tpp-160) REVERT: A 427 MET cc_start: 0.8386 (tpp) cc_final: 0.7993 (tpp) REVERT: A 457 ILE cc_start: 0.8789 (tt) cc_final: 0.8547 (tt) REVERT: A 504 LYS cc_start: 0.8749 (tttt) cc_final: 0.8414 (tmtt) REVERT: A 506 GLN cc_start: 0.8804 (tt0) cc_final: 0.8509 (tt0) REVERT: A 510 VAL cc_start: 0.8181 (OUTLIER) cc_final: 0.7809 (t) REVERT: A 517 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7859 (mp0) REVERT: A 525 ILE cc_start: 0.8500 (tp) cc_final: 0.7873 (pt) REVERT: A 530 ARG cc_start: 0.7819 (ptm160) cc_final: 0.7605 (ptm160) REVERT: A 586 GLN cc_start: 0.8217 (tp40) cc_final: 0.7715 (tm-30) REVERT: A 594 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.7214 (tp-100) REVERT: A 619 GLU cc_start: 0.7326 (mp0) cc_final: 0.7011 (tp30) REVERT: A 621 ASN cc_start: 0.8225 (m110) cc_final: 0.7983 (m-40) REVERT: A 625 GLN cc_start: 0.7695 (pt0) cc_final: 0.7032 (tt0) REVERT: A 632 SER cc_start: 0.8320 (t) cc_final: 0.7925 (t) REVERT: A 636 GLU cc_start: 0.7955 (tp30) cc_final: 0.7529 (tp30) REVERT: A 697 GLU cc_start: 0.7395 (tp30) cc_final: 0.7069 (tp30) REVERT: A 710 GLN cc_start: 0.7767 (pt0) cc_final: 0.7407 (pp30) REVERT: A 712 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7968 (tt) REVERT: B 1 MET cc_start: 0.6272 (ppp) cc_final: 0.5119 (ppp) REVERT: B 12 PHE cc_start: 0.7377 (t80) cc_final: 0.6941 (m-80) REVERT: B 41 GLU cc_start: 0.7604 (tt0) cc_final: 0.7383 (tt0) REVERT: B 53 LEU cc_start: 0.8612 (mt) cc_final: 0.7673 (mm) REVERT: B 57 MET cc_start: 0.8362 (mmt) cc_final: 0.7856 (mmt) REVERT: B 83 VAL cc_start: 0.8229 (m) cc_final: 0.7989 (p) REVERT: B 133 LYS cc_start: 0.7506 (mttt) cc_final: 0.7250 (mttp) REVERT: B 200 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7587 (pp) REVERT: B 235 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7484 (mp0) REVERT: B 238 ASN cc_start: 0.8267 (m-40) cc_final: 0.7997 (m110) REVERT: B 244 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8115 (tp) REVERT: B 259 CYS cc_start: 0.7240 (m) cc_final: 0.7011 (m) REVERT: B 262 ASN cc_start: 0.7554 (p0) cc_final: 0.7348 (p0) REVERT: B 338 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6695 (pm20) REVERT: B 350 VAL cc_start: 0.7133 (m) cc_final: 0.6932 (m) REVERT: B 384 HIS cc_start: 0.5354 (OUTLIER) cc_final: 0.5075 (p-80) REVERT: B 397 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7401 (mm) REVERT: B 403 PHE cc_start: 0.8067 (t80) cc_final: 0.7827 (t80) REVERT: B 439 ASP cc_start: 0.7623 (t0) cc_final: 0.7282 (t0) REVERT: B 471 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7882 (pp) REVERT: B 487 ARG cc_start: 0.6497 (ptt-90) cc_final: 0.5657 (ptt180) REVERT: B 507 LYS cc_start: 0.7949 (mtmt) cc_final: 0.7699 (mtmm) REVERT: B 511 ARG cc_start: 0.7792 (mtp85) cc_final: 0.7479 (mtt180) REVERT: B 516 VAL cc_start: 0.8405 (m) cc_final: 0.8113 (p) REVERT: B 583 LYS cc_start: 0.8368 (mtmm) cc_final: 0.8161 (mttt) REVERT: B 586 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7392 (pp20) REVERT: B 589 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7790 (tp30) REVERT: B 613 HIS cc_start: 0.7844 (OUTLIER) cc_final: 0.7401 (p90) REVERT: B 631 ARG cc_start: 0.7331 (mtt180) cc_final: 0.6822 (mpp80) REVERT: B 638 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7878 (tm-30) REVERT: B 668 ILE cc_start: 0.8478 (mm) cc_final: 0.8127 (mt) REVERT: B 672 THR cc_start: 0.8089 (p) cc_final: 0.7779 (m) REVERT: B 681 ASP cc_start: 0.8412 (t0) cc_final: 0.7592 (t70) REVERT: B 682 LYS cc_start: 0.8548 (pttp) cc_final: 0.8196 (ttpp) REVERT: B 696 TRP cc_start: 0.8526 (p-90) cc_final: 0.8301 (p-90) REVERT: B 707 ASN cc_start: 0.8015 (t0) cc_final: 0.7357 (t0) REVERT: C 405 GLN cc_start: 0.7931 (pp30) cc_final: 0.6989 (pp30) REVERT: C 409 GLN cc_start: 0.7783 (mt0) cc_final: 0.7308 (mt0) REVERT: C 412 GLU cc_start: 0.7610 (tt0) cc_final: 0.7350 (tt0) REVERT: C 473 ARG cc_start: 0.7215 (tmt170) cc_final: 0.6802 (tmt170) REVERT: C 474 HIS cc_start: 0.8022 (m90) cc_final: 0.7632 (m-70) REVERT: C 524 HIS cc_start: 0.7992 (t-170) cc_final: 0.7698 (t-90) REVERT: C 545 MET cc_start: 0.5660 (mtt) cc_final: 0.5290 (mtt) REVERT: D 23 LEU cc_start: 0.8596 (mm) cc_final: 0.8208 (mp) REVERT: D 33 ARG cc_start: 0.8134 (mmm-85) cc_final: 0.7883 (mtp85) REVERT: D 42 LEU cc_start: 0.8721 (tt) cc_final: 0.8514 (tp) REVERT: D 53 LYS cc_start: 0.8831 (mtmt) cc_final: 0.8574 (ttmt) REVERT: D 56 VAL cc_start: 0.8878 (t) cc_final: 0.8656 (p) REVERT: D 77 LYS cc_start: 0.8105 (mttt) cc_final: 0.7840 (mttt) REVERT: D 154 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7336 (mt-10) REVERT: D 163 MET cc_start: 0.7592 (ttm) cc_final: 0.7304 (ttm) REVERT: D 177 GLN cc_start: 0.7885 (mt0) cc_final: 0.7087 (tm-30) REVERT: D 180 SER cc_start: 0.8580 (m) cc_final: 0.8314 (p) REVERT: D 204 LEU cc_start: 0.8760 (mt) cc_final: 0.8497 (mt) REVERT: D 215 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.8244 (t80) REVERT: D 216 MET cc_start: 0.8576 (tpp) cc_final: 0.8322 (mmp) REVERT: D 247 LYS cc_start: 0.8227 (tttt) cc_final: 0.7961 (tttm) REVERT: D 252 GLU cc_start: 0.7556 (mt-10) cc_final: 0.6938 (mt-10) REVERT: D 261 PHE cc_start: 0.8766 (t80) cc_final: 0.8373 (t80) REVERT: D 281 TYR cc_start: 0.8470 (p90) cc_final: 0.8078 (p90) REVERT: D 313 TYR cc_start: 0.8631 (m-80) cc_final: 0.8248 (m-80) REVERT: D 357 SER cc_start: 0.8341 (m) cc_final: 0.8072 (p) REVERT: D 395 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7385 (tm-30) REVERT: D 402 ARG cc_start: 0.6614 (mpt180) cc_final: 0.6227 (mtt90) REVERT: D 404 THR cc_start: 0.8469 (m) cc_final: 0.8094 (p) REVERT: D 450 ASP cc_start: 0.7581 (t0) cc_final: 0.7215 (t0) REVERT: E 37 ILE cc_start: 0.8447 (mm) cc_final: 0.8116 (mm) REVERT: E 38 LEU cc_start: 0.8120 (mt) cc_final: 0.7408 (mp) REVERT: E 40 LYS cc_start: 0.8267 (tppt) cc_final: 0.7981 (mmmm) REVERT: E 66 ASP cc_start: 0.7817 (t0) cc_final: 0.7430 (t0) REVERT: E 81 LEU cc_start: 0.8561 (tp) cc_final: 0.8336 (tp) REVERT: E 90 TYR cc_start: 0.7835 (t80) cc_final: 0.7272 (t80) REVERT: E 94 GLU cc_start: 0.8172 (tp30) cc_final: 0.7920 (tp30) REVERT: E 116 LYS cc_start: 0.7895 (ttmm) cc_final: 0.7531 (tttm) REVERT: E 157 LYS cc_start: 0.8479 (tttt) cc_final: 0.8193 (tttt) REVERT: E 159 MET cc_start: 0.8575 (mmt) cc_final: 0.8240 (mmp) REVERT: E 172 SER cc_start: 0.8626 (t) cc_final: 0.8320 (p) REVERT: E 229 LYS cc_start: 0.8244 (tttt) cc_final: 0.7961 (tttt) REVERT: E 230 GLU cc_start: 0.7629 (tp30) cc_final: 0.7380 (tp30) REVERT: E 233 THR cc_start: 0.7810 (m) cc_final: 0.7585 (p) REVERT: E 250 ILE cc_start: 0.8258 (mt) cc_final: 0.8054 (mm) REVERT: E 328 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7859 (tt) REVERT: E 336 LEU cc_start: 0.8272 (tp) cc_final: 0.8003 (tt) REVERT: E 338 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7527 (mm-30) REVERT: F 18 ASN cc_start: 0.8426 (t0) cc_final: 0.8171 (t0) REVERT: F 106 SER cc_start: 0.8379 (m) cc_final: 0.8156 (t) REVERT: F 113 GLU cc_start: 0.8066 (tt0) cc_final: 0.7839 (tt0) REVERT: F 116 LYS cc_start: 0.8799 (mmmm) cc_final: 0.8471 (mtpp) REVERT: F 117 ASP cc_start: 0.8257 (t0) cc_final: 0.8056 (t0) REVERT: F 139 LYS cc_start: 0.8843 (mttt) cc_final: 0.8586 (mtpp) REVERT: F 146 ARG cc_start: 0.8569 (tmm-80) cc_final: 0.8154 (ttt180) REVERT: F 178 MET cc_start: 0.8018 (mmm) cc_final: 0.7807 (mmp) REVERT: F 197 ASP cc_start: 0.8104 (t0) cc_final: 0.7818 (t0) REVERT: F 208 ASP cc_start: 0.7823 (t70) cc_final: 0.7369 (t70) REVERT: F 217 VAL cc_start: 0.8697 (t) cc_final: 0.8471 (p) REVERT: G 16 MET cc_start: 0.8823 (mmm) cc_final: 0.8442 (mmp) REVERT: K 116 TYR cc_start: 0.7771 (t80) cc_final: 0.7555 (t80) REVERT: K 118 MET cc_start: 0.7157 (tpp) cc_final: 0.6367 (tpp) REVERT: K 135 LYS cc_start: 0.8779 (tttt) cc_final: 0.8460 (tttt) REVERT: K 139 ILE cc_start: 0.8300 (mm) cc_final: 0.7577 (tp) REVERT: K 151 LYS cc_start: 0.7683 (mttt) cc_final: 0.7317 (mttt) REVERT: K 163 LYS cc_start: 0.7454 (mttt) cc_final: 0.7204 (mttt) REVERT: K 164 PHE cc_start: 0.8475 (p90) cc_final: 0.8087 (p90) REVERT: K 188 LYS cc_start: 0.8339 (tttt) cc_final: 0.7934 (tmtt) REVERT: K 201 GLU cc_start: 0.7520 (tp30) cc_final: 0.7110 (tp30) REVERT: K 209 GLU cc_start: 0.8292 (tp30) cc_final: 0.7637 (tp30) REVERT: K 213 LYS cc_start: 0.8420 (tptt) cc_final: 0.7669 (tptt) REVERT: K 245 GLU cc_start: 0.8079 (mp0) cc_final: 0.7416 (mp0) REVERT: K 250 GLU cc_start: 0.7032 (tp30) cc_final: 0.6611 (tp30) REVERT: K 252 LEU cc_start: 0.7400 (mt) cc_final: 0.6765 (mt) REVERT: K 258 ARG cc_start: 0.7514 (ttp-170) cc_final: 0.6915 (ttp-170) REVERT: K 263 MET cc_start: 0.4893 (OUTLIER) cc_final: 0.4351 (ptt) outliers start: 94 outliers final: 70 residues processed: 845 average time/residue: 0.5066 time to fit residues: 638.0352 Evaluate side-chains 873 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 788 time to evaluate : 2.451 ------------------------------------------------------------------------------- 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 443 VAL Chi-restraints excluded: chain A residue 446 ILE 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 594 GLN Chi-restraints excluded: chain A residue 629 HIS 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 28 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 205 VAL Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 384 HIS 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 471 LEU Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 499 ASN 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 B residue 702 THR 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 446 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 127 LYS 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 353 GLN Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain E residue 12 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 139 CYS Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 152 LYS Chi-restraints excluded: chain F residue 248 HIS 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 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 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 47 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 184 optimal weight: 4.9990 chunk 236 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 39 optimal weight: 0.2980 chunk 140 optimal weight: 0.5980 chunk 172 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 chunk 139 optimal weight: 0.0270 chunk 259 optimal weight: 0.3980 overall best weight: 0.3838 ------------------------------------------------------------------------------- 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 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 ASN E 50 HIS E 324 HIS ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.150231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.122672 restraints weight = 38879.960| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.61 r_work: 0.3432 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24160 Z= 0.134 Angle : 0.707 18.379 32876 Z= 0.344 Chirality : 0.043 0.230 3677 Planarity : 0.004 0.060 4022 Dihedral : 14.253 179.299 3595 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.58 % Allowed : 24.85 % Favored : 71.57 % 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: 1.08 (0.14), residues: 1350 sheet: -0.10 (0.27), residues: 360 loop : -1.16 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 342 HIS 0.014 0.001 HIS B 613 PHE 0.022 0.001 PHE B 403 TYR 0.045 0.002 TYR C 533 ARG 0.012 0.001 ARG A 325 Details of bonding type rmsd hydrogen bonds : bond 0.03431 ( 1083) hydrogen bonds : angle 4.22302 ( 3076) metal coordination : bond 0.00972 ( 28) metal coordination : angle 4.96221 ( 45) covalent geometry : bond 0.00304 (24132) covalent geometry : angle 0.68371 (32831) ********************** 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 882 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 793 time to evaluate : 2.462 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 98 ASP cc_start: 0.7652 (m-30) cc_final: 0.7087 (m-30) REVERT: A 103 ILE cc_start: 0.8760 (pt) cc_final: 0.8488 (tp) REVERT: A 105 GLU cc_start: 0.8008 (pm20) cc_final: 0.7624 (pm20) REVERT: A 117 LYS cc_start: 0.8431 (tttt) cc_final: 0.7593 (ttpt) REVERT: A 138 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7613 (tm-30) REVERT: A 150 ASP cc_start: 0.7863 (t0) cc_final: 0.7569 (t0) REVERT: A 153 MET cc_start: 0.7585 (mmm) cc_final: 0.7159 (mmm) REVERT: A 155 PHE cc_start: 0.8090 (t80) cc_final: 0.7748 (t80) REVERT: A 157 LYS cc_start: 0.8472 (tppt) cc_final: 0.8174 (ttmm) REVERT: A 165 LYS cc_start: 0.8297 (mttm) cc_final: 0.7919 (mttp) REVERT: A 279 GLU cc_start: 0.7740 (mp0) cc_final: 0.7390 (mp0) REVERT: A 282 LYS cc_start: 0.8733 (tttt) cc_final: 0.8226 (ttmm) REVERT: A 285 ILE cc_start: 0.8711 (pt) cc_final: 0.8416 (pt) REVERT: A 298 ARG cc_start: 0.8222 (mmm160) cc_final: 0.7838 (tpp80) REVERT: A 309 ASP cc_start: 0.7199 (p0) cc_final: 0.6732 (p0) REVERT: A 321 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7311 (mm-30) REVERT: A 351 VAL cc_start: 0.8392 (t) cc_final: 0.8139 (p) REVERT: A 372 GLU cc_start: 0.7119 (mp0) cc_final: 0.6588 (mp0) REVERT: A 375 LYS cc_start: 0.8608 (ttpt) cc_final: 0.8278 (ttmm) REVERT: A 425 ARG cc_start: 0.7885 (tpp-160) cc_final: 0.7509 (tpp-160) REVERT: A 427 MET cc_start: 0.8396 (tpp) cc_final: 0.8005 (tpp) REVERT: A 457 ILE cc_start: 0.8772 (tt) cc_final: 0.8530 (tt) REVERT: A 504 LYS cc_start: 0.8754 (tttt) cc_final: 0.8467 (tmtt) REVERT: A 510 VAL cc_start: 0.8173 (OUTLIER) cc_final: 0.7788 (t) REVERT: A 517 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7896 (mp0) REVERT: A 518 PHE cc_start: 0.8716 (m-80) cc_final: 0.8498 (m-80) REVERT: A 525 ILE cc_start: 0.8517 (tp) cc_final: 0.7873 (pt) REVERT: A 530 ARG cc_start: 0.7809 (ptm160) cc_final: 0.7585 (ptm160) REVERT: A 586 GLN cc_start: 0.8215 (tp40) cc_final: 0.7696 (tm-30) REVERT: A 594 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.7183 (tp-100) REVERT: A 619 GLU cc_start: 0.7344 (mp0) cc_final: 0.7003 (tp30) REVERT: A 621 ASN cc_start: 0.8235 (m110) cc_final: 0.7986 (m-40) REVERT: A 625 GLN cc_start: 0.7640 (pt0) cc_final: 0.6995 (tt0) REVERT: A 632 SER cc_start: 0.8345 (t) cc_final: 0.7932 (t) REVERT: A 636 GLU cc_start: 0.7982 (tp30) cc_final: 0.7492 (tp30) REVERT: A 697 GLU cc_start: 0.7416 (tp30) cc_final: 0.7087 (tp30) REVERT: A 710 GLN cc_start: 0.7772 (pt0) cc_final: 0.7386 (pp30) REVERT: A 715 LYS cc_start: 0.8630 (ttmt) cc_final: 0.8106 (tptp) REVERT: B 1 MET cc_start: 0.6282 (ppp) cc_final: 0.5096 (ppp) REVERT: B 12 PHE cc_start: 0.7381 (t80) cc_final: 0.6918 (m-80) REVERT: B 41 GLU cc_start: 0.7752 (tt0) cc_final: 0.7433 (tt0) REVERT: B 53 LEU cc_start: 0.8644 (mt) cc_final: 0.7671 (mm) REVERT: B 57 MET cc_start: 0.8470 (mmt) cc_final: 0.7929 (mmt) REVERT: B 133 LYS cc_start: 0.7489 (mttt) cc_final: 0.7241 (mttp) REVERT: B 200 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7608 (pp) REVERT: B 235 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7521 (mp0) REVERT: B 238 ASN cc_start: 0.8265 (m-40) cc_final: 0.7990 (m110) REVERT: B 244 ILE cc_start: 0.8410 (tp) cc_final: 0.8097 (tp) REVERT: B 259 CYS cc_start: 0.7247 (m) cc_final: 0.7023 (m) REVERT: B 262 ASN cc_start: 0.7530 (p0) cc_final: 0.7304 (p0) REVERT: B 384 HIS cc_start: 0.5306 (OUTLIER) cc_final: 0.5012 (p-80) REVERT: B 397 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7391 (mm) REVERT: B 439 ASP cc_start: 0.7614 (t0) cc_final: 0.7265 (t0) REVERT: B 471 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7826 (pp) REVERT: B 487 ARG cc_start: 0.6617 (ptt-90) cc_final: 0.5822 (ptt180) REVERT: B 507 LYS cc_start: 0.7923 (mtmt) cc_final: 0.7674 (mtmm) REVERT: B 511 ARG cc_start: 0.7778 (mtp85) cc_final: 0.7459 (mtt180) REVERT: B 516 VAL cc_start: 0.8410 (m) cc_final: 0.8116 (p) REVERT: B 589 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7832 (tp30) REVERT: B 613 HIS cc_start: 0.7799 (OUTLIER) cc_final: 0.7393 (p90) REVERT: B 631 ARG cc_start: 0.7453 (mtt180) cc_final: 0.6922 (mpp80) REVERT: B 638 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7896 (tm-30) REVERT: B 668 ILE cc_start: 0.8489 (mm) cc_final: 0.8136 (mt) REVERT: B 672 THR cc_start: 0.8109 (p) cc_final: 0.7817 (m) REVERT: B 678 VAL cc_start: 0.8641 (OUTLIER) cc_final: 0.8398 (p) REVERT: B 681 ASP cc_start: 0.8421 (t0) cc_final: 0.7583 (t70) REVERT: B 682 LYS cc_start: 0.8537 (pttp) cc_final: 0.8182 (ttpp) REVERT: B 707 ASN cc_start: 0.8046 (t0) cc_final: 0.7343 (t0) REVERT: B 711 ASP cc_start: 0.7910 (m-30) cc_final: 0.7604 (m-30) REVERT: C 405 GLN cc_start: 0.7927 (pp30) cc_final: 0.7174 (pp30) REVERT: C 409 GLN cc_start: 0.7804 (mt0) cc_final: 0.7517 (mt0) REVERT: C 412 GLU cc_start: 0.7624 (tt0) cc_final: 0.7355 (tt0) REVERT: C 424 SER cc_start: 0.8662 (p) cc_final: 0.8335 (t) REVERT: C 473 ARG cc_start: 0.7290 (tmt170) cc_final: 0.6788 (tmt170) REVERT: C 474 HIS cc_start: 0.8065 (m90) cc_final: 0.7759 (m90) REVERT: C 524 HIS cc_start: 0.8022 (t-90) cc_final: 0.7719 (t-90) REVERT: C 545 MET cc_start: 0.5694 (mtt) cc_final: 0.5333 (mtt) REVERT: D 23 LEU cc_start: 0.8603 (mm) cc_final: 0.8219 (mp) REVERT: D 33 ARG cc_start: 0.8147 (mmm-85) cc_final: 0.7886 (mtp85) REVERT: D 53 LYS cc_start: 0.8827 (mtmt) cc_final: 0.8446 (mtpt) REVERT: D 56 VAL cc_start: 0.8874 (t) cc_final: 0.8646 (p) REVERT: D 66 LEU cc_start: 0.8488 (mt) cc_final: 0.8268 (mt) REVERT: D 77 LYS cc_start: 0.8135 (mttt) cc_final: 0.7833 (mttt) REVERT: D 154 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7336 (mt-10) REVERT: D 177 GLN cc_start: 0.7908 (mt0) cc_final: 0.7224 (tm-30) REVERT: D 180 SER cc_start: 0.8578 (m) cc_final: 0.8278 (p) REVERT: D 194 PRO cc_start: 0.8431 (Cg_endo) cc_final: 0.8231 (Cg_exo) REVERT: D 204 LEU cc_start: 0.8740 (mt) cc_final: 0.8475 (mt) REVERT: D 215 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.8284 (t80) REVERT: D 216 MET cc_start: 0.8606 (tpp) cc_final: 0.8350 (mmp) REVERT: D 229 ASP cc_start: 0.7774 (t70) cc_final: 0.7557 (t70) REVERT: D 247 LYS cc_start: 0.8254 (tttt) cc_final: 0.7960 (tttm) REVERT: D 252 GLU cc_start: 0.7599 (mt-10) cc_final: 0.6941 (mt-10) REVERT: D 261 PHE cc_start: 0.8775 (t80) cc_final: 0.8375 (t80) REVERT: D 275 LYS cc_start: 0.8636 (pttt) cc_final: 0.8205 (ptmm) REVERT: D 277 LYS cc_start: 0.8652 (mttt) cc_final: 0.8360 (mttt) REVERT: D 281 TYR cc_start: 0.8488 (p90) cc_final: 0.8117 (p90) REVERT: D 313 TYR cc_start: 0.8658 (m-80) cc_final: 0.8269 (m-80) REVERT: D 357 SER cc_start: 0.8465 (m) cc_final: 0.8153 (p) REVERT: D 395 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7384 (tm-30) REVERT: D 402 ARG cc_start: 0.6592 (mpt180) cc_final: 0.6227 (mtt90) REVERT: D 404 THR cc_start: 0.8420 (m) cc_final: 0.8053 (p) REVERT: D 450 ASP cc_start: 0.7632 (t0) cc_final: 0.7253 (t0) REVERT: E 37 ILE cc_start: 0.8432 (mm) cc_final: 0.8116 (mm) REVERT: E 40 LYS cc_start: 0.8244 (tppt) cc_final: 0.7950 (mmmm) REVERT: E 66 ASP cc_start: 0.7809 (t0) cc_final: 0.7409 (t0) REVERT: E 81 LEU cc_start: 0.8539 (tp) cc_final: 0.8320 (tp) REVERT: E 90 TYR cc_start: 0.7834 (t80) cc_final: 0.7291 (t80) REVERT: E 94 GLU cc_start: 0.8173 (tp30) cc_final: 0.7918 (tp30) REVERT: E 116 LYS cc_start: 0.8050 (ttmm) cc_final: 0.7719 (tttm) REVERT: E 157 LYS cc_start: 0.8480 (tttt) cc_final: 0.8277 (tttt) REVERT: E 159 MET cc_start: 0.8581 (mmt) cc_final: 0.8229 (mmp) REVERT: E 172 SER cc_start: 0.8628 (t) cc_final: 0.8338 (p) REVERT: E 229 LYS cc_start: 0.8211 (tttt) cc_final: 0.7939 (tttt) REVERT: E 230 GLU cc_start: 0.7618 (tp30) cc_final: 0.7058 (tp30) REVERT: E 233 THR cc_start: 0.7795 (m) cc_final: 0.7536 (p) REVERT: E 250 ILE cc_start: 0.8241 (mt) cc_final: 0.8034 (mm) REVERT: E 328 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7869 (tt) REVERT: E 336 LEU cc_start: 0.8260 (tp) cc_final: 0.7996 (tt) REVERT: E 338 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7555 (mm-30) REVERT: F 106 SER cc_start: 0.8379 (m) cc_final: 0.8150 (t) REVERT: F 113 GLU cc_start: 0.8076 (tt0) cc_final: 0.7848 (tt0) REVERT: F 116 LYS cc_start: 0.8754 (mmmm) cc_final: 0.8433 (mtpp) REVERT: F 139 LYS cc_start: 0.8821 (mttt) cc_final: 0.8573 (mtpp) REVERT: F 146 ARG cc_start: 0.8540 (tmm-80) cc_final: 0.8142 (ttt180) REVERT: F 178 MET cc_start: 0.8010 (mmm) cc_final: 0.7760 (mmt) REVERT: F 197 ASP cc_start: 0.8127 (t0) cc_final: 0.7826 (t0) REVERT: F 208 ASP cc_start: 0.7872 (t70) cc_final: 0.7433 (t70) REVERT: F 217 VAL cc_start: 0.8695 (t) cc_final: 0.8425 (p) REVERT: G 16 MET cc_start: 0.8849 (mmm) cc_final: 0.8480 (mmp) REVERT: G 25 GLU cc_start: 0.7629 (pt0) cc_final: 0.7405 (pt0) REVERT: K 118 MET cc_start: 0.7145 (tpp) cc_final: 0.6364 (tpp) REVERT: K 135 LYS cc_start: 0.8799 (tttt) cc_final: 0.8462 (tttt) REVERT: K 139 ILE cc_start: 0.8301 (mm) cc_final: 0.7582 (tp) REVERT: K 151 LYS cc_start: 0.7610 (mttt) cc_final: 0.7250 (mttt) REVERT: K 163 LYS cc_start: 0.7450 (mttt) cc_final: 0.7201 (mttt) REVERT: K 164 PHE cc_start: 0.8490 (p90) cc_final: 0.8117 (p90) REVERT: K 188 LYS cc_start: 0.8336 (tttt) cc_final: 0.7932 (tmtt) REVERT: K 201 GLU cc_start: 0.7546 (tp30) cc_final: 0.7159 (tp30) REVERT: K 209 GLU cc_start: 0.8315 (tp30) cc_final: 0.7652 (tp30) REVERT: K 213 LYS cc_start: 0.8407 (tptt) cc_final: 0.7658 (tptt) REVERT: K 245 GLU cc_start: 0.8085 (mp0) cc_final: 0.7401 (mp0) REVERT: K 250 GLU cc_start: 0.7036 (tp30) cc_final: 0.6617 (tp30) REVERT: K 252 LEU cc_start: 0.7379 (mt) cc_final: 0.6774 (mt) REVERT: K 258 ARG cc_start: 0.7479 (ttp-170) cc_final: 0.6882 (ttp-170) REVERT: K 263 MET cc_start: 0.4946 (OUTLIER) cc_final: 0.4341 (ptt) outliers start: 89 outliers final: 68 residues processed: 842 average time/residue: 0.4231 time to fit residues: 523.1100 Evaluate side-chains 863 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 783 time to evaluate : 2.634 ------------------------------------------------------------------------------- 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 443 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 629 HIS 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 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 235 GLU Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 384 HIS 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 471 LEU Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 499 ASN 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 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 B residue 702 THR 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 446 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 127 LYS Chi-restraints excluded: chain D residue 178 LEU 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 353 GLN Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain E residue 12 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 139 CYS Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 152 LYS Chi-restraints excluded: chain F residue 173 GLN Chi-restraints excluded: chain F residue 248 HIS 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 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 182 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 93 optimal weight: 0.0470 chunk 260 optimal weight: 6.9990 chunk 268 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 225 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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** A 677 GLN ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 509 GLN E 50 HIS E 324 HIS ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.149489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.122217 restraints weight = 38429.700| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.54 r_work: 0.3428 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24160 Z= 0.149 Angle : 0.718 19.274 32876 Z= 0.350 Chirality : 0.044 0.223 3677 Planarity : 0.005 0.069 4022 Dihedral : 14.255 179.528 3593 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.66 % Allowed : 25.41 % Favored : 70.93 % 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: 0.09 (0.16), residues: 2776 helix: 1.09 (0.14), residues: 1350 sheet: -0.12 (0.27), residues: 361 loop : -1.18 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 342 HIS 0.014 0.001 HIS B 613 PHE 0.024 0.001 PHE C 475 TYR 0.046 0.002 TYR C 533 ARG 0.014 0.001 ARG A 325 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 1083) hydrogen bonds : angle 4.23706 ( 3076) metal coordination : bond 0.00804 ( 28) metal coordination : angle 5.11422 ( 45) covalent geometry : bond 0.00338 (24132) covalent geometry : angle 0.69327 (32831) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14470.67 seconds wall clock time: 249 minutes 28.01 seconds (14968.01 seconds total)