Starting phenix.real_space_refine on Mon Feb 19 02:48:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebu_27998/02_2024/8ebu_27998_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebu_27998/02_2024/8ebu_27998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebu_27998/02_2024/8ebu_27998.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebu_27998/02_2024/8ebu_27998.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebu_27998/02_2024/8ebu_27998_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebu_27998/02_2024/8ebu_27998_updated.pdb" } 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 Residue "A TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 109": "NH1" <-> "NH2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 520": "NH1" <-> "NH2" Residue "A TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 574": "NH1" <-> "NH2" Residue "A TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 676": "NH1" <-> "NH2" Residue "A ARG 678": "NH1" <-> "NH2" Residue "A TYR 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 30": "NH1" <-> "NH2" Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B ARG 112": "NH1" <-> "NH2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 166": "NH1" <-> "NH2" Residue "B TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 334": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 378": "NH1" <-> "NH2" Residue "B ARG 424": "NH1" <-> "NH2" Residue "B ARG 487": "NH1" <-> "NH2" Residue "B ARG 497": "NH1" <-> "NH2" Residue "B ARG 592": "NH1" <-> "NH2" Residue "B ARG 669": "NH1" <-> "NH2" Residue "B ARG 695": "NH1" <-> "NH2" Residue "B PHE 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 911": "OE1" <-> "OE2" Residue "K TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 211": "NH1" <-> "NH2" Residue "K ARG 237": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23543 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4882 Classifications: {'peptide': 604} Link IDs: {'PTRANS': 24, 'TRANS': 579} Chain breaks: 2 Chain: "B" Number of atoms: 5457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5457 Classifications: {'peptide': 677} Link IDs: {'PTRANS': 29, 'TRANS': 647} Chain breaks: 1 Chain: "C" Number of atoms: 1444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1444 Classifications: {'peptide': 179} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 172} Chain breaks: 1 Chain: "D" Number of atoms: 3483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3483 Classifications: {'peptide': 434} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 412} Chain breaks: 1 Chain: "E" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2989 Classifications: {'peptide': 380} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 361} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2034 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 1 Chain: "G" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "H" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 303 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain breaks: 1 Chain: "K" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1450 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 166} Chain: "L" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 496 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "M" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 469 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5825 SG CYS B 116 55.952 39.988 41.090 1.00125.15 S ATOM 6134 SG CYS B 155 52.333 36.397 36.791 1.00126.77 S ATOM 5965 SG CYS B 134 53.794 42.600 35.650 1.00119.97 S ATOM 6423 SG CYS B 190 49.618 41.350 39.627 1.00118.76 S ATOM 17933 SG CYS E 345 41.827 61.151 132.535 1.00 53.91 S ATOM 17955 SG CYS E 348 43.604 64.300 133.735 1.00 43.62 S ATOM 18112 SG CYS E 368 41.879 64.252 130.312 1.00 45.52 S ATOM 18133 SG CYS E 371 45.038 62.236 130.910 1.00 40.96 S ATOM 18053 SG CYS E 360 40.833 50.582 126.921 1.00 57.69 S ATOM 18071 SG CYS E 363 41.126 50.067 130.685 1.00 61.60 S ATOM 18220 SG CYS E 382 43.731 52.125 128.803 1.00 43.88 S ATOM 18237 SG CYS E 385 43.624 48.395 128.291 1.00 42.71 S ATOM 17497 SG CYS E 291 80.132 38.822 120.915 1.00 50.76 S ATOM 17519 SG CYS E 294 83.655 37.423 120.505 1.00 63.45 S ATOM 17608 SG CYS E 305 82.372 39.983 118.017 1.00 52.10 S ATOM 17631 SG CYS E 308 80.907 36.507 118.037 1.00 57.40 S ATOM 20133 SG CYS F 268 60.437 38.234 111.588 1.00 32.82 S ATOM 20152 SG CYS F 271 57.912 40.031 113.751 1.00 35.10 S ATOM 20237 SG CYS F 282 57.928 36.223 113.703 1.00 69.28 S ATOM 20257 SG CYS F 285 56.763 38.118 110.659 1.00 68.43 S ATOM 20025 SG CYS F 255 62.252 34.521 123.735 1.00 47.32 S ATOM 20042 SG CYS F 257 59.734 31.713 123.202 1.00 56.61 S ATOM 20191 SG CYS F 276 63.496 30.887 123.579 1.00 49.54 S ATOM 21147 SG CYS K 105 44.962 102.777 24.284 1.00103.00 S ATOM 21171 SG CYS K 108 44.497 102.477 20.518 1.00 98.85 S ATOM 21319 SG CYS K 126 47.124 100.350 22.324 1.00 98.15 S ATOM 21341 SG CYS K 129 47.618 104.079 21.816 1.00103.44 S Time building chain proxies: 12.40, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.37 Conformation dependent library (CDL) restraints added in 4.8 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... running ksdssp... Secondary structure from input PDB file: 116 helices and 21 sheets defined 44.5% alpha, 9.6% beta 20 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 10.25 Creating SS restraints... Processing helix chain 'A' and resid 93 through 103 removed outlier: 3.518A pdb=" N ALA A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 153 through 161 Processing helix chain 'A' and resid 182 through 189 removed outlier: 3.750A pdb=" N GLN A 186 " --> pdb=" O PRO A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 196 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 192 through 196' Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 274 through 286 removed outlier: 3.615A pdb=" N ILE A 277 " --> pdb=" O GLN A 274 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLU A 278 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A 279 " --> pdb=" O MET A 276 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 280 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS A 284 " --> pdb=" O GLN A 281 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE A 285 " --> pdb=" O LYS A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 327 Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 370 through 381 Processing helix chain 'A' and resid 421 through 432 removed outlier: 3.881A pdb=" N THR A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 446 Processing helix chain 'A' and resid 452 through 457 removed outlier: 3.838A pdb=" N THR A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 removed outlier: 3.569A pdb=" N LEU A 483 " --> pdb=" O LEU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 498 Processing helix chain 'A' and resid 516 through 524 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 531 through 535 Processing helix chain 'A' and resid 538 through 553 Processing helix chain 'A' and resid 565 through 575 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 587 through 597 removed outlier: 4.062A pdb=" N LYS A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 642 Processing helix chain 'A' and resid 668 through 676 Processing helix chain 'A' and resid 678 through 683 Processing helix chain 'A' and resid 706 through 716 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 19 through 34 Processing helix chain 'B' and resid 48 through 62 Processing helix chain 'B' and resid 77 through 98 Processing helix chain 'B' and resid 119 through 122 No H-bonds generated for 'chain 'B' and resid 119 through 122' Processing helix chain 'B' and resid 127 through 137 removed outlier: 4.676A pdb=" N ASP B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLY B 132 " --> pdb=" O LYS B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 146 Processing helix chain 'B' and resid 157 through 164 removed outlier: 4.570A pdb=" N ALA B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 187 Processing helix chain 'B' and resid 191 through 198 Processing helix chain 'B' and resid 209 through 213 removed outlier: 4.077A pdb=" N LEU B 213 " --> pdb=" O HIS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 221 removed outlier: 3.913A 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 239 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 253 through 271 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) Processing helix chain 'B' and resid 327 through 330 No H-bonds generated for 'chain 'B' and resid 327 through 330' Processing helix chain 'B' and resid 336 through 345 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 356 through 364 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) Processing helix chain 'B' and resid 370 through 386 removed outlier: 4.026A pdb=" N ALA B 376 " --> pdb=" O ARG B 373 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG B 380 " --> pdb=" O GLU B 377 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU B 382 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LEU B 383 " --> pdb=" O ARG B 380 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS B 384 " --> pdb=" O SER B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 409 Processing helix chain 'B' and resid 442 through 448 Proline residue: B 446 - end of helix No H-bonds generated for 'chain 'B' and resid 442 through 448' Processing helix chain 'B' and resid 467 through 470 No H-bonds generated for 'chain 'B' and resid 467 through 470' Processing helix chain 'B' and resid 508 through 510 No H-bonds generated for 'chain 'B' and resid 508 through 510' Processing helix chain 'B' and resid 514 through 528 Processing helix chain 'B' and resid 542 through 554 Processing helix chain 'B' and resid 558 through 564 removed outlier: 3.555A pdb=" N ASN B 564 " --> pdb=" O ASN B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 589 Processing helix chain 'B' and resid 603 through 607 Processing helix chain 'B' and resid 633 through 643 Processing helix chain 'B' and resid 648 through 667 removed outlier: 4.147A pdb=" N ARG B 666 " --> pdb=" O GLN B 662 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ALA B 667 " --> pdb=" O CYS B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 685 Processing helix chain 'B' and resid 687 through 692 removed outlier: 4.325A pdb=" N LYS B 692 " --> pdb=" O ASP B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 698 No H-bonds generated for 'chain 'B' and resid 695 through 698' Processing helix chain 'B' and resid 710 through 724 Processing helix chain 'C' and resid 124 through 132 Processing helix chain 'C' and resid 139 through 146 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 399 through 412 Processing helix chain 'C' and resid 424 through 434 Processing helix chain 'C' and resid 455 through 478 Processing helix chain 'C' and resid 484 through 515 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 521 through 546 removed outlier: 4.340A pdb=" N ILE C 525 " --> pdb=" O LEU C 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 28 through 36 removed outlier: 3.754A pdb=" N GLY D 36 " --> pdb=" O ASP D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 47 Processing helix chain 'D' and resid 50 through 58 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 72 Processing helix chain 'D' and resid 78 through 93 removed outlier: 4.448A pdb=" N LYS D 81 " --> pdb=" O GLU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 122 Processing helix chain 'D' and resid 145 through 164 Processing helix chain 'D' and resid 173 through 182 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 208 through 226 removed outlier: 4.630A pdb=" N GLN D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N SER D 225 " --> pdb=" O GLN D 221 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG D 226 " --> pdb=" O THR D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 241 Processing helix chain 'D' and resid 256 through 268 Processing helix chain 'D' and resid 285 through 290 Processing helix chain 'D' and resid 322 through 329 Processing helix chain 'D' and resid 348 through 356 Processing helix chain 'D' and resid 361 through 370 Processing helix chain 'D' and resid 385 through 398 removed outlier: 4.234A pdb=" N ARG D 398 " --> pdb=" O TRP D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 428 Processing helix chain 'D' and resid 445 through 461 removed outlier: 4.343A 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 18 through 20 No H-bonds generated for 'chain 'E' and resid 18 through 20' Processing helix chain 'E' and resid 30 through 41 Processing helix chain 'E' and resid 69 through 72 Processing helix chain 'E' and resid 80 through 98 Processing helix chain 'E' and resid 124 through 136 removed outlier: 4.369A pdb=" N ASP E 136 " --> pdb=" O LYS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 156 Processing helix chain 'E' and resid 182 through 191 Processing helix chain 'E' and resid 206 through 215 Processing helix chain 'E' and resid 225 through 236 Processing helix chain 'E' and resid 273 through 277 removed outlier: 4.008A pdb=" N ASP E 277 " --> pdb=" O MET E 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 273 through 277' Processing helix chain 'E' and resid 315 through 325 removed outlier: 4.453A pdb=" N SER E 321 " --> pdb=" O HIS E 317 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR E 322 " --> pdb=" O LEU E 318 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N HIS E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N HIS E 324 " --> pdb=" O ARG E 320 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU E 325 " --> pdb=" O SER E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 377 Processing helix chain 'E' and resid 383 through 386 No H-bonds generated for 'chain 'E' and resid 383 through 386' Processing helix chain 'F' and resid 19 through 28 Processing helix chain 'F' and resid 34 through 51 Processing helix chain 'F' and resid 102 through 120 Processing helix chain 'F' and resid 133 through 150 Processing helix chain 'F' and resid 174 through 186 Processing helix chain 'F' and resid 201 through 210 Processing helix chain 'F' and resid 220 through 230 removed outlier: 4.570A pdb=" N LEU F 224 " --> pdb=" O PRO F 221 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL F 230 " --> pdb=" O LEU F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 240 removed outlier: 3.888A pdb=" N GLN F 240 " --> pdb=" O ASP F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 286 No H-bonds generated for 'chain 'F' and resid 284 through 286' Processing helix chain 'G' and resid 14 through 26 Processing helix chain 'G' and resid 47 through 63 removed outlier: 3.743A pdb=" N VAL G 50 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ASN G 51 " --> pdb=" O GLU G 48 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL G 52 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU G 53 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP G 62 " --> pdb=" O GLU G 59 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN G 63 " --> pdb=" O LEU G 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 890 through 901 removed outlier: 3.588A pdb=" N ALA H 894 " --> pdb=" O THR H 890 " (cutoff:3.500A) Processing helix chain 'H' and resid 909 through 915 Processing helix chain 'H' and resid 936 through 938 No H-bonds generated for 'chain 'H' and resid 936 through 938' Processing helix chain 'K' and resid 116 through 121 Processing helix chain 'K' and resid 141 through 148 Processing helix chain 'K' and resid 152 through 156 Processing helix chain 'K' and resid 183 through 194 Processing helix chain 'K' and resid 197 through 231 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= A, 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= B, 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= C, first strand: chain 'A' and resid 389 through 392 removed outlier: 6.839A pdb=" N VAL A 405 " --> pdb=" O CYS A 390 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N PHE A 392 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE A 407 " --> 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: 6.579A pdb=" N GLY A 336 " --> pdb=" O GLY A 465 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N THR A 467 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE A 338 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL A 339 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU A 490 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 688 through 690 removed outlier: 3.581A pdb=" N LYS A 688 " --> pdb=" O CYS A 507 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ALA A 657 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N ALA A 508 " --> pdb=" O ALA A 657 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE A 659 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N VAL A 510 " --> pdb=" O PHE A 659 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N SER A 661 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N CYS A 512 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 663 " --> pdb=" O CYS A 512 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 623 " --> pdb=" O PHE A 658 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 558 through 561 Processing sheet with id= F, first strand: chain 'B' and resid 2 through 5 Processing sheet with id= G, first strand: chain 'B' and resid 38 through 41 removed outlier: 3.656A pdb=" N SER B 458 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 69 through 71 Processing sheet with id= I, first strand: chain 'B' and resid 106 through 108 removed outlier: 6.898A pdb=" N VAL B 204 " --> pdb=" O LEU B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 249 through 251 removed outlier: 3.774A pdb=" N VAL B 249 " --> pdb=" O PHE B 435 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 436 " --> pdb=" O THR B 415 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR B 415 " --> pdb=" O SER B 436 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 490 through 495 removed outlier: 8.065A pdb=" N GLY B 675 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N MET B 493 " --> pdb=" O GLY B 675 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N MET B 677 " --> pdb=" O MET B 493 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ILE B 495 " --> pdb=" O MET B 677 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE B 679 " --> pdb=" O ILE B 495 " (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= L, first strand: chain 'D' and resid 96 through 100 removed outlier: 3.668A pdb=" N ILE D 109 " --> pdb=" O HIS D 97 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 248 through 250 Processing sheet with id= N, first strand: chain 'D' and resid 307 through 310 removed outlier: 3.768A pdb=" N ARG D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLN D 345 " --> pdb=" O MET D 334 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N MET D 334 " --> pdb=" O GLN D 345 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 407 through 409 removed outlier: 3.575A pdb=" N MET D 441 " --> pdb=" O TYR D 409 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 113 through 118 removed outlier: 6.714A pdb=" N ILE E 106 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N SER E 164 " --> pdb=" O HIS E 60 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N TYR E 62 " --> pdb=" O SER E 164 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLU E 166 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N VAL E 64 " --> pdb=" O GLU E 166 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU E 168 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ASP E 66 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ILE E 170 " --> pdb=" O ASP E 66 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 332 through 335 Processing sheet with id= R, first strand: chain 'F' and resid 67 through 71 removed outlier: 6.432A pdb=" N VAL F 59 " --> pdb=" O LEU F 70 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLU F 156 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU F 10 " --> pdb=" O GLU F 156 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS F 158 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL F 12 " --> pdb=" O LYS F 158 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ARG F 160 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL F 14 " --> pdb=" O ARG F 160 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU F 162 " --> pdb=" O VAL F 14 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ASP F 16 " --> pdb=" O LEU F 162 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE F 164 " --> pdb=" O ASP F 16 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU F 190 " --> pdb=" O ILE F 161 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL F 163 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ASP F 192 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LYS F 165 " --> pdb=" O ASP F 192 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N CYS F 194 " --> pdb=" O LYS F 165 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 8 through 11 removed outlier: 3.651A pdb=" N GLN G 36 " --> pdb=" O PHE G 44 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'K' and resid 138 through 140 Processing sheet with id= U, first strand: chain 'K' and resid 256 through 260 848 hydrogen bonds defined for protein. 2364 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: 8.26 Time building geometry restraints manager: 11.20 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: 73.68 - 85.75: 12 85.75 - 97.82: 0 97.82 - 109.89: 3211 109.89 - 121.96: 24784 121.96 - 134.04: 4824 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: 1200 2.73 - 3.27: 23784 3.27 - 3.82: 39763 3.82 - 4.36: 46985 4.36 - 4.90: 78880 Nonbonded interactions: 190612 Sorted by model distance: nonbonded pdb=" O PHE A 378 " pdb=" OG SER A 382 " model vdw 2.188 2.440 nonbonded pdb=" O ASP A 309 " pdb=" OG1 THR A 383 " model vdw 2.213 2.440 nonbonded pdb=" OG SER E 243 " pdb=" O ALA F 288 " model vdw 2.214 2.440 nonbonded pdb=" OG1 THR B 482 " pdb=" OE2 GLU B 699 " model vdw 2.222 2.440 nonbonded pdb=" OG1 THR B 76 " pdb=" OE1 GLU B 79 " model vdw 2.223 2.440 ... (remaining 190607 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.350 Check model and map are aligned: 0.350 Set scattering table: 0.240 Process input model: 79.770 Find NCS groups from input model: 0.910 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24132 Z= 0.140 Angle : 0.492 8.224 32831 Z= 0.287 Chirality : 0.038 0.145 3677 Planarity : 0.003 0.052 4022 Dihedral : 13.040 175.786 9147 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.02 % Allowed : 6.23 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.17), residues: 2776 helix: 1.86 (0.15), residues: 1288 sheet: 0.52 (0.29), residues: 365 loop : -0.99 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 511 HIS 0.005 0.001 HIS B 613 PHE 0.011 0.001 PHE A 659 TYR 0.013 0.001 TYR A 534 ARG 0.003 0.000 ARG A 676 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1001 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 926 time to evaluate : 2.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 0.4247 time to fit residues: 600.7920 Evaluate side-chains 808 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 769 time to evaluate : 2.878 ------------------------------------------------------------------------------- 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: 0.3980 chunk 212 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 143 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 254 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN A 459 GLN ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 ASN A 668 GLN A 677 GLN B 210 HIS ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN C 474 HIS ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN D 117 ASN ** D 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN D 202 GLN ** D 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 GLN D 363 GLN E 332 GLN ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN ** F 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 HIS ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24132 Z= 0.254 Angle : 0.602 8.684 32831 Z= 0.311 Chirality : 0.043 0.196 3677 Planarity : 0.004 0.050 4022 Dihedral : 14.362 179.761 3646 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.74 % Allowed : 15.60 % Favored : 79.65 % 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: 0.41 (0.16), residues: 2776 helix: 1.44 (0.15), residues: 1290 sheet: 0.08 (0.27), residues: 375 loop : -1.05 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 511 HIS 0.023 0.001 HIS C 474 PHE 0.028 0.002 PHE D 215 TYR 0.022 0.002 TYR A 534 ARG 0.007 0.001 ARG D 115 *********************** 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 943 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 825 time to evaluate : 2.708 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: 0.6648 (m-30) cc_final: 0.6373 (m-30) REVERT: A 117 LYS cc_start: 0.8007 (tttt) cc_final: 0.7442 (ttpt) REVERT: A 150 ASP cc_start: 0.7094 (t0) cc_final: 0.6879 (t0) REVERT: A 157 LYS cc_start: 0.8211 (tppt) cc_final: 0.7918 (ttmm) REVERT: A 165 LYS cc_start: 0.7821 (mttm) cc_final: 0.7570 (mttp) REVERT: A 271 GLU cc_start: 0.7021 (pp20) cc_final: 0.4940 (tm-30) REVERT: A 282 LYS cc_start: 0.8676 (tttt) cc_final: 0.8169 (ttmm) REVERT: A 296 ASP cc_start: 0.6048 (t0) cc_final: 0.5738 (t0) REVERT: A 308 ILE cc_start: 0.7531 (tp) cc_final: 0.7278 (tt) REVERT: A 309 ASP cc_start: 0.5743 (p0) cc_final: 0.5148 (p0) REVERT: A 316 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7932 (pp) REVERT: A 334 ARG cc_start: 0.7355 (ptp-170) cc_final: 0.7121 (ptp-170) REVERT: A 375 LYS cc_start: 0.8361 (ttpt) cc_final: 0.8047 (ttmm) REVERT: A 383 THR cc_start: 0.8387 (p) cc_final: 0.8185 (p) REVERT: A 487 LYS cc_start: 0.8223 (ttmt) cc_final: 0.8012 (ttpp) REVERT: A 506 GLN cc_start: 0.8132 (tt0) cc_final: 0.7741 (tt0) REVERT: A 537 ASN cc_start: 0.7639 (t0) cc_final: 0.7406 (t0) REVERT: A 570 GLU cc_start: 0.5916 (OUTLIER) cc_final: 0.5603 (pm20) REVERT: A 625 GLN cc_start: 0.7472 (pt0) cc_final: 0.6283 (tt0) REVERT: A 642 ARG cc_start: 0.7684 (mtt-85) cc_final: 0.7387 (mmt-90) REVERT: A 658 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.7393 (p90) REVERT: A 659 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.6824 (p90) REVERT: B 27 GLU cc_start: 0.7086 (tm-30) cc_final: 0.6818 (tm-30) REVERT: B 28 LEU cc_start: 0.7363 (tp) cc_final: 0.7065 (tp) REVERT: B 53 LEU cc_start: 0.8057 (mt) cc_final: 0.7260 (mm) REVERT: B 57 MET cc_start: 0.7214 (mmt) cc_final: 0.6853 (mmt) REVERT: B 61 ARG cc_start: 0.6576 (tpm170) cc_final: 0.5920 (tpm170) REVERT: B 91 LEU cc_start: 0.7292 (OUTLIER) cc_final: 0.7082 (mm) REVERT: B 176 ASN cc_start: 0.5842 (t0) cc_final: 0.5540 (t0) REVERT: B 244 ILE cc_start: 0.8513 (tp) cc_final: 0.8197 (tp) REVERT: B 338 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6377 (mp0) REVERT: B 469 LYS cc_start: 0.7359 (ptpt) cc_final: 0.7072 (ptpp) REVERT: B 514 ILE cc_start: 0.8293 (tp) cc_final: 0.8047 (mm) REVERT: B 583 LYS cc_start: 0.7558 (ptpp) cc_final: 0.7246 (mtmm) REVERT: B 589 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6824 (mm-30) REVERT: B 603 LYS cc_start: 0.7196 (ptmm) cc_final: 0.6921 (ptmm) REVERT: B 668 ILE cc_start: 0.8029 (mm) cc_final: 0.7685 (mt) REVERT: B 672 THR cc_start: 0.7793 (p) cc_final: 0.7554 (m) REVERT: B 682 LYS cc_start: 0.7967 (pttp) cc_final: 0.7642 (ttpp) REVERT: C 424 SER cc_start: 0.7932 (p) cc_final: 0.7675 (p) REVERT: C 441 MET cc_start: 0.5259 (mmm) cc_final: 0.4942 (mmt) REVERT: C 442 GLN cc_start: 0.2612 (OUTLIER) cc_final: 0.1583 (pt0) REVERT: C 524 HIS cc_start: 0.7218 (t-170) cc_final: 0.6769 (t-90) REVERT: C 528 MET cc_start: 0.7253 (mtp) cc_final: 0.6879 (mtm) REVERT: C 529 LEU cc_start: 0.8805 (mt) cc_final: 0.7923 (mt) REVERT: C 545 MET cc_start: 0.5347 (mtt) cc_final: 0.5122 (mtt) REVERT: D 53 LYS cc_start: 0.8827 (mtmt) cc_final: 0.8417 (mtpp) REVERT: D 57 MET cc_start: 0.8079 (mmm) cc_final: 0.7851 (mmm) REVERT: D 76 LYS cc_start: 0.6930 (mttm) cc_final: 0.6726 (mttt) REVERT: D 89 LEU cc_start: 0.8369 (tp) cc_final: 0.8162 (tt) REVERT: D 113 ILE cc_start: 0.7492 (OUTLIER) cc_final: 0.7284 (mp) REVERT: D 117 ASN cc_start: 0.7271 (m-40) cc_final: 0.6997 (m-40) REVERT: D 120 ILE cc_start: 0.8340 (mt) cc_final: 0.8089 (mm) REVERT: D 156 TRP cc_start: 0.8637 (t-100) cc_final: 0.8249 (t-100) REVERT: D 177 GLN cc_start: 0.7704 (mt0) cc_final: 0.7170 (tm-30) REVERT: D 180 SER cc_start: 0.8406 (m) cc_final: 0.7943 (p) REVERT: D 216 MET cc_start: 0.8033 (tpp) cc_final: 0.7785 (mmp) REVERT: D 243 SER cc_start: 0.8759 (m) cc_final: 0.8282 (p) REVERT: D 261 PHE cc_start: 0.8668 (t80) cc_final: 0.8381 (t80) REVERT: D 263 GLN cc_start: 0.7186 (mm-40) cc_final: 0.6762 (mm-40) REVERT: D 267 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7159 (mt-10) REVERT: D 312 ASN cc_start: 0.8141 (p0) cc_final: 0.7927 (p0) REVERT: D 313 TYR cc_start: 0.8173 (m-80) cc_final: 0.7959 (m-80) REVERT: D 365 ILE cc_start: 0.8349 (mt) cc_final: 0.8138 (mm) REVERT: D 395 GLU cc_start: 0.7042 (tm-30) cc_final: 0.6808 (tm-30) REVERT: D 402 ARG cc_start: 0.6383 (mpt180) cc_final: 0.5905 (mtt90) REVERT: D 407 VAL cc_start: 0.8254 (t) cc_final: 0.7995 (m) REVERT: D 439 ARG cc_start: 0.8206 (mtm180) cc_final: 0.7786 (mtm180) REVERT: E 37 ILE cc_start: 0.8294 (mm) cc_final: 0.8032 (mm) REVERT: E 38 LEU cc_start: 0.8042 (mt) cc_final: 0.7740 (mt) REVERT: E 40 LYS cc_start: 0.8108 (tppt) cc_final: 0.7892 (mmmm) REVERT: E 137 MET cc_start: 0.7336 (ttp) cc_final: 0.7057 (ttp) REVERT: E 172 SER cc_start: 0.7989 (t) cc_final: 0.7761 (p) REVERT: E 226 SER cc_start: 0.7628 (p) cc_final: 0.7394 (p) REVERT: E 229 LYS cc_start: 0.7596 (tttt) cc_final: 0.7369 (tttt) REVERT: E 251 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7506 (mmm160) REVERT: E 328 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7431 (tt) REVERT: E 336 LEU cc_start: 0.8253 (tp) cc_final: 0.8051 (tt) REVERT: F 39 ASP cc_start: 0.6561 (m-30) cc_final: 0.6285 (m-30) REVERT: F 113 GLU cc_start: 0.7217 (tt0) cc_final: 0.6941 (tt0) REVERT: F 116 LYS cc_start: 0.8728 (mmmm) cc_final: 0.8268 (mtpp) REVERT: F 139 LYS cc_start: 0.8795 (mttt) cc_final: 0.8463 (mtmt) REVERT: F 146 ARG cc_start: 0.8591 (tmm-80) cc_final: 0.8028 (ttt180) REVERT: F 178 MET cc_start: 0.7627 (mmm) cc_final: 0.7325 (mmp) REVERT: F 208 ASP cc_start: 0.6304 (t70) cc_final: 0.5966 (t0) REVERT: F 237 GLN cc_start: 0.7578 (mt0) cc_final: 0.7295 (mt0) REVERT: F 240 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7424 (mp10) REVERT: G 23 LEU cc_start: 0.8798 (mt) cc_final: 0.8591 (mp) REVERT: G 60 LEU cc_start: 0.8641 (tp) cc_final: 0.8409 (tt) REVERT: K 151 LYS cc_start: 0.7951 (mttt) cc_final: 0.7570 (mttt) REVERT: K 163 LYS cc_start: 0.7145 (mttt) cc_final: 0.6926 (mttt) REVERT: K 179 LYS cc_start: 0.7919 (mttt) cc_final: 0.7699 (mtmm) REVERT: K 209 GLU cc_start: 0.7671 (tp30) cc_final: 0.7214 (tp30) REVERT: K 213 LYS cc_start: 0.7949 (tptt) cc_final: 0.7529 (tptt) outliers start: 118 outliers final: 62 residues processed: 887 average time/residue: 0.4075 time to fit residues: 529.0659 Evaluate side-chains 857 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 784 time to evaluate : 2.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 715 LYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 84 ILE 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 338 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 386 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 500 ASP Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 428 SER 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 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 284 THR Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 139 CYS Chi-restraints excluded: chain E residue 145 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 E residue 370 ASP Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 192 ASP 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 255 CYS Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 141 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 173 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 254 optimal weight: 0.0570 chunk 275 optimal weight: 9.9990 chunk 226 optimal weight: 0.0570 chunk 252 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 ASN A 683 GLN B 92 ASN B 210 HIS B 237 HIS B 238 ASN B 241 ASN ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 ASN ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 HIS D 211 GLN D 260 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 HIS E 332 GLN ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN F 187 GLN ** F 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 54 GLN K 119 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24132 Z= 0.188 Angle : 0.583 12.710 32831 Z= 0.297 Chirality : 0.042 0.177 3677 Planarity : 0.004 0.062 4022 Dihedral : 14.312 179.323 3626 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.62 % Allowed : 18.82 % Favored : 76.56 % 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: 0.33 (0.16), residues: 2776 helix: 1.39 (0.15), residues: 1299 sheet: 0.05 (0.27), residues: 374 loop : -1.13 (0.18), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 511 HIS 0.010 0.001 HIS A 71 PHE 0.023 0.001 PHE F 278 TYR 0.040 0.001 TYR C 533 ARG 0.007 0.000 ARG A 325 *********************** 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 909 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 794 time to evaluate : 2.749 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: 0.6686 (m-30) cc_final: 0.6415 (m-30) REVERT: A 117 LYS cc_start: 0.7790 (tttt) cc_final: 0.7540 (ttpt) REVERT: A 157 LYS cc_start: 0.8169 (tppt) cc_final: 0.7917 (ttmm) REVERT: A 165 LYS cc_start: 0.7835 (mttm) cc_final: 0.7558 (mttp) REVERT: A 273 LYS cc_start: 0.7845 (mttt) cc_final: 0.7613 (mttt) REVERT: A 282 LYS cc_start: 0.8539 (tttt) cc_final: 0.8157 (ttmm) REVERT: A 296 ASP cc_start: 0.6205 (t0) cc_final: 0.5957 (t0) REVERT: A 316 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.8019 (pp) REVERT: A 334 ARG cc_start: 0.7360 (ptp-170) cc_final: 0.7029 (ptp-170) REVERT: A 506 GLN cc_start: 0.8143 (tt0) cc_final: 0.7833 (tt0) REVERT: A 525 ILE cc_start: 0.8502 (tp) cc_final: 0.8123 (pt) REVERT: A 537 ASN cc_start: 0.7606 (t0) cc_final: 0.7351 (t0) REVERT: A 625 GLN cc_start: 0.6960 (pt0) cc_final: 0.6519 (tt0) REVERT: A 658 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7356 (p90) REVERT: A 659 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.6742 (p90) REVERT: B 12 PHE cc_start: 0.6704 (t80) cc_final: 0.6290 (m-80) REVERT: B 25 MET cc_start: 0.6094 (mmm) cc_final: 0.5854 (mmm) REVERT: B 53 LEU cc_start: 0.8145 (mt) cc_final: 0.7400 (mm) REVERT: B 57 MET cc_start: 0.7136 (mmt) cc_final: 0.6834 (mmt) REVERT: B 92 ASN cc_start: 0.7441 (m-40) cc_final: 0.7050 (m-40) REVERT: B 122 THR cc_start: 0.7135 (OUTLIER) cc_final: 0.6867 (p) REVERT: B 133 LYS cc_start: 0.7468 (mtmt) cc_final: 0.7200 (mttp) REVERT: B 176 ASN cc_start: 0.5981 (t0) cc_final: 0.5713 (t0) REVERT: B 244 ILE cc_start: 0.8478 (tp) cc_final: 0.8214 (tp) REVERT: B 342 TRP cc_start: 0.6877 (t-100) cc_final: 0.6475 (t-100) REVERT: B 469 LYS cc_start: 0.7321 (ptpt) cc_final: 0.7045 (ptpp) REVERT: B 583 LYS cc_start: 0.7537 (ptpp) cc_final: 0.7223 (mtmm) REVERT: B 668 ILE cc_start: 0.8088 (mm) cc_final: 0.7655 (mt) REVERT: B 672 THR cc_start: 0.7811 (p) cc_final: 0.7450 (m) REVERT: B 682 LYS cc_start: 0.7905 (pttp) cc_final: 0.7631 (ttpp) REVERT: C 405 GLN cc_start: 0.7699 (pp30) cc_final: 0.6238 (pp30) REVERT: C 409 GLN cc_start: 0.7341 (mt0) cc_final: 0.6886 (mt0) REVERT: C 441 MET cc_start: 0.5513 (mmm) cc_final: 0.5285 (mmt) REVERT: C 442 GLN cc_start: 0.2622 (OUTLIER) cc_final: 0.1571 (pt0) REVERT: C 475 PHE cc_start: 0.8512 (t80) cc_final: 0.7726 (t80) REVERT: C 524 HIS cc_start: 0.7221 (t-170) cc_final: 0.6987 (t-90) REVERT: C 529 LEU cc_start: 0.8885 (mt) cc_final: 0.8673 (mt) REVERT: C 545 MET cc_start: 0.5359 (mtt) cc_final: 0.5123 (mtt) REVERT: D 53 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8396 (mtmm) REVERT: D 89 LEU cc_start: 0.8406 (tp) cc_final: 0.8141 (tt) REVERT: D 120 ILE cc_start: 0.8323 (mt) cc_final: 0.8122 (mm) REVERT: D 129 TRP cc_start: 0.8068 (m-10) cc_final: 0.7570 (m100) REVERT: D 177 GLN cc_start: 0.7667 (mt0) cc_final: 0.7203 (tm-30) REVERT: D 180 SER cc_start: 0.8378 (m) cc_final: 0.7918 (p) REVERT: D 243 SER cc_start: 0.8887 (m) cc_final: 0.8477 (p) REVERT: D 261 PHE cc_start: 0.8596 (t80) cc_final: 0.8310 (t80) REVERT: D 263 GLN cc_start: 0.7243 (mm-40) cc_final: 0.6770 (mm-40) REVERT: D 275 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8040 (pttt) REVERT: D 313 TYR cc_start: 0.8153 (m-80) cc_final: 0.7946 (m-80) REVERT: D 365 ILE cc_start: 0.8367 (mt) cc_final: 0.8101 (mm) REVERT: D 395 GLU cc_start: 0.7057 (tm-30) cc_final: 0.6800 (tm-30) REVERT: D 402 ARG cc_start: 0.6356 (mpt180) cc_final: 0.5748 (mtt90) REVERT: D 407 VAL cc_start: 0.8175 (t) cc_final: 0.7938 (m) REVERT: E 37 ILE cc_start: 0.8292 (mm) cc_final: 0.8031 (mm) REVERT: E 38 LEU cc_start: 0.8016 (mt) cc_final: 0.7701 (mt) REVERT: E 40 LYS cc_start: 0.8087 (tppt) cc_final: 0.7875 (mmmm) REVERT: E 81 LEU cc_start: 0.8573 (tp) cc_final: 0.8243 (tp) REVERT: E 172 SER cc_start: 0.7964 (t) cc_final: 0.7723 (p) REVERT: E 250 ILE cc_start: 0.8076 (mt) cc_final: 0.7771 (mm) REVERT: E 328 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7547 (tm) REVERT: F 39 ASP cc_start: 0.6530 (m-30) cc_final: 0.6233 (m-30) REVERT: F 56 LYS cc_start: 0.7959 (mtpp) cc_final: 0.7630 (mtpp) REVERT: F 113 GLU cc_start: 0.7236 (tt0) cc_final: 0.6956 (tt0) REVERT: F 116 LYS cc_start: 0.8654 (mmmm) cc_final: 0.8040 (mtpp) REVERT: F 139 LYS cc_start: 0.8805 (mttt) cc_final: 0.8466 (mtmt) REVERT: F 146 ARG cc_start: 0.8330 (tmm-80) cc_final: 0.7972 (ttt180) REVERT: F 178 MET cc_start: 0.7587 (mmm) cc_final: 0.7363 (mmp) REVERT: F 208 ASP cc_start: 0.6347 (t70) cc_final: 0.6052 (t0) REVERT: F 240 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7390 (mp10) REVERT: G 16 MET cc_start: 0.7934 (mmm) cc_final: 0.7522 (mmm) REVERT: K 141 LYS cc_start: 0.8499 (tttt) cc_final: 0.8101 (ttmm) REVERT: K 151 LYS cc_start: 0.7968 (mttt) cc_final: 0.7630 (mttt) REVERT: K 163 LYS cc_start: 0.7158 (mttt) cc_final: 0.6932 (mttt) REVERT: K 209 GLU cc_start: 0.7609 (tp30) cc_final: 0.7125 (tp30) REVERT: K 213 LYS cc_start: 0.7937 (tptt) cc_final: 0.7547 (tptt) REVERT: K 272 LYS cc_start: 0.6286 (ttmm) cc_final: 0.5825 (tptt) outliers start: 115 outliers final: 74 residues processed: 845 average time/residue: 0.4147 time to fit residues: 514.0985 Evaluate side-chains 858 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 776 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 144 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 393 THR Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 42 MET 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 122 THR 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 334 ARG Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 386 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 500 ASP Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 430 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 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 260 ASN Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain D residue 284 THR 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 421 LEU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 187 LYS Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 33 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 176 ASN Chi-restraints excluded: chain F residue 217 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 F residue 267 VAL Chi-restraints excluded: chain G residue 38 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 251 optimal weight: 0.5980 chunk 191 optimal weight: 0.8980 chunk 132 optimal weight: 0.0470 chunk 28 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 255 optimal weight: 0.7980 chunk 270 optimal weight: 0.7980 chunk 133 optimal weight: 0.5980 chunk 242 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 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 114 HIS A 551 HIS ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 ASN A 677 GLN B 60 GLN ** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 GLN C 145 ASN C 474 HIS D 117 ASN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 GLN E 365 ASN F 108 ASN F 187 GLN F 219 GLN ** F 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 260 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24132 Z= 0.207 Angle : 0.602 10.289 32831 Z= 0.307 Chirality : 0.042 0.278 3677 Planarity : 0.004 0.056 4022 Dihedral : 14.297 178.879 3617 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 5.19 % Allowed : 19.34 % Favored : 75.47 % 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: 0.26 (0.16), residues: 2776 helix: 1.30 (0.15), residues: 1293 sheet: -0.01 (0.27), residues: 371 loop : -1.10 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 511 HIS 0.011 0.001 HIS C 474 PHE 0.028 0.001 PHE D 272 TYR 0.045 0.002 TYR C 533 ARG 0.007 0.001 ARG B 487 *********************** 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 916 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 787 time to evaluate : 2.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASP cc_start: 0.6718 (m-30) cc_final: 0.6358 (m-30) REVERT: A 117 LYS cc_start: 0.7789 (tttt) cc_final: 0.7496 (ttpt) REVERT: A 148 VAL cc_start: 0.8663 (p) cc_final: 0.8306 (m) REVERT: A 157 LYS cc_start: 0.8185 (tppt) cc_final: 0.7929 (ttmm) REVERT: A 165 LYS cc_start: 0.7912 (mttm) cc_final: 0.7650 (mttp) REVERT: A 273 LYS cc_start: 0.7881 (mttt) cc_final: 0.7679 (mttt) REVERT: A 282 LYS cc_start: 0.8544 (tttt) cc_final: 0.8149 (ttmm) REVERT: A 296 ASP cc_start: 0.6262 (t0) cc_final: 0.5966 (t0) REVERT: A 309 ASP cc_start: 0.5935 (p0) cc_final: 0.5165 (p0) REVERT: A 375 LYS cc_start: 0.8408 (ttpt) cc_final: 0.7999 (ttmm) REVERT: A 506 GLN cc_start: 0.8160 (tt0) cc_final: 0.7910 (tt0) REVERT: A 525 ILE cc_start: 0.8457 (tp) cc_final: 0.8084 (pt) REVERT: A 537 ASN cc_start: 0.7601 (t0) cc_final: 0.7389 (t0) REVERT: A 658 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.7258 (p90) REVERT: A 659 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.7042 (p90) REVERT: B 12 PHE cc_start: 0.6584 (t80) cc_final: 0.6216 (m-80) REVERT: B 25 MET cc_start: 0.6019 (mmm) cc_final: 0.5734 (mmm) REVERT: B 53 LEU cc_start: 0.8175 (mt) cc_final: 0.7361 (mm) REVERT: B 57 MET cc_start: 0.7119 (mmt) cc_final: 0.6769 (mmt) REVERT: B 91 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.7072 (mm) REVERT: B 92 ASN cc_start: 0.7447 (m-40) cc_final: 0.7053 (m-40) REVERT: B 122 THR cc_start: 0.7103 (OUTLIER) cc_final: 0.6839 (p) REVERT: B 133 LYS cc_start: 0.7555 (mtmt) cc_final: 0.7248 (mtmt) REVERT: B 176 ASN cc_start: 0.5967 (t0) cc_final: 0.5491 (t0) REVERT: B 178 ASP cc_start: 0.6908 (p0) cc_final: 0.6237 (p0) REVERT: B 238 ASN cc_start: 0.8143 (m110) cc_final: 0.7891 (m110) REVERT: B 244 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8228 (tp) REVERT: B 262 ASN cc_start: 0.6662 (p0) cc_final: 0.6326 (p0) REVERT: B 469 LYS cc_start: 0.7373 (ptpt) cc_final: 0.7057 (ptpp) REVERT: B 507 LYS cc_start: 0.8229 (mtmt) cc_final: 0.8019 (mtmm) REVERT: B 583 LYS cc_start: 0.7599 (ptpp) cc_final: 0.7294 (mtmm) REVERT: B 589 GLU cc_start: 0.7117 (tp30) cc_final: 0.6730 (mm-30) REVERT: B 613 HIS cc_start: 0.7718 (OUTLIER) cc_final: 0.7434 (p90) REVERT: B 668 ILE cc_start: 0.8083 (mm) cc_final: 0.7700 (mt) REVERT: B 672 THR cc_start: 0.7804 (p) cc_final: 0.7493 (m) REVERT: B 682 LYS cc_start: 0.7905 (pttp) cc_final: 0.7628 (ttpp) REVERT: B 711 ASP cc_start: 0.7070 (m-30) cc_final: 0.6865 (m-30) REVERT: C 405 GLN cc_start: 0.7750 (pp30) cc_final: 0.6559 (pp30) REVERT: C 409 GLN cc_start: 0.7288 (mt0) cc_final: 0.6986 (mt0) REVERT: C 441 MET cc_start: 0.5445 (mmm) cc_final: 0.5121 (tpp) REVERT: C 524 HIS cc_start: 0.7200 (t-170) cc_final: 0.6962 (t-90) REVERT: C 545 MET cc_start: 0.5440 (mtt) cc_final: 0.5193 (mtt) REVERT: D 53 LYS cc_start: 0.8778 (mtmt) cc_final: 0.8378 (mtmm) REVERT: D 81 LYS cc_start: 0.8519 (tttt) cc_final: 0.8175 (ttpp) REVERT: D 89 LEU cc_start: 0.8448 (tp) cc_final: 0.8186 (tt) REVERT: D 120 ILE cc_start: 0.8361 (mt) cc_final: 0.8153 (mm) REVERT: D 129 TRP cc_start: 0.8133 (m-10) cc_final: 0.7641 (m100) REVERT: D 207 ASP cc_start: 0.7265 (p0) cc_final: 0.7004 (p0) REVERT: D 215 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7872 (t80) REVERT: D 218 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7439 (tt0) REVERT: D 243 SER cc_start: 0.8889 (m) cc_final: 0.8448 (p) REVERT: D 365 ILE cc_start: 0.8380 (mt) cc_final: 0.8148 (mm) REVERT: D 395 GLU cc_start: 0.7095 (tm-30) cc_final: 0.6780 (tm-30) REVERT: D 402 ARG cc_start: 0.6374 (mpt180) cc_final: 0.5771 (mtt90) REVERT: D 407 VAL cc_start: 0.8234 (t) cc_final: 0.8014 (m) REVERT: E 37 ILE cc_start: 0.8339 (mm) cc_final: 0.8079 (mm) REVERT: E 38 LEU cc_start: 0.8049 (mt) cc_final: 0.7699 (mt) REVERT: E 40 LYS cc_start: 0.8106 (tppt) cc_final: 0.7900 (mmmm) REVERT: E 81 LEU cc_start: 0.8591 (tp) cc_final: 0.8240 (tp) REVERT: E 157 LYS cc_start: 0.7892 (tmmt) cc_final: 0.7513 (ptmm) REVERT: E 158 HIS cc_start: 0.6464 (m90) cc_final: 0.6171 (m-70) REVERT: E 172 SER cc_start: 0.8154 (t) cc_final: 0.7856 (p) REVERT: E 250 ILE cc_start: 0.8224 (mt) cc_final: 0.7925 (mm) REVERT: E 328 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7576 (tm) REVERT: F 39 ASP cc_start: 0.6563 (m-30) cc_final: 0.6253 (m-30) REVERT: F 56 LYS cc_start: 0.8027 (mtpp) cc_final: 0.7663 (mtpp) REVERT: F 113 GLU cc_start: 0.7225 (tt0) cc_final: 0.6958 (tt0) REVERT: F 116 LYS cc_start: 0.8713 (mmmm) cc_final: 0.8016 (mtpp) REVERT: F 139 LYS cc_start: 0.8813 (mttt) cc_final: 0.8482 (mtmt) REVERT: F 146 ARG cc_start: 0.8385 (tmm-80) cc_final: 0.8000 (ttt180) REVERT: F 158 LYS cc_start: 0.8328 (mtmt) cc_final: 0.7988 (mtmt) REVERT: F 208 ASP cc_start: 0.6405 (t70) cc_final: 0.6097 (t0) REVERT: F 240 GLN cc_start: 0.7724 (mm110) cc_final: 0.7276 (mt0) REVERT: G 16 MET cc_start: 0.7861 (mmm) cc_final: 0.7569 (mmm) REVERT: K 141 LYS cc_start: 0.8548 (tttt) cc_final: 0.8150 (ttmm) REVERT: K 151 LYS cc_start: 0.7973 (mttt) cc_final: 0.7540 (mttt) REVERT: K 188 LYS cc_start: 0.7857 (tttt) cc_final: 0.7550 (tmtt) REVERT: K 209 GLU cc_start: 0.7604 (tp30) cc_final: 0.7097 (tp30) REVERT: K 213 LYS cc_start: 0.7957 (tptt) cc_final: 0.7544 (tptt) REVERT: K 263 MET cc_start: 0.3316 (ptt) cc_final: 0.3030 (ptt) outliers start: 129 outliers final: 92 residues processed: 846 average time/residue: 0.4049 time to fit residues: 501.3909 Evaluate side-chains 871 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 770 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 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 655 TYR 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 712 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 42 MET 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 122 THR 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 244 ILE Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 603 LYS 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 430 THR Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 506 CYS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 213 TRP Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 218 GLN Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 260 ASN 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 E residue 22 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 139 CYS Chi-restraints excluded: chain E residue 187 LYS Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 173 GLN Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 217 VAL 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 267 VAL Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 38 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 225 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 230 optimal weight: 0.9980 chunk 187 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS ** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 ASN D 263 GLN ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 54 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24132 Z= 0.231 Angle : 0.608 13.615 32831 Z= 0.311 Chirality : 0.043 0.201 3677 Planarity : 0.004 0.065 4022 Dihedral : 14.310 179.251 3610 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 5.11 % Allowed : 20.71 % Favored : 74.19 % 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: 0.21 (0.16), residues: 2776 helix: 1.27 (0.15), residues: 1298 sheet: -0.09 (0.27), residues: 367 loop : -1.11 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 539 HIS 0.009 0.001 HIS K 266 PHE 0.027 0.002 PHE B 403 TYR 0.042 0.002 TYR C 533 ARG 0.009 0.001 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 789 time to evaluate : 4.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASP cc_start: 0.6755 (m-30) cc_final: 0.6411 (m-30) REVERT: A 117 LYS cc_start: 0.7805 (tttt) cc_final: 0.7549 (ttpt) REVERT: A 148 VAL cc_start: 0.8787 (p) cc_final: 0.8474 (m) REVERT: A 157 LYS cc_start: 0.8216 (tppt) cc_final: 0.7935 (ttmm) REVERT: A 165 LYS cc_start: 0.7961 (mttm) cc_final: 0.7685 (mttp) REVERT: A 282 LYS cc_start: 0.8562 (tttt) cc_final: 0.8151 (ttmm) REVERT: A 296 ASP cc_start: 0.6419 (t0) cc_final: 0.6031 (t0) REVERT: A 375 LYS cc_start: 0.8328 (ttpt) cc_final: 0.8016 (ttmm) REVERT: A 419 ARG cc_start: 0.7474 (ttm110) cc_final: 0.7150 (mtp-110) REVERT: A 506 GLN cc_start: 0.8194 (tt0) cc_final: 0.7850 (tt0) REVERT: A 525 ILE cc_start: 0.8459 (tp) cc_final: 0.8055 (pt) REVERT: A 537 ASN cc_start: 0.7590 (t0) cc_final: 0.7336 (t0) REVERT: A 679 PHE cc_start: 0.8420 (t80) cc_final: 0.8155 (t80) REVERT: A 697 GLU cc_start: 0.6815 (tp30) cc_final: 0.6403 (tp30) REVERT: A 711 GLN cc_start: 0.7556 (pp30) cc_final: 0.7056 (pp30) REVERT: A 715 LYS cc_start: 0.7531 (ptpp) cc_final: 0.6945 (ptpp) REVERT: B 12 PHE cc_start: 0.6685 (t80) cc_final: 0.6264 (m-80) REVERT: B 25 MET cc_start: 0.6199 (mmm) cc_final: 0.5997 (mmm) REVERT: B 53 LEU cc_start: 0.8208 (mt) cc_final: 0.7348 (mm) REVERT: B 57 MET cc_start: 0.7213 (mmt) cc_final: 0.7002 (mmt) REVERT: B 91 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.7090 (mm) REVERT: B 122 THR cc_start: 0.7113 (OUTLIER) cc_final: 0.6844 (p) REVERT: B 133 LYS cc_start: 0.7617 (mtmt) cc_final: 0.7284 (mtmt) REVERT: B 176 ASN cc_start: 0.5970 (t0) cc_final: 0.5528 (t0) REVERT: B 178 ASP cc_start: 0.7005 (p0) cc_final: 0.6354 (p0) REVERT: B 238 ASN cc_start: 0.8194 (m110) cc_final: 0.7923 (m110) REVERT: B 244 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8316 (tp) REVERT: B 262 ASN cc_start: 0.6922 (p0) cc_final: 0.6543 (p0) REVERT: B 469 LYS cc_start: 0.7463 (ptpt) cc_final: 0.7147 (ptpp) REVERT: B 514 ILE cc_start: 0.8228 (tp) cc_final: 0.8007 (mm) REVERT: B 613 HIS cc_start: 0.8025 (OUTLIER) cc_final: 0.7535 (p90) REVERT: B 668 ILE cc_start: 0.8107 (mm) cc_final: 0.7662 (mt) REVERT: B 672 THR cc_start: 0.7819 (p) cc_final: 0.7479 (m) REVERT: B 682 LYS cc_start: 0.7852 (pttp) cc_final: 0.7597 (ttpp) REVERT: C 405 GLN cc_start: 0.7823 (pp30) cc_final: 0.7038 (pp30) REVERT: C 409 GLN cc_start: 0.7333 (mt0) cc_final: 0.7022 (mt0) REVERT: C 441 MET cc_start: 0.5463 (mmm) cc_final: 0.5143 (tpp) REVERT: C 524 HIS cc_start: 0.7255 (t-170) cc_final: 0.6943 (t-90) REVERT: C 545 MET cc_start: 0.5429 (mtt) cc_final: 0.5202 (mtt) REVERT: D 77 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7398 (mmtt) REVERT: D 81 LYS cc_start: 0.8487 (tttt) cc_final: 0.8126 (ttpp) REVERT: D 89 LEU cc_start: 0.8509 (tp) cc_final: 0.8236 (tt) REVERT: D 129 TRP cc_start: 0.8195 (m-10) cc_final: 0.7727 (m100) REVERT: D 162 PHE cc_start: 0.7484 (t80) cc_final: 0.7260 (t80) REVERT: D 194 PRO cc_start: 0.7462 (Cg_endo) cc_final: 0.7216 (Cg_exo) REVERT: D 207 ASP cc_start: 0.7380 (p0) cc_final: 0.7174 (p0) REVERT: D 215 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7823 (t80) REVERT: D 218 GLN cc_start: 0.7749 (mt0) cc_final: 0.7449 (tt0) REVERT: D 243 SER cc_start: 0.8761 (m) cc_final: 0.8559 (p) REVERT: D 365 ILE cc_start: 0.8385 (mt) cc_final: 0.8155 (mm) REVERT: D 395 GLU cc_start: 0.7087 (tm-30) cc_final: 0.6775 (tm-30) REVERT: D 402 ARG cc_start: 0.6505 (mpt180) cc_final: 0.5837 (mtt90) REVERT: D 407 VAL cc_start: 0.8304 (t) cc_final: 0.8075 (m) REVERT: E 37 ILE cc_start: 0.8449 (mm) cc_final: 0.8183 (mm) REVERT: E 38 LEU cc_start: 0.8101 (mt) cc_final: 0.7713 (mt) REVERT: E 40 LYS cc_start: 0.8177 (tppt) cc_final: 0.7934 (mmmm) REVERT: E 81 LEU cc_start: 0.8599 (tp) cc_final: 0.8296 (tp) REVERT: E 172 SER cc_start: 0.8167 (t) cc_final: 0.7851 (p) REVERT: E 230 GLU cc_start: 0.7150 (tp30) cc_final: 0.6923 (tp30) REVERT: E 250 ILE cc_start: 0.8225 (mt) cc_final: 0.7934 (mm) REVERT: E 328 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7645 (tm) REVERT: E 336 LEU cc_start: 0.8191 (tt) cc_final: 0.7953 (tt) REVERT: E 343 ARG cc_start: 0.7782 (mmm160) cc_final: 0.7578 (mmt180) REVERT: F 39 ASP cc_start: 0.6557 (m-30) cc_final: 0.6284 (m-30) REVERT: F 56 LYS cc_start: 0.8075 (mtpp) cc_final: 0.7814 (mtpp) REVERT: F 113 GLU cc_start: 0.7221 (tt0) cc_final: 0.6966 (tt0) REVERT: F 116 LYS cc_start: 0.8767 (mmmm) cc_final: 0.8033 (mtpp) REVERT: F 139 LYS cc_start: 0.8837 (mttt) cc_final: 0.8505 (mtmt) REVERT: F 146 ARG cc_start: 0.8424 (tmm-80) cc_final: 0.8010 (ttt180) REVERT: F 158 LYS cc_start: 0.8324 (mtmt) cc_final: 0.7970 (mtmt) REVERT: F 208 ASP cc_start: 0.6462 (t70) cc_final: 0.6096 (t0) REVERT: F 240 GLN cc_start: 0.7909 (mm110) cc_final: 0.7521 (mt0) REVERT: G 16 MET cc_start: 0.7888 (mmm) cc_final: 0.7565 (mmm) REVERT: K 151 LYS cc_start: 0.8116 (mttt) cc_final: 0.7836 (mttt) REVERT: K 188 LYS cc_start: 0.7925 (tttt) cc_final: 0.7625 (tmtt) REVERT: K 209 GLU cc_start: 0.7626 (tp30) cc_final: 0.7102 (tp30) REVERT: K 213 LYS cc_start: 0.7981 (tptt) cc_final: 0.7548 (tptt) REVERT: K 258 ARG cc_start: 0.6892 (ttp-170) cc_final: 0.6596 (ttp-170) REVERT: K 263 MET cc_start: 0.3742 (OUTLIER) cc_final: 0.3371 (ptt) outliers start: 127 outliers final: 95 residues processed: 853 average time/residue: 0.4234 time to fit residues: 531.3616 Evaluate side-chains 881 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 778 time to evaluate : 2.715 ------------------------------------------------------------------------------- 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 129 VAL Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 469 THR 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 655 TYR 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 B residue 37 HIS 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 122 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 603 LYS 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 430 THR 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 506 CYS Chi-restraints excluded: chain D residue 77 LYS 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 178 LEU Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 213 TRP Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 139 CYS Chi-restraints excluded: chain E residue 190 LYS 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 370 ASP Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 173 GLN Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 234 ASP 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 10 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain K residue 122 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 91 optimal weight: 0.8980 chunk 243 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 270 optimal weight: 0.9980 chunk 224 optimal weight: 0.1980 chunk 125 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 142 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 GLN A 656 ASN B 60 GLN B 118 HIS ** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 509 GLN D 117 ASN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 HIS G 54 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24132 Z= 0.222 Angle : 0.605 10.918 32831 Z= 0.310 Chirality : 0.043 0.183 3677 Planarity : 0.004 0.058 4022 Dihedral : 14.337 179.598 3609 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 5.07 % Allowed : 22.11 % Favored : 72.82 % 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: 0.13 (0.16), residues: 2776 helix: 1.20 (0.15), residues: 1297 sheet: -0.19 (0.27), residues: 365 loop : -1.14 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 539 HIS 0.009 0.001 HIS K 266 PHE 0.030 0.001 PHE B 403 TYR 0.042 0.002 TYR C 533 ARG 0.012 0.001 ARG A 325 *********************** 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 912 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 786 time to evaluate : 2.655 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 98 ASP cc_start: 0.6773 (m-30) cc_final: 0.6430 (m-30) REVERT: A 117 LYS cc_start: 0.7813 (tttt) cc_final: 0.7573 (ttpt) REVERT: A 148 VAL cc_start: 0.8782 (p) cc_final: 0.8465 (m) REVERT: A 157 LYS cc_start: 0.8223 (tppt) cc_final: 0.7936 (ttmm) REVERT: A 165 LYS cc_start: 0.7972 (mttm) cc_final: 0.7699 (mttp) REVERT: A 282 LYS cc_start: 0.8556 (tttt) cc_final: 0.8155 (ttmm) REVERT: A 296 ASP cc_start: 0.6569 (t0) cc_final: 0.6154 (t0) REVERT: A 309 ASP cc_start: 0.5935 (p0) cc_final: 0.5169 (p0) REVERT: A 496 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8313 (tp) REVERT: A 506 GLN cc_start: 0.8237 (tt0) cc_final: 0.7890 (tt0) REVERT: A 525 ILE cc_start: 0.8462 (tp) cc_final: 0.8024 (pt) REVERT: A 537 ASN cc_start: 0.7572 (t0) cc_final: 0.7333 (t0) REVERT: A 679 PHE cc_start: 0.8417 (t80) cc_final: 0.8189 (t80) REVERT: A 697 GLU cc_start: 0.6810 (tp30) cc_final: 0.6425 (tp30) REVERT: A 712 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8304 (tt) REVERT: B 12 PHE cc_start: 0.6729 (t80) cc_final: 0.6347 (m-80) REVERT: B 53 LEU cc_start: 0.8223 (mt) cc_final: 0.7345 (mm) REVERT: B 57 MET cc_start: 0.7258 (mmt) cc_final: 0.7045 (mmt) REVERT: B 91 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.7075 (mm) REVERT: B 122 THR cc_start: 0.7081 (OUTLIER) cc_final: 0.6786 (p) REVERT: B 133 LYS cc_start: 0.7416 (mtmt) cc_final: 0.7129 (mtmt) REVERT: B 176 ASN cc_start: 0.5907 (t0) cc_final: 0.5520 (t0) REVERT: B 178 ASP cc_start: 0.6947 (p0) cc_final: 0.6317 (p0) REVERT: B 238 ASN cc_start: 0.8181 (m110) cc_final: 0.7944 (m110) REVERT: B 244 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8289 (tp) REVERT: B 469 LYS cc_start: 0.7487 (ptpt) cc_final: 0.7184 (ptpp) REVERT: B 511 ARG cc_start: 0.7847 (mtp85) cc_final: 0.7527 (mtt180) REVERT: B 514 ILE cc_start: 0.8221 (tp) cc_final: 0.8004 (mm) REVERT: B 613 HIS cc_start: 0.7984 (OUTLIER) cc_final: 0.7485 (p90) REVERT: B 668 ILE cc_start: 0.8066 (mm) cc_final: 0.7601 (mt) REVERT: B 672 THR cc_start: 0.7801 (p) cc_final: 0.7495 (m) REVERT: B 682 LYS cc_start: 0.7862 (pttp) cc_final: 0.7619 (ttpp) REVERT: C 405 GLN cc_start: 0.7824 (pp30) cc_final: 0.7017 (pp30) REVERT: C 409 GLN cc_start: 0.7355 (mt0) cc_final: 0.7045 (mt0) REVERT: C 441 MET cc_start: 0.5452 (mmm) cc_final: 0.5133 (tpp) REVERT: C 474 HIS cc_start: 0.6473 (m90) cc_final: 0.6226 (m-70) REVERT: C 524 HIS cc_start: 0.7263 (t-170) cc_final: 0.6830 (t-90) REVERT: C 528 MET cc_start: 0.7083 (mtp) cc_final: 0.6799 (mtm) REVERT: D 53 LYS cc_start: 0.8755 (mtmt) cc_final: 0.8439 (mtmm) REVERT: D 76 LYS cc_start: 0.7119 (mttm) cc_final: 0.6888 (mttm) REVERT: D 77 LYS cc_start: 0.7626 (mmtt) cc_final: 0.7379 (mmtt) REVERT: D 81 LYS cc_start: 0.8456 (tttt) cc_final: 0.8106 (ttpp) REVERT: D 89 LEU cc_start: 0.8559 (tp) cc_final: 0.8309 (tt) REVERT: D 129 TRP cc_start: 0.8232 (m-10) cc_final: 0.7742 (m100) REVERT: D 177 GLN cc_start: 0.7648 (mt0) cc_final: 0.7242 (tm-30) REVERT: D 180 SER cc_start: 0.8490 (m) cc_final: 0.8105 (p) REVERT: D 194 PRO cc_start: 0.7587 (Cg_endo) cc_final: 0.7349 (Cg_exo) REVERT: D 207 ASP cc_start: 0.7558 (p0) cc_final: 0.7296 (p0) REVERT: D 215 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7813 (t80) REVERT: D 275 LYS cc_start: 0.8375 (pttt) cc_final: 0.7898 (pttm) REVERT: D 277 LYS cc_start: 0.8511 (mttt) cc_final: 0.8151 (mtmt) REVERT: D 365 ILE cc_start: 0.8388 (mt) cc_final: 0.8153 (mm) REVERT: D 395 GLU cc_start: 0.7097 (tm-30) cc_final: 0.6789 (tm-30) REVERT: D 402 ARG cc_start: 0.6575 (mpt180) cc_final: 0.5963 (mtt90) REVERT: D 407 VAL cc_start: 0.8319 (t) cc_final: 0.8101 (m) REVERT: E 37 ILE cc_start: 0.8455 (mm) cc_final: 0.8196 (mm) REVERT: E 38 LEU cc_start: 0.8096 (mt) cc_final: 0.7733 (mt) REVERT: E 40 LYS cc_start: 0.8164 (tppt) cc_final: 0.7925 (mmmm) REVERT: E 81 LEU cc_start: 0.8623 (tp) cc_final: 0.8276 (tp) REVERT: E 157 LYS cc_start: 0.7788 (ttpp) cc_final: 0.7433 (ptmm) REVERT: E 172 SER cc_start: 0.8184 (t) cc_final: 0.7875 (p) REVERT: E 230 GLU cc_start: 0.7142 (tp30) cc_final: 0.6819 (tp30) REVERT: E 250 ILE cc_start: 0.8266 (mt) cc_final: 0.8003 (mm) REVERT: E 328 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7683 (tm) REVERT: F 39 ASP cc_start: 0.6628 (m-30) cc_final: 0.6323 (m-30) REVERT: F 56 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7758 (mtpp) REVERT: F 113 GLU cc_start: 0.7207 (tt0) cc_final: 0.6958 (tt0) REVERT: F 116 LYS cc_start: 0.8746 (mmmm) cc_final: 0.8054 (mtpp) REVERT: F 139 LYS cc_start: 0.8834 (mttt) cc_final: 0.8503 (mtmt) REVERT: F 146 ARG cc_start: 0.8448 (tmm-80) cc_final: 0.8004 (ttt180) REVERT: F 158 LYS cc_start: 0.8330 (mtmt) cc_final: 0.7932 (mtmt) REVERT: F 178 MET cc_start: 0.7615 (mmm) cc_final: 0.7415 (mmp) REVERT: F 208 ASP cc_start: 0.6505 (t70) cc_final: 0.6168 (t0) REVERT: F 240 GLN cc_start: 0.7886 (mm110) cc_final: 0.7523 (mt0) REVERT: G 16 MET cc_start: 0.7899 (mmm) cc_final: 0.7584 (mmm) REVERT: K 151 LYS cc_start: 0.8121 (mttt) cc_final: 0.7804 (mttt) REVERT: K 188 LYS cc_start: 0.8035 (tttt) cc_final: 0.7729 (tmtt) REVERT: K 209 GLU cc_start: 0.7632 (tp30) cc_final: 0.7093 (tp30) REVERT: K 213 LYS cc_start: 0.7992 (tptt) cc_final: 0.7568 (tptt) REVERT: K 258 ARG cc_start: 0.6911 (ttp-170) cc_final: 0.6605 (ttp-170) REVERT: K 263 MET cc_start: 0.3774 (OUTLIER) cc_final: 0.3284 (ptt) outliers start: 126 outliers final: 92 residues processed: 840 average time/residue: 0.4132 time to fit residues: 506.2403 Evaluate side-chains 866 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 765 time to evaluate : 3.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 496 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 571 TYR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 42 MET 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 122 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 446 GLN Chi-restraints excluded: chain C residue 449 ILE 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 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 321 SER 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 417 ASP Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 109 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 E residue 370 ASP Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 9 ASN Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 173 GLN Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 236 ASP Chi-restraints excluded: chain F residue 247 VAL 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 10 ILE Chi-restraints excluded: chain G residue 38 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 261 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 197 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 228 optimal weight: 0.8980 chunk 151 optimal weight: 0.7980 chunk 269 optimal weight: 0.6980 chunk 168 optimal weight: 0.9990 chunk 164 optimal weight: 0.3980 chunk 124 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 509 GLN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 GLN E 324 HIS F 277 ASN G 54 GLN K 197 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24132 Z= 0.230 Angle : 0.637 10.145 32831 Z= 0.323 Chirality : 0.043 0.205 3677 Planarity : 0.004 0.064 4022 Dihedral : 14.354 179.796 3607 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 5.07 % Allowed : 23.12 % Favored : 71.81 % 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: 1.19 (0.15), residues: 1289 sheet: -0.23 (0.27), residues: 368 loop : -1.15 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 539 HIS 0.009 0.001 HIS K 266 PHE 0.032 0.002 PHE B 403 TYR 0.045 0.002 TYR C 533 ARG 0.008 0.001 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 783 time to evaluate : 2.755 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 87 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6694 (mt-10) REVERT: A 98 ASP cc_start: 0.6804 (m-30) cc_final: 0.6469 (m-30) REVERT: A 148 VAL cc_start: 0.8836 (p) cc_final: 0.8498 (m) REVERT: A 157 LYS cc_start: 0.8229 (tppt) cc_final: 0.7949 (ttmm) REVERT: A 165 LYS cc_start: 0.7985 (mttm) cc_final: 0.7725 (mttp) REVERT: A 282 LYS cc_start: 0.8572 (tttt) cc_final: 0.8170 (ttmm) REVERT: A 309 ASP cc_start: 0.6013 (p0) cc_final: 0.5246 (p0) REVERT: A 375 LYS cc_start: 0.8386 (ttpt) cc_final: 0.7990 (ttmm) REVERT: A 379 LYS cc_start: 0.7842 (mmtt) cc_final: 0.7432 (mmmm) REVERT: A 419 ARG cc_start: 0.7410 (ttm110) cc_final: 0.7096 (mtp-110) REVERT: A 506 GLN cc_start: 0.8234 (tt0) cc_final: 0.7854 (tt0) REVERT: A 525 ILE cc_start: 0.8493 (tp) cc_final: 0.7993 (pt) REVERT: A 537 ASN cc_start: 0.7571 (t0) cc_final: 0.7310 (t0) REVERT: A 679 PHE cc_start: 0.8419 (t80) cc_final: 0.8208 (t80) REVERT: A 697 GLU cc_start: 0.6866 (tp30) cc_final: 0.6475 (tp30) REVERT: A 712 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8335 (tt) REVERT: B 12 PHE cc_start: 0.6750 (t80) cc_final: 0.6378 (m-80) REVERT: B 53 LEU cc_start: 0.8296 (mt) cc_final: 0.7464 (mm) REVERT: B 122 THR cc_start: 0.7161 (OUTLIER) cc_final: 0.6866 (p) REVERT: B 176 ASN cc_start: 0.5923 (t0) cc_final: 0.5562 (t0) REVERT: B 178 ASP cc_start: 0.7034 (p0) cc_final: 0.6438 (p0) REVERT: B 238 ASN cc_start: 0.8182 (m110) cc_final: 0.7960 (m110) REVERT: B 244 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8288 (tp) REVERT: B 262 ASN cc_start: 0.6701 (p0) cc_final: 0.6150 (p0) REVERT: B 511 ARG cc_start: 0.7847 (mtp85) cc_final: 0.7504 (mtt180) REVERT: B 514 ILE cc_start: 0.8222 (tp) cc_final: 0.8013 (mm) REVERT: B 613 HIS cc_start: 0.7929 (OUTLIER) cc_final: 0.7356 (p90) REVERT: B 668 ILE cc_start: 0.8020 (mm) cc_final: 0.7691 (mt) REVERT: B 672 THR cc_start: 0.7798 (p) cc_final: 0.7480 (m) REVERT: B 682 LYS cc_start: 0.7872 (pttp) cc_final: 0.7625 (ttpp) REVERT: C 405 GLN cc_start: 0.7866 (pp30) cc_final: 0.7079 (pp30) REVERT: C 409 GLN cc_start: 0.7379 (mt0) cc_final: 0.7096 (mt0) REVERT: C 412 GLU cc_start: 0.7023 (tt0) cc_final: 0.6703 (tt0) REVERT: C 441 MET cc_start: 0.5400 (mmm) cc_final: 0.5104 (tpp) REVERT: C 524 HIS cc_start: 0.7259 (t-170) cc_final: 0.6942 (t-90) REVERT: D 23 LEU cc_start: 0.8539 (mm) cc_final: 0.8216 (mp) REVERT: D 53 LYS cc_start: 0.8754 (mtmt) cc_final: 0.8488 (ttmt) REVERT: D 77 LYS cc_start: 0.7603 (mmtt) cc_final: 0.7365 (mmtt) REVERT: D 81 LYS cc_start: 0.8470 (tttt) cc_final: 0.8116 (ttpp) REVERT: D 89 LEU cc_start: 0.8593 (tp) cc_final: 0.8346 (tt) REVERT: D 98 THR cc_start: 0.8754 (m) cc_final: 0.8365 (p) REVERT: D 129 TRP cc_start: 0.8252 (m-10) cc_final: 0.7748 (m100) REVERT: D 177 GLN cc_start: 0.7689 (mt0) cc_final: 0.7428 (tm-30) REVERT: D 180 SER cc_start: 0.8471 (m) cc_final: 0.8265 (p) REVERT: D 194 PRO cc_start: 0.7743 (Cg_endo) cc_final: 0.7470 (Cg_exo) REVERT: D 207 ASP cc_start: 0.7581 (p0) cc_final: 0.7301 (p0) REVERT: D 215 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7825 (t80) REVERT: D 247 LYS cc_start: 0.7673 (tttm) cc_final: 0.7446 (tttm) REVERT: D 365 ILE cc_start: 0.8430 (mt) cc_final: 0.8168 (mm) REVERT: D 395 GLU cc_start: 0.7086 (tm-30) cc_final: 0.6790 (tm-30) REVERT: D 402 ARG cc_start: 0.6582 (mpt180) cc_final: 0.5906 (mtt90) REVERT: E 34 ILE cc_start: 0.8179 (pt) cc_final: 0.7971 (pt) REVERT: E 37 ILE cc_start: 0.8464 (mm) cc_final: 0.8185 (mm) REVERT: E 38 LEU cc_start: 0.8098 (mt) cc_final: 0.7731 (mt) REVERT: E 40 LYS cc_start: 0.8166 (tppt) cc_final: 0.7933 (mmmm) REVERT: E 81 LEU cc_start: 0.8610 (tp) cc_final: 0.8298 (tp) REVERT: E 172 SER cc_start: 0.8190 (t) cc_final: 0.7858 (p) REVERT: E 230 GLU cc_start: 0.7129 (tp30) cc_final: 0.6815 (tp30) REVERT: E 250 ILE cc_start: 0.8275 (mt) cc_final: 0.8019 (mm) REVERT: E 328 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7699 (tm) REVERT: F 39 ASP cc_start: 0.6644 (m-30) cc_final: 0.6346 (m-30) REVERT: F 55 ASN cc_start: 0.8194 (m-40) cc_final: 0.7770 (m-40) REVERT: F 56 LYS cc_start: 0.8128 (mtpp) cc_final: 0.7377 (mtpp) REVERT: F 113 GLU cc_start: 0.7212 (tt0) cc_final: 0.6975 (tt0) REVERT: F 116 LYS cc_start: 0.8740 (mmmm) cc_final: 0.8249 (mtpp) REVERT: F 131 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8467 (p) REVERT: F 139 LYS cc_start: 0.8836 (mttt) cc_final: 0.8481 (mtmt) REVERT: F 146 ARG cc_start: 0.8338 (tmm-80) cc_final: 0.7913 (ttt180) REVERT: F 158 LYS cc_start: 0.8279 (mtmt) cc_final: 0.7896 (mtmt) REVERT: F 178 MET cc_start: 0.7525 (mmm) cc_final: 0.7266 (mmp) REVERT: F 208 ASP cc_start: 0.6560 (t70) cc_final: 0.6204 (t0) REVERT: F 240 GLN cc_start: 0.7978 (mm110) cc_final: 0.7678 (mt0) REVERT: G 16 MET cc_start: 0.7911 (mmm) cc_final: 0.7591 (mmm) REVERT: G 27 ASN cc_start: 0.8230 (m-40) cc_final: 0.7999 (t0) REVERT: K 151 LYS cc_start: 0.8142 (mttt) cc_final: 0.7839 (mttt) REVERT: K 188 LYS cc_start: 0.8057 (tttt) cc_final: 0.7755 (tmtt) REVERT: K 209 GLU cc_start: 0.7643 (tp30) cc_final: 0.7112 (tp30) REVERT: K 213 LYS cc_start: 0.8031 (tptt) cc_final: 0.7580 (tptt) REVERT: K 258 ARG cc_start: 0.6914 (ttp-170) cc_final: 0.6602 (ttp-170) REVERT: K 263 MET cc_start: 0.3923 (OUTLIER) cc_final: 0.3473 (ptt) outliers start: 126 outliers final: 96 residues processed: 834 average time/residue: 0.4194 time to fit residues: 510.7748 Evaluate side-chains 880 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 776 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 479 ASP 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 571 TYR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 446 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 506 CYS 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 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 321 SER Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain E residue 12 GLU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 109 THR 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 334 ILE Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 9 ASN Chi-restraints excluded: chain F residue 33 THR 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 176 ASN Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 248 HIS Chi-restraints excluded: chain F residue 255 CYS Chi-restraints excluded: chain F residue 260 ASN Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain 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 197 GLN 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 166 optimal weight: 0.9980 chunk 107 optimal weight: 0.2980 chunk 161 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 GLN C 474 HIS C 509 GLN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS E 324 HIS F 277 ASN G 54 GLN K 197 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24132 Z= 0.249 Angle : 0.655 10.382 32831 Z= 0.333 Chirality : 0.044 0.199 3677 Planarity : 0.004 0.068 4022 Dihedral : 14.404 179.933 3605 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.83 % Allowed : 24.05 % Favored : 71.13 % 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: 1.10 (0.15), residues: 1291 sheet: -0.29 (0.27), residues: 369 loop : -1.13 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 539 HIS 0.009 0.001 HIS K 266 PHE 0.029 0.002 PHE B 403 TYR 0.044 0.002 TYR C 533 ARG 0.009 0.001 ARG C 542 *********************** 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 910 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 790 time to evaluate : 2.656 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: 0.6808 (m-30) cc_final: 0.6490 (m-30) REVERT: A 148 VAL cc_start: 0.8823 (p) cc_final: 0.8500 (m) REVERT: A 157 LYS cc_start: 0.8252 (tppt) cc_final: 0.7956 (ttmm) REVERT: A 165 LYS cc_start: 0.7997 (mttm) cc_final: 0.7689 (mttp) REVERT: A 282 LYS cc_start: 0.8554 (tttt) cc_final: 0.8177 (ttmm) REVERT: A 309 ASP cc_start: 0.6148 (p0) cc_final: 0.5454 (p0) REVERT: A 457 ILE cc_start: 0.8620 (tt) cc_final: 0.8256 (mm) REVERT: A 506 GLN cc_start: 0.8234 (tt0) cc_final: 0.7893 (tt0) REVERT: A 517 GLU cc_start: 0.7231 (mp0) cc_final: 0.6986 (mm-30) REVERT: A 525 ILE cc_start: 0.8493 (tp) cc_final: 0.7971 (pt) REVERT: A 537 ASN cc_start: 0.7575 (t0) cc_final: 0.7325 (t0) REVERT: A 570 GLU cc_start: 0.6381 (pt0) cc_final: 0.6174 (mt-10) REVERT: A 679 PHE cc_start: 0.8443 (t80) cc_final: 0.8209 (t80) REVERT: A 697 GLU cc_start: 0.6917 (tp30) cc_final: 0.6581 (tp30) REVERT: A 712 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8375 (tt) REVERT: B 1 MET cc_start: 0.6001 (ppp) cc_final: 0.5699 (ppp) REVERT: B 12 PHE cc_start: 0.6774 (t80) cc_final: 0.6412 (m-80) REVERT: B 41 GLU cc_start: 0.6547 (tt0) cc_final: 0.6250 (tt0) REVERT: B 53 LEU cc_start: 0.8396 (mt) cc_final: 0.8146 (mm) REVERT: B 122 THR cc_start: 0.6535 (OUTLIER) cc_final: 0.6256 (p) REVERT: B 176 ASN cc_start: 0.5909 (t0) cc_final: 0.5581 (t0) REVERT: B 178 ASP cc_start: 0.7047 (p0) cc_final: 0.6429 (p0) REVERT: B 238 ASN cc_start: 0.8176 (m110) cc_final: 0.7958 (m110) REVERT: B 244 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8324 (tp) REVERT: B 262 ASN cc_start: 0.6573 (p0) cc_final: 0.6153 (p0) REVERT: B 352 GLU cc_start: 0.7676 (mp0) cc_final: 0.6249 (pm20) REVERT: B 511 ARG cc_start: 0.7830 (mtp85) cc_final: 0.7510 (mtt180) REVERT: B 514 ILE cc_start: 0.8241 (tp) cc_final: 0.8027 (mm) REVERT: B 613 HIS cc_start: 0.8005 (OUTLIER) cc_final: 0.7437 (p90) REVERT: B 668 ILE cc_start: 0.8025 (mm) cc_final: 0.7664 (mt) REVERT: B 672 THR cc_start: 0.7755 (p) cc_final: 0.7449 (m) REVERT: B 682 LYS cc_start: 0.7874 (pttp) cc_final: 0.7630 (ttpp) REVERT: C 405 GLN cc_start: 0.7842 (pp30) cc_final: 0.6830 (pp30) REVERT: C 409 GLN cc_start: 0.7444 (mt0) cc_final: 0.7033 (mt0) REVERT: C 412 GLU cc_start: 0.7157 (tt0) cc_final: 0.6875 (tt0) REVERT: C 441 MET cc_start: 0.5380 (mmm) cc_final: 0.5071 (tpp) REVERT: C 524 HIS cc_start: 0.7248 (t-170) cc_final: 0.6812 (t-90) REVERT: C 528 MET cc_start: 0.7095 (mtp) cc_final: 0.6814 (mtm) REVERT: D 23 LEU cc_start: 0.8503 (mm) cc_final: 0.8201 (mp) REVERT: D 53 LYS cc_start: 0.8769 (mtmt) cc_final: 0.8203 (mtpp) REVERT: D 77 LYS cc_start: 0.7625 (mmtt) cc_final: 0.7369 (mmtt) REVERT: D 89 LEU cc_start: 0.8630 (tp) cc_final: 0.8392 (tt) REVERT: D 98 THR cc_start: 0.8747 (m) cc_final: 0.8388 (p) REVERT: D 129 TRP cc_start: 0.8288 (m-10) cc_final: 0.7786 (m100) REVERT: D 180 SER cc_start: 0.8617 (m) cc_final: 0.8339 (p) REVERT: D 194 PRO cc_start: 0.7874 (Cg_endo) cc_final: 0.7669 (Cg_exo) REVERT: D 207 ASP cc_start: 0.7625 (p0) cc_final: 0.7351 (p0) REVERT: D 247 LYS cc_start: 0.7738 (tttm) cc_final: 0.7412 (tttm) REVERT: D 258 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8426 (tp) REVERT: D 365 ILE cc_start: 0.8429 (mt) cc_final: 0.8172 (mm) REVERT: D 395 GLU cc_start: 0.7134 (tm-30) cc_final: 0.6787 (tm-30) REVERT: D 402 ARG cc_start: 0.6644 (mpt180) cc_final: 0.5937 (mtt90) REVERT: E 31 LYS cc_start: 0.7350 (ptmt) cc_final: 0.7136 (ptmt) REVERT: E 37 ILE cc_start: 0.8529 (mm) cc_final: 0.8274 (mm) REVERT: E 38 LEU cc_start: 0.8097 (mt) cc_final: 0.7728 (mt) REVERT: E 40 LYS cc_start: 0.8158 (tppt) cc_final: 0.7934 (mmmm) REVERT: E 81 LEU cc_start: 0.8619 (tp) cc_final: 0.8314 (tp) REVERT: E 172 SER cc_start: 0.8187 (t) cc_final: 0.7840 (p) REVERT: E 187 LYS cc_start: 0.7410 (ttpt) cc_final: 0.7209 (ttpt) REVERT: E 230 GLU cc_start: 0.7151 (tp30) cc_final: 0.6810 (tp30) REVERT: E 250 ILE cc_start: 0.8261 (mt) cc_final: 0.8023 (mm) REVERT: E 328 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7739 (tm) REVERT: F 39 ASP cc_start: 0.6666 (m-30) cc_final: 0.6360 (m-30) REVERT: F 55 ASN cc_start: 0.8219 (m-40) cc_final: 0.7793 (m-40) REVERT: F 113 GLU cc_start: 0.7217 (tt0) cc_final: 0.6986 (tt0) REVERT: F 116 LYS cc_start: 0.8758 (mmmm) cc_final: 0.8268 (mtpp) REVERT: F 139 LYS cc_start: 0.8837 (mttt) cc_final: 0.8490 (mtmt) REVERT: F 146 ARG cc_start: 0.8349 (tmm-80) cc_final: 0.7984 (ttt180) REVERT: F 158 LYS cc_start: 0.8273 (mtmt) cc_final: 0.7868 (mtmt) REVERT: F 208 ASP cc_start: 0.6595 (t70) cc_final: 0.6236 (t0) REVERT: F 237 GLN cc_start: 0.7639 (mt0) cc_final: 0.7390 (tt0) REVERT: F 240 GLN cc_start: 0.7978 (mm110) cc_final: 0.7718 (mt0) REVERT: G 16 MET cc_start: 0.7920 (mmm) cc_final: 0.7376 (mmm) REVERT: G 27 ASN cc_start: 0.8258 (m-40) cc_final: 0.8049 (t0) REVERT: K 188 LYS cc_start: 0.8093 (tttt) cc_final: 0.7785 (tmtt) REVERT: K 209 GLU cc_start: 0.7652 (tp30) cc_final: 0.7097 (tp30) REVERT: K 213 LYS cc_start: 0.8064 (tptt) cc_final: 0.7484 (tptt) REVERT: K 258 ARG cc_start: 0.6887 (ttp-170) cc_final: 0.6561 (ttp-170) REVERT: K 263 MET cc_start: 0.3976 (ptt) cc_final: 0.3544 (ptt) outliers start: 120 outliers final: 102 residues processed: 840 average time/residue: 0.4209 time to fit residues: 515.7507 Evaluate side-chains 887 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 779 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 497 GLN Chi-restraints excluded: chain A residue 502 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 603 ASN Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 469 LYS Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 603 LYS 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 698 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 100 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 213 TRP Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 321 SER 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 417 ASP Chi-restraints excluded: chain E residue 12 GLU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 109 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 E residue 334 ILE Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 33 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 210 THR Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain F residue 236 ASP Chi-restraints excluded: chain F residue 248 HIS Chi-restraints excluded: chain F residue 255 CYS Chi-restraints excluded: chain F residue 260 ASN Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain 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 201 GLU Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 227 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 245 optimal weight: 0.8980 chunk 258 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 151 optimal weight: 0.0770 chunk 109 optimal weight: 0.9980 chunk 197 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 227 optimal weight: 0.3980 chunk 237 optimal weight: 3.9990 chunk 250 optimal weight: 3.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 GLN ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 GLN C 474 HIS C 509 GLN ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS E 256 GLN E 293 GLN E 324 HIS G 54 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24132 Z= 0.220 Angle : 0.665 15.980 32831 Z= 0.335 Chirality : 0.043 0.194 3677 Planarity : 0.004 0.069 4022 Dihedral : 14.361 179.752 3601 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.70 % Allowed : 24.77 % Favored : 70.53 % 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: -0.01 (0.16), residues: 2776 helix: 1.08 (0.15), residues: 1303 sheet: -0.30 (0.27), residues: 368 loop : -1.18 (0.18), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 539 HIS 0.010 0.001 HIS K 266 PHE 0.036 0.001 PHE B 403 TYR 0.047 0.002 TYR C 533 ARG 0.011 0.001 ARG C 542 *********************** 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 897 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 780 time to evaluate : 2.762 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: 0.6801 (m-30) cc_final: 0.6482 (m-30) REVERT: A 148 VAL cc_start: 0.8820 (p) cc_final: 0.8485 (m) REVERT: A 157 LYS cc_start: 0.8234 (tppt) cc_final: 0.7936 (ttmm) REVERT: A 165 LYS cc_start: 0.7999 (mttm) cc_final: 0.7672 (mttp) REVERT: A 276 MET cc_start: 0.7629 (tpp) cc_final: 0.7093 (tpp) REVERT: A 282 LYS cc_start: 0.8570 (tttt) cc_final: 0.8151 (ttmm) REVERT: A 309 ASP cc_start: 0.6093 (p0) cc_final: 0.5347 (p0) REVERT: A 375 LYS cc_start: 0.8430 (ttpt) cc_final: 0.8077 (ttmm) REVERT: A 379 LYS cc_start: 0.7830 (mmtt) cc_final: 0.7415 (mmmm) REVERT: A 427 MET cc_start: 0.7410 (tpp) cc_final: 0.7198 (tpp) REVERT: A 457 ILE cc_start: 0.8570 (tt) cc_final: 0.8247 (mm) REVERT: A 506 GLN cc_start: 0.8235 (tt0) cc_final: 0.7998 (tt0) REVERT: A 517 GLU cc_start: 0.7221 (mp0) cc_final: 0.6999 (mm-30) REVERT: A 525 ILE cc_start: 0.8490 (tp) cc_final: 0.7959 (pt) REVERT: A 537 ASN cc_start: 0.7603 (t0) cc_final: 0.7354 (t0) REVERT: A 697 GLU cc_start: 0.6929 (tp30) cc_final: 0.6609 (tp30) REVERT: B 1 MET cc_start: 0.6022 (ppp) cc_final: 0.5647 (ppp) REVERT: B 12 PHE cc_start: 0.6770 (t80) cc_final: 0.6476 (m-80) REVERT: B 25 MET cc_start: 0.5976 (mmp) cc_final: 0.5745 (mmm) REVERT: B 53 LEU cc_start: 0.8389 (mt) cc_final: 0.8119 (mm) REVERT: B 122 THR cc_start: 0.6508 (OUTLIER) cc_final: 0.6225 (p) REVERT: B 178 ASP cc_start: 0.7150 (p0) cc_final: 0.6398 (p0) REVERT: B 238 ASN cc_start: 0.8166 (m110) cc_final: 0.7944 (m110) REVERT: B 244 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8313 (tp) REVERT: B 262 ASN cc_start: 0.6500 (p0) cc_final: 0.6070 (p0) REVERT: B 511 ARG cc_start: 0.7806 (mtp85) cc_final: 0.7476 (mtt180) REVERT: B 613 HIS cc_start: 0.7912 (OUTLIER) cc_final: 0.7308 (p90) REVERT: B 668 ILE cc_start: 0.8018 (mm) cc_final: 0.7646 (mt) REVERT: B 672 THR cc_start: 0.7740 (p) cc_final: 0.7455 (m) REVERT: B 682 LYS cc_start: 0.7857 (pttp) cc_final: 0.7614 (ttpp) REVERT: C 405 GLN cc_start: 0.7857 (pp30) cc_final: 0.6819 (pp30) REVERT: C 409 GLN cc_start: 0.7427 (mt0) cc_final: 0.7023 (mt0) REVERT: C 412 GLU cc_start: 0.7184 (tt0) cc_final: 0.6872 (tt0) REVERT: C 441 MET cc_start: 0.5372 (mmm) cc_final: 0.5086 (tpp) REVERT: C 475 PHE cc_start: 0.8349 (t80) cc_final: 0.8139 (t80) REVERT: C 524 HIS cc_start: 0.7230 (t-170) cc_final: 0.6790 (t-90) REVERT: C 528 MET cc_start: 0.6987 (mtp) cc_final: 0.6735 (mtm) REVERT: D 23 LEU cc_start: 0.8512 (mm) cc_final: 0.8191 (mp) REVERT: D 34 LEU cc_start: 0.8611 (tp) cc_final: 0.8372 (tt) REVERT: D 53 LYS cc_start: 0.8750 (mtmt) cc_final: 0.8181 (mtpp) REVERT: D 77 LYS cc_start: 0.7476 (mmtt) cc_final: 0.7211 (mmtt) REVERT: D 89 LEU cc_start: 0.8632 (tp) cc_final: 0.8405 (tt) REVERT: D 98 THR cc_start: 0.8698 (m) cc_final: 0.8357 (p) REVERT: D 129 TRP cc_start: 0.8282 (m-10) cc_final: 0.7814 (m100) REVERT: D 180 SER cc_start: 0.8618 (m) cc_final: 0.8376 (p) REVERT: D 194 PRO cc_start: 0.7899 (Cg_endo) cc_final: 0.7618 (Cg_exo) REVERT: D 207 ASP cc_start: 0.7623 (p0) cc_final: 0.7351 (p0) REVERT: D 215 PHE cc_start: 0.7885 (t80) cc_final: 0.7514 (t80) REVERT: D 247 LYS cc_start: 0.7520 (tttm) cc_final: 0.7291 (tttm) REVERT: D 258 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8430 (tp) REVERT: D 266 ARG cc_start: 0.8375 (ttt-90) cc_final: 0.8129 (ttt180) REVERT: D 365 ILE cc_start: 0.8421 (mt) cc_final: 0.8168 (mm) REVERT: D 395 GLU cc_start: 0.7076 (tm-30) cc_final: 0.6761 (tm-30) REVERT: D 402 ARG cc_start: 0.6604 (mpt180) cc_final: 0.5913 (mtt90) REVERT: E 37 ILE cc_start: 0.8516 (mm) cc_final: 0.8254 (mm) REVERT: E 38 LEU cc_start: 0.8107 (mt) cc_final: 0.7735 (mt) REVERT: E 40 LYS cc_start: 0.8132 (tppt) cc_final: 0.7905 (mmmm) REVERT: E 81 LEU cc_start: 0.8605 (tp) cc_final: 0.8285 (tp) REVERT: E 118 THR cc_start: 0.7871 (t) cc_final: 0.7665 (t) REVERT: E 157 LYS cc_start: 0.7799 (ttpp) cc_final: 0.7575 (ttpp) REVERT: E 172 SER cc_start: 0.8163 (t) cc_final: 0.7840 (p) REVERT: E 229 LYS cc_start: 0.7586 (tptt) cc_final: 0.7352 (tptt) REVERT: E 230 GLU cc_start: 0.7105 (tp30) cc_final: 0.6779 (tp30) REVERT: E 250 ILE cc_start: 0.8220 (mt) cc_final: 0.8012 (mm) REVERT: E 328 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7741 (tm) REVERT: F 39 ASP cc_start: 0.6639 (m-30) cc_final: 0.6336 (m-30) REVERT: F 55 ASN cc_start: 0.8213 (m-40) cc_final: 0.7823 (m-40) REVERT: F 113 GLU cc_start: 0.7213 (tt0) cc_final: 0.6988 (tt0) REVERT: F 116 LYS cc_start: 0.8762 (mmmm) cc_final: 0.8253 (mtpp) REVERT: F 139 LYS cc_start: 0.8845 (mttt) cc_final: 0.8496 (mtpp) REVERT: F 146 ARG cc_start: 0.8299 (tmm-80) cc_final: 0.7940 (ttt180) REVERT: F 158 LYS cc_start: 0.8301 (mtmt) cc_final: 0.7894 (mtmt) REVERT: F 208 ASP cc_start: 0.6566 (t70) cc_final: 0.6185 (t0) REVERT: F 237 GLN cc_start: 0.7633 (mt0) cc_final: 0.7376 (tt0) REVERT: F 240 GLN cc_start: 0.7950 (mm110) cc_final: 0.7717 (mt0) REVERT: G 16 MET cc_start: 0.7926 (mmm) cc_final: 0.7370 (mmm) REVERT: K 188 LYS cc_start: 0.8112 (tttt) cc_final: 0.7784 (tmtt) REVERT: K 197 GLN cc_start: 0.8464 (tm-30) cc_final: 0.8254 (tm-30) REVERT: K 209 GLU cc_start: 0.7649 (tp30) cc_final: 0.7262 (tp30) REVERT: K 213 LYS cc_start: 0.8055 (tptt) cc_final: 0.7542 (tptt) REVERT: K 245 GLU cc_start: 0.7499 (mp0) cc_final: 0.7169 (mp0) REVERT: K 252 LEU cc_start: 0.7055 (mt) cc_final: 0.6590 (mt) REVERT: K 263 MET cc_start: 0.3824 (OUTLIER) cc_final: 0.3274 (ptt) outliers start: 117 outliers final: 92 residues processed: 834 average time/residue: 0.4313 time to fit residues: 527.2753 Evaluate side-chains 870 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 772 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 497 GLN 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 603 ASN Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 656 ASN 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 85 GLU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 122 THR 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 244 ILE Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 469 LYS Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 612 HIS Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 446 GLN Chi-restraints excluded: chain C residue 449 ILE 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 196 ILE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 213 TRP Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 321 SER 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 417 ASP Chi-restraints excluded: chain E residue 12 GLU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 109 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 370 ASP Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 173 GLN Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain F residue 236 ASP Chi-restraints excluded: chain F residue 248 HIS Chi-restraints excluded: chain F residue 255 CYS Chi-restraints excluded: chain F residue 260 ASN Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain G residue 38 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 263 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 165 optimal weight: 0.1980 chunk 265 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 chunk 126 optimal weight: 0.5980 chunk 184 optimal weight: 0.5980 chunk 278 optimal weight: 1.9990 chunk 256 optimal weight: 0.0470 chunk 222 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 171 optimal weight: 0.2980 chunk 136 optimal weight: 1.9990 overall best weight: 0.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 GLN A 668 GLN B 60 GLN B 92 ASN ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 509 GLN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 HIS F 18 ASN F 48 HIS F 277 ASN G 54 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24132 Z= 0.193 Angle : 0.661 14.872 32831 Z= 0.334 Chirality : 0.043 0.214 3677 Planarity : 0.004 0.074 4022 Dihedral : 14.311 179.627 3599 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.86 % Allowed : 25.45 % Favored : 70.69 % 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: 0.01 (0.16), residues: 2776 helix: 1.09 (0.15), residues: 1302 sheet: -0.25 (0.28), residues: 358 loop : -1.18 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 539 HIS 0.010 0.001 HIS K 266 PHE 0.034 0.001 PHE B 403 TYR 0.047 0.001 TYR C 533 ARG 0.013 0.001 ARG C 542 ********************** 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 870 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 774 time to evaluate : 2.701 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 98 ASP cc_start: 0.6930 (m-30) cc_final: 0.6606 (m-30) REVERT: A 148 VAL cc_start: 0.8777 (p) cc_final: 0.8438 (m) REVERT: A 157 LYS cc_start: 0.8203 (tppt) cc_final: 0.7913 (ttmm) REVERT: A 165 LYS cc_start: 0.7972 (mttm) cc_final: 0.7646 (mttp) REVERT: A 282 LYS cc_start: 0.8551 (tttt) cc_final: 0.8123 (ttmm) REVERT: A 309 ASP cc_start: 0.6105 (p0) cc_final: 0.5254 (p0) REVERT: A 379 LYS cc_start: 0.7795 (mmtt) cc_final: 0.7411 (mmmm) REVERT: A 427 MET cc_start: 0.7437 (tpp) cc_final: 0.7178 (tpp) REVERT: A 457 ILE cc_start: 0.8532 (tt) cc_final: 0.8208 (mm) REVERT: A 496 LEU cc_start: 0.8274 (tp) cc_final: 0.8066 (tp) REVERT: A 506 GLN cc_start: 0.8226 (tt0) cc_final: 0.7911 (tt0) REVERT: A 525 ILE cc_start: 0.8486 (tp) cc_final: 0.7952 (pt) REVERT: A 537 ASN cc_start: 0.7611 (t0) cc_final: 0.7343 (t0) REVERT: A 697 GLU cc_start: 0.6929 (tp30) cc_final: 0.6614 (tp30) REVERT: B 1 MET cc_start: 0.5993 (ppp) cc_final: 0.5532 (ppp) REVERT: B 12 PHE cc_start: 0.6754 (t80) cc_final: 0.6457 (m-80) REVERT: B 122 THR cc_start: 0.6806 (OUTLIER) cc_final: 0.6518 (p) REVERT: B 178 ASP cc_start: 0.6821 (p0) cc_final: 0.6609 (p0) REVERT: B 244 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8283 (tp) REVERT: B 262 ASN cc_start: 0.6357 (p0) cc_final: 0.5871 (p0) REVERT: B 488 VAL cc_start: 0.8558 (m) cc_final: 0.8340 (p) REVERT: B 511 ARG cc_start: 0.7793 (mtp85) cc_final: 0.7477 (mtt180) REVERT: B 554 GLU cc_start: 0.6979 (tm-30) cc_final: 0.6750 (tm-30) REVERT: B 613 HIS cc_start: 0.7741 (OUTLIER) cc_final: 0.7190 (p90) REVERT: B 668 ILE cc_start: 0.7963 (mm) cc_final: 0.7579 (mt) REVERT: B 672 THR cc_start: 0.7724 (p) cc_final: 0.7474 (m) REVERT: B 681 ASP cc_start: 0.7785 (t0) cc_final: 0.7130 (t70) REVERT: B 682 LYS cc_start: 0.7850 (pttp) cc_final: 0.7478 (ttpp) REVERT: C 405 GLN cc_start: 0.7860 (pp30) cc_final: 0.6817 (pp30) REVERT: C 409 GLN cc_start: 0.7408 (mt0) cc_final: 0.6993 (mt0) REVERT: C 412 GLU cc_start: 0.7172 (tt0) cc_final: 0.6892 (tt0) REVERT: C 441 MET cc_start: 0.5355 (mmm) cc_final: 0.5049 (tpp) REVERT: C 524 HIS cc_start: 0.7236 (t-170) cc_final: 0.6780 (t-90) REVERT: C 528 MET cc_start: 0.6987 (mtp) cc_final: 0.6731 (mtm) REVERT: D 23 LEU cc_start: 0.8451 (mm) cc_final: 0.8075 (mp) REVERT: D 76 LYS cc_start: 0.7009 (mttm) cc_final: 0.6792 (mttm) REVERT: D 77 LYS cc_start: 0.7438 (mmtt) cc_final: 0.7192 (mmtt) REVERT: D 98 THR cc_start: 0.8672 (m) cc_final: 0.8355 (p) REVERT: D 129 TRP cc_start: 0.8255 (m-10) cc_final: 0.7831 (m100) REVERT: D 180 SER cc_start: 0.8528 (m) cc_final: 0.8232 (p) REVERT: D 206 LEU cc_start: 0.7767 (tp) cc_final: 0.7486 (tp) REVERT: D 207 ASP cc_start: 0.7573 (p0) cc_final: 0.7186 (p0) REVERT: D 247 LYS cc_start: 0.7553 (tttm) cc_final: 0.7304 (tttm) REVERT: D 249 TYR cc_start: 0.7645 (m-80) cc_final: 0.7373 (m-80) REVERT: D 258 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8442 (tp) REVERT: D 281 TYR cc_start: 0.8149 (p90) cc_final: 0.7899 (p90) REVERT: D 365 ILE cc_start: 0.8413 (mt) cc_final: 0.8164 (mm) REVERT: D 395 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6698 (tm-30) REVERT: D 402 ARG cc_start: 0.6511 (mpt180) cc_final: 0.5877 (mtt90) REVERT: E 34 ILE cc_start: 0.8166 (pt) cc_final: 0.7931 (pt) REVERT: E 37 ILE cc_start: 0.8486 (mm) cc_final: 0.8250 (mm) REVERT: E 38 LEU cc_start: 0.8101 (mt) cc_final: 0.7727 (mt) REVERT: E 40 LYS cc_start: 0.8122 (tppt) cc_final: 0.7898 (mmmm) REVERT: E 81 LEU cc_start: 0.8587 (tp) cc_final: 0.8300 (tp) REVERT: E 90 TYR cc_start: 0.7008 (t80) cc_final: 0.6560 (t80) REVERT: E 118 THR cc_start: 0.7800 (t) cc_final: 0.7599 (t) REVERT: E 157 LYS cc_start: 0.7785 (ttpp) cc_final: 0.7569 (ttpp) REVERT: E 172 SER cc_start: 0.8164 (t) cc_final: 0.7846 (p) REVERT: E 230 GLU cc_start: 0.7060 (tp30) cc_final: 0.6737 (tp30) REVERT: E 328 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7730 (tm) REVERT: E 353 LYS cc_start: 0.8000 (mttt) cc_final: 0.7541 (mmtt) REVERT: F 39 ASP cc_start: 0.6601 (m-30) cc_final: 0.6312 (m-30) REVERT: F 54 SER cc_start: 0.7941 (m) cc_final: 0.7510 (t) REVERT: F 55 ASN cc_start: 0.8017 (m-40) cc_final: 0.7745 (m110) REVERT: F 113 GLU cc_start: 0.7208 (tt0) cc_final: 0.6977 (tt0) REVERT: F 116 LYS cc_start: 0.8755 (mmmm) cc_final: 0.8370 (mtpp) REVERT: F 139 LYS cc_start: 0.8822 (mttt) cc_final: 0.8465 (mtpp) REVERT: F 146 ARG cc_start: 0.8242 (tmm-80) cc_final: 0.7870 (ttt180) REVERT: F 158 LYS cc_start: 0.8271 (mtmt) cc_final: 0.7888 (mtmt) REVERT: F 208 ASP cc_start: 0.6526 (t70) cc_final: 0.6148 (t0) REVERT: F 237 GLN cc_start: 0.7683 (mt0) cc_final: 0.7387 (tt0) REVERT: F 240 GLN cc_start: 0.7926 (mm110) cc_final: 0.7625 (mp10) REVERT: G 8 VAL cc_start: 0.8279 (t) cc_final: 0.8054 (p) REVERT: K 117 LEU cc_start: 0.8516 (mm) cc_final: 0.8146 (mp) REVERT: K 188 LYS cc_start: 0.8092 (tttt) cc_final: 0.7765 (tmtt) REVERT: K 209 GLU cc_start: 0.7722 (tp30) cc_final: 0.7032 (tp30) REVERT: K 213 LYS cc_start: 0.8055 (tptt) cc_final: 0.7656 (tptt) REVERT: K 245 GLU cc_start: 0.7430 (mp0) cc_final: 0.7116 (mp0) REVERT: K 252 LEU cc_start: 0.7013 (mt) cc_final: 0.6732 (mt) REVERT: K 263 MET cc_start: 0.3700 (OUTLIER) cc_final: 0.3043 (ptt) outliers start: 96 outliers final: 76 residues processed: 820 average time/residue: 0.4318 time to fit residues: 521.0852 Evaluate side-chains 842 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 760 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 502 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 603 ASN Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 122 THR 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 244 ILE Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 469 LYS Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 446 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 213 TRP Chi-restraints excluded: chain D residue 258 LEU 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 417 ASP Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 109 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 370 ASP Chi-restraints excluded: chain F residue 33 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 217 VAL Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain F residue 255 CYS Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain 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 176 optimal weight: 1.9990 chunk 236 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 204 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 0.1980 chunk 222 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 228 optimal weight: 0.9980 chunk 28 optimal weight: 0.3980 chunk 40 optimal weight: 0.0050 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN A 497 GLN ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 GLN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 HIS E 293 GLN E 324 HIS F 277 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.150122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.122666 restraints weight = 38845.334| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.55 r_work: 0.3423 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24132 Z= 0.207 Angle : 0.686 16.272 32831 Z= 0.342 Chirality : 0.043 0.196 3677 Planarity : 0.004 0.064 4022 Dihedral : 14.305 179.565 3597 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.74 % Allowed : 26.34 % Favored : 69.92 % 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: -0.02 (0.16), residues: 2776 helix: 1.05 (0.15), residues: 1302 sheet: -0.22 (0.28), residues: 361 loop : -1.18 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 539 HIS 0.010 0.001 HIS K 266 PHE 0.041 0.002 PHE C 475 TYR 0.048 0.001 TYR C 533 ARG 0.011 0.001 ARG C 542 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8295.00 seconds wall clock time: 148 minutes 46.87 seconds (8926.87 seconds total)