Starting phenix.real_space_refine on Sat Sep 28 00:15:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cm9_7457/09_2024/6cm9_7457.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cm9_7457/09_2024/6cm9_7457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cm9_7457/09_2024/6cm9_7457.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cm9_7457/09_2024/6cm9_7457.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cm9_7457/09_2024/6cm9_7457.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cm9_7457/09_2024/6cm9_7457.cif" } resolution = 3.73 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 102 5.16 5 C 11256 2.51 5 N 3014 2.21 5 O 3303 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 17683 Number of models: 1 Model: "" Number of chains: 11 Chain: "L" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "T" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 1, 'TRANS': 11} Chain: "B" Number of atoms: 4513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4513 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 25, 'TRANS': 544} Chain: "C" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1330 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 3, 'TRANS': 161} Chain: "G" Number of atoms: 4633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4633 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 13, 'TRANS': 571} Chain: "H" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 3, 'TRANS': 159} Chain: "M" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3362 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 20, 'TRANS': 394} Chain breaks: 1 Chain: "S" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1197 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 1, 'TRANS': 140} Chain: "N" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1089 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 118} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.78, per 1000 atoms: 0.55 Number of scatterers: 17683 At special positions: 0 Unit cell: (139.777, 152.581, 130.174, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 102 16.00 P 6 15.00 Mg 2 11.99 O 3303 8.00 N 3014 7.00 C 11256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.22 Conformation dependent library (CDL) restraints added in 2.3 seconds 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4198 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 18 sheets defined 52.7% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'B' and resid 15 through 22 Processing helix chain 'B' and resid 26 through 41 removed outlier: 3.728A pdb=" N LYS B 30 " --> pdb=" O LYS B 26 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 55 removed outlier: 3.599A pdb=" N VAL B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 55 " --> pdb=" O PHE B 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 50 through 55' Processing helix chain 'B' and resid 65 through 76 Processing helix chain 'B' and resid 82 through 86 removed outlier: 3.959A pdb=" N ILE B 85 " --> pdb=" O ASP B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 99 through 111 removed outlier: 3.553A pdb=" N ARG B 103 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 131 removed outlier: 3.576A pdb=" N LEU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 152 removed outlier: 3.698A pdb=" N ARG B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 160 removed outlier: 4.085A pdb=" N VAL B 156 " --> pdb=" O ASN B 152 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 167 Processing helix chain 'B' and resid 174 through 191 removed outlier: 3.853A pdb=" N SER B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 Processing helix chain 'B' and resid 217 through 222 removed outlier: 3.680A pdb=" N PHE B 221 " --> pdb=" O TRP B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 245 removed outlier: 4.030A pdb=" N ARG B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 250 removed outlier: 3.701A pdb=" N SER B 249 " --> pdb=" O PRO B 246 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS B 250 " --> pdb=" O ARG B 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 246 through 250' Processing helix chain 'B' and resid 254 through 267 Processing helix chain 'B' and resid 275 through 282 removed outlier: 3.527A pdb=" N THR B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 291 removed outlier: 3.645A pdb=" N LEU B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 297 through 310 removed outlier: 4.120A pdb=" N VAL B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 removed outlier: 4.592A pdb=" N HIS B 319 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU B 320 " --> pdb=" O LEU B 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 316 through 320' Processing helix chain 'B' and resid 321 through 325 Processing helix chain 'B' and resid 331 through 345 removed outlier: 4.315A pdb=" N GLU B 337 " --> pdb=" O TYR B 333 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU B 339 " --> pdb=" O LYS B 335 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 349 No H-bonds generated for 'chain 'B' and resid 347 through 349' Processing helix chain 'B' and resid 350 through 359 removed outlier: 3.521A pdb=" N VAL B 354 " --> pdb=" O ASN B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 384 Processing helix chain 'B' and resid 387 through 400 Processing helix chain 'B' and resid 403 through 419 removed outlier: 4.364A pdb=" N VAL B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 441 through 455 removed outlier: 3.920A pdb=" N ALA B 446 " --> pdb=" O PRO B 442 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 466 removed outlier: 3.678A pdb=" N LEU B 465 " --> pdb=" O ASN B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 470 Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.544A pdb=" N ASP B 475 " --> pdb=" O GLY B 472 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS B 476 " --> pdb=" O PHE B 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 472 through 476' Processing helix chain 'B' and resid 477 through 495 removed outlier: 3.976A pdb=" N GLN B 481 " --> pdb=" O SER B 477 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 511 removed outlier: 3.765A pdb=" N GLN B 504 " --> pdb=" O GLN B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 533 Processing helix chain 'B' and resid 536 through 541 Processing helix chain 'B' and resid 559 through 564 Processing helix chain 'B' and resid 569 through 574 removed outlier: 3.529A pdb=" N TYR B 574 " --> pdb=" O LEU B 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 39 Processing helix chain 'C' and resid 75 through 79 removed outlier: 3.833A pdb=" N TRP C 78 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG C 79 " --> pdb=" O PRO C 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 75 through 79' Processing helix chain 'C' and resid 96 through 111 removed outlier: 4.018A pdb=" N ASN C 101 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N GLU C 102 " --> pdb=" O GLU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 144 Processing helix chain 'C' and resid 165 through 178 Processing helix chain 'G' and resid 6 through 16 removed outlier: 3.614A pdb=" N THR G 16 " --> pdb=" O ARG G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 40 removed outlier: 4.155A pdb=" N GLU G 25 " --> pdb=" O ALA G 21 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU G 30 " --> pdb=" O MET G 26 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU G 40 " --> pdb=" O SER G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 59 Processing helix chain 'G' and resid 67 through 75 removed outlier: 4.090A pdb=" N LEU G 73 " --> pdb=" O GLU G 69 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA G 75 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 93 removed outlier: 3.661A pdb=" N LYS G 82 " --> pdb=" O LYS G 78 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU G 93 " --> pdb=" O ALA G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 102 removed outlier: 3.588A pdb=" N LEU G 102 " --> pdb=" O VAL G 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 99 through 102' Processing helix chain 'G' and resid 103 through 111 Processing helix chain 'G' and resid 117 through 130 removed outlier: 3.734A pdb=" N LEU G 126 " --> pdb=" O ALA G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 143 removed outlier: 5.793A pdb=" N GLY G 140 " --> pdb=" O ARG G 136 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N GLU G 141 " --> pdb=" O ASP G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 168 removed outlier: 3.552A pdb=" N LYS G 155 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS G 156 " --> pdb=" O TYR G 152 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU G 159 " --> pdb=" O LYS G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 175 Processing helix chain 'G' and resid 187 through 205 removed outlier: 3.667A pdb=" N LEU G 191 " --> pdb=" O ASN G 187 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER G 205 " --> pdb=" O MET G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 213 Processing helix chain 'G' and resid 215 through 229 removed outlier: 3.573A pdb=" N LEU G 219 " --> pdb=" O LEU G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 242 through 256 removed outlier: 3.626A pdb=" N ARG G 248 " --> pdb=" O PHE G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 261 through 267 Processing helix chain 'G' and resid 267 through 275 removed outlier: 3.632A pdb=" N LEU G 271 " --> pdb=" O MET G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 299 removed outlier: 3.713A pdb=" N ASN G 286 " --> pdb=" O LYS G 282 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP G 298 " --> pdb=" O LEU G 294 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE G 299 " --> pdb=" O THR G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 318 removed outlier: 3.699A pdb=" N ARG G 306 " --> pdb=" O GLU G 302 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL G 307 " --> pdb=" O SER G 303 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU G 308 " --> pdb=" O GLY G 304 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU G 318 " --> pdb=" O GLY G 314 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 335 Processing helix chain 'G' and resid 343 through 345 No H-bonds generated for 'chain 'G' and resid 343 through 345' Processing helix chain 'G' and resid 346 through 353 removed outlier: 3.534A pdb=" N CYS G 353 " --> pdb=" O THR G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 354 through 356 No H-bonds generated for 'chain 'G' and resid 354 through 356' Processing helix chain 'G' and resid 358 through 373 Processing helix chain 'G' and resid 377 through 391 removed outlier: 3.624A pdb=" N MET G 382 " --> pdb=" O ILE G 378 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS G 383 " --> pdb=" O ARG G 379 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU G 384 " --> pdb=" O GLY G 380 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP G 390 " --> pdb=" O LEU G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 396 through 411 removed outlier: 3.886A pdb=" N PHE G 405 " --> pdb=" O ALA G 401 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS G 410 " --> pdb=" O LEU G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 415 through 429 Processing helix chain 'G' and resid 436 through 448 removed outlier: 4.279A pdb=" N ASN G 440 " --> pdb=" O ASP G 436 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 464 removed outlier: 3.925A pdb=" N ARG G 458 " --> pdb=" O TYR G 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 469 through 488 removed outlier: 3.536A pdb=" N VAL G 473 " --> pdb=" O GLN G 469 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TRP G 478 " --> pdb=" O GLN G 474 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASP G 485 " --> pdb=" O GLY G 481 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU G 486 " --> pdb=" O GLU G 482 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU G 487 " --> pdb=" O TYR G 483 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL G 488 " --> pdb=" O GLY G 484 " (cutoff:3.500A) Processing helix chain 'G' and resid 503 through 515 removed outlier: 3.715A pdb=" N LEU G 509 " --> pdb=" O VAL G 505 " (cutoff:3.500A) Processing helix chain 'G' and resid 521 through 533 Processing helix chain 'G' and resid 543 through 551 removed outlier: 3.732A pdb=" N VAL G 547 " --> pdb=" O ARG G 543 " (cutoff:3.500A) Processing helix chain 'G' and resid 556 through 573 removed outlier: 3.727A pdb=" N VAL G 564 " --> pdb=" O GLN G 560 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU G 569 " --> pdb=" O GLU G 565 " (cutoff:3.500A) Processing helix chain 'G' and resid 577 through 581 removed outlier: 3.543A pdb=" N LEU G 580 " --> pdb=" O ARG G 577 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU G 581 " --> pdb=" O SER G 578 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 577 through 581' Processing helix chain 'H' and resid 29 through 38 Processing helix chain 'H' and resid 74 through 81 removed outlier: 3.823A pdb=" N TRP H 78 " --> pdb=" O ARG H 75 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG H 79 " --> pdb=" O PRO H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 111 Processing helix chain 'H' and resid 135 through 144 removed outlier: 3.638A pdb=" N ILE H 139 " --> pdb=" O ASN H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 148 Processing helix chain 'H' and resid 165 through 176 Processing helix chain 'M' and resid 26 through 31 removed outlier: 3.819A pdb=" N VAL M 30 " --> pdb=" O MET M 27 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU M 31 " --> pdb=" O SER M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 42 removed outlier: 3.695A pdb=" N ILE M 36 " --> pdb=" O HIS M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 95 Processing helix chain 'M' and resid 99 through 104 removed outlier: 3.815A pdb=" N ILE M 103 " --> pdb=" O GLU M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 117 removed outlier: 3.848A pdb=" N TYR M 111 " --> pdb=" O PHE M 107 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU M 112 " --> pdb=" O VAL M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 132 Processing helix chain 'M' and resid 150 through 155 removed outlier: 3.811A pdb=" N THR M 154 " --> pdb=" O PRO M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 224 Processing helix chain 'M' and resid 243 through 251 removed outlier: 3.570A pdb=" N ASP M 250 " --> pdb=" O ARG M 246 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 40 removed outlier: 3.833A pdb=" N LYS S 29 " --> pdb=" O ASP S 25 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG S 33 " --> pdb=" O LYS S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 96 removed outlier: 3.702A pdb=" N LEU S 81 " --> pdb=" O GLU S 77 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE S 95 " --> pdb=" O LEU S 91 " (cutoff:3.500A) Processing helix chain 'S' and resid 100 through 105 Processing helix chain 'S' and resid 106 through 116 removed outlier: 3.568A pdb=" N PHE S 112 " --> pdb=" O GLU S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 128 through 141 removed outlier: 4.102A pdb=" N VAL S 132 " --> pdb=" O LYS S 128 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 23 Processing helix chain 'N' and resid 80 through 95 removed outlier: 3.593A pdb=" N GLY N 95 " --> pdb=" O LEU N 91 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 119 removed outlier: 3.709A pdb=" N GLN N 107 " --> pdb=" O SER N 103 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY N 119 " --> pdb=" O TYR N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 193 through 199 Processing sheet with id=AA1, first strand: chain 'C' and resid 19 through 22 removed outlier: 3.895A pdb=" N TYR C 58 " --> pdb=" O ILE C 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 90 through 91 removed outlier: 6.997A pdb=" N PHE C 90 " --> pdb=" O PHE C 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 236 through 237 Processing sheet with id=AA4, first strand: chain 'H' and resid 18 through 22 removed outlier: 5.998A pdb=" N MET H 18 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N TRP H 66 " --> pdb=" O MET H 18 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE H 20 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL H 68 " --> pdb=" O ILE H 20 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N MET H 22 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL H 65 " --> pdb=" O GLU H 54 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU H 54 " --> pdb=" O VAL H 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 91 through 93 Processing sheet with id=AA6, first strand: chain 'M' and resid 17 through 20 removed outlier: 3.574A pdb=" N ILE M 17 " --> pdb=" O VAL M 8 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA M 5 " --> pdb=" O THR M 70 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET M 58 " --> pdb=" O ALA M 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'M' and resid 193 through 194 removed outlier: 6.843A pdb=" N ILE M 198 " --> pdb=" O LEU M 264 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE M 176 " --> pdb=" O SER M 197 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL M 175 " --> pdb=" O ILE M 412 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 235 through 238 removed outlier: 3.614A pdb=" N LYS M 237 " --> pdb=" O SER M 266 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE M 198 " --> pdb=" O LEU M 264 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL M 171 " --> pdb=" O TRP M 408 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 179 through 183 removed outlier: 7.081A pdb=" N VAL M 179 " --> pdb=" O GLY M 416 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR M 418 " --> pdb=" O VAL M 179 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU M 181 " --> pdb=" O TYR M 418 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N LEU M 420 " --> pdb=" O LEU M 181 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL M 183 " --> pdb=" O LEU M 420 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 253 through 255 removed outlier: 3.710A pdb=" N ILE M 253 " --> pdb=" O LEU M 212 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY M 213 " --> pdb=" O TYR M 394 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR M 394 " --> pdb=" O GLY M 213 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 277 through 280 removed outlier: 3.621A pdb=" N ILE M 291 " --> pdb=" O PHE M 360 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ARG M 357 " --> pdb=" O PHE M 325 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE M 325 " --> pdb=" O ARG M 357 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N HIS M 359 " --> pdb=" O PRO M 323 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP M 321 " --> pdb=" O GLY M 361 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 306 through 312 removed outlier: 6.969A pdb=" N THR M 306 " --> pdb=" O PRO M 349 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ASN M 308 " --> pdb=" O SER M 347 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N SER M 347 " --> pdb=" O ASN M 308 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS M 333 " --> pdb=" O VAL M 342 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 385 through 386 Processing sheet with id=AB6, first strand: chain 'S' and resid 4 through 5 Processing sheet with id=AB7, first strand: chain 'S' and resid 49 through 51 removed outlier: 3.827A pdb=" N ILE S 71 " --> pdb=" O LYS S 56 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 118 through 119 Processing sheet with id=AB9, first strand: chain 'N' and resid 101 through 102 removed outlier: 3.501A pdb=" N LEU N 181 " --> pdb=" O HIS N 102 " (cutoff:3.500A) 738 hydrogen bonds defined for protein. 2127 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.67 Time building geometry restraints manager: 5.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5201 1.33 - 1.45: 2779 1.45 - 1.57: 9851 1.57 - 1.69: 10 1.69 - 1.81: 166 Bond restraints: 18007 Sorted by residual: bond pdb=" C LEU G 176 " pdb=" N PRO G 177 " ideal model delta sigma weight residual 1.334 1.374 -0.040 8.40e-03 1.42e+04 2.26e+01 bond pdb=" CG1 ILE S 35 " pdb=" CD1 ILE S 35 " ideal model delta sigma weight residual 1.513 1.426 0.087 3.90e-02 6.57e+02 4.98e+00 bond pdb=" CB VAL M 77 " pdb=" CG2 VAL M 77 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.71e+00 bond pdb=" CB VAL B 262 " pdb=" CG2 VAL B 262 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.06e+00 bond pdb=" CB VAL M 332 " pdb=" CG2 VAL M 332 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 3.96e+00 ... (remaining 18002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 23253 2.19 - 4.38: 954 4.38 - 6.57: 116 6.57 - 8.76: 34 8.76 - 10.94: 11 Bond angle restraints: 24368 Sorted by residual: angle pdb=" N VAL B 47 " pdb=" CA VAL B 47 " pdb=" C VAL B 47 " ideal model delta sigma weight residual 111.91 106.87 5.04 8.90e-01 1.26e+00 3.20e+01 angle pdb=" C LYS H 59 " pdb=" N ASN H 60 " pdb=" CA ASN H 60 " ideal model delta sigma weight residual 121.54 130.83 -9.29 1.91e+00 2.74e-01 2.36e+01 angle pdb=" C ASN M 308 " pdb=" N ASN M 309 " pdb=" CA ASN M 309 " ideal model delta sigma weight residual 121.54 130.49 -8.95 1.91e+00 2.74e-01 2.20e+01 angle pdb=" N GLY N 130 " pdb=" CA GLY N 130 " pdb=" C GLY N 130 " ideal model delta sigma weight residual 112.34 121.54 -9.20 2.04e+00 2.40e-01 2.03e+01 angle pdb=" CA HIS L 166 " pdb=" C HIS L 166 " pdb=" N PRO L 167 " ideal model delta sigma weight residual 118.16 121.24 -3.08 7.00e-01 2.04e+00 1.94e+01 ... (remaining 24363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.58: 10916 34.58 - 69.16: 70 69.16 - 103.74: 16 103.74 - 138.32: 3 138.32 - 172.91: 3 Dihedral angle restraints: 11008 sinusoidal: 4546 harmonic: 6462 Sorted by residual: dihedral pdb=" O5' GTP H1001 " pdb=" O3A GTP H1001 " pdb=" PA GTP H1001 " pdb=" PB GTP H1001 " ideal model delta sinusoidal sigma weight residual -85.88 87.03 -172.91 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O5' GTP C1001 " pdb=" O3A GTP C1001 " pdb=" PA GTP C1001 " pdb=" PB GTP C1001 " ideal model delta sinusoidal sigma weight residual 274.12 109.86 164.26 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" C8 GTP H1001 " pdb=" C1' GTP H1001 " pdb=" N9 GTP H1001 " pdb=" O4' GTP H1001 " ideal model delta sinusoidal sigma weight residual 104.59 -38.21 142.80 1 2.00e+01 2.50e-03 4.31e+01 ... (remaining 11005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1923 0.057 - 0.114: 716 0.114 - 0.171: 128 0.171 - 0.228: 17 0.228 - 0.285: 6 Chirality restraints: 2790 Sorted by residual: chirality pdb=" CA ASN M 309 " pdb=" N ASN M 309 " pdb=" C ASN M 309 " pdb=" CB ASN M 309 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB VAL B 47 " pdb=" CA VAL B 47 " pdb=" CG1 VAL B 47 " pdb=" CG2 VAL B 47 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CG LEU B 197 " pdb=" CB LEU B 197 " pdb=" CD1 LEU B 197 " pdb=" CD2 LEU B 197 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 2787 not shown) Planarity restraints: 3085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS L 166 " 0.057 5.00e-02 4.00e+02 8.59e-02 1.18e+01 pdb=" N PRO L 167 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO L 167 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO L 167 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 75 " 0.043 5.00e-02 4.00e+02 6.41e-02 6.58e+00 pdb=" N PRO H 76 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO H 76 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO H 76 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 343 " 0.018 2.00e-02 2.50e+03 1.60e-02 6.44e+00 pdb=" CG TRP M 343 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP M 343 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP M 343 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP M 343 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP M 343 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP M 343 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 343 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 343 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP M 343 " 0.002 2.00e-02 2.50e+03 ... (remaining 3082 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 85 2.51 - 3.10: 12070 3.10 - 3.70: 26825 3.70 - 4.30: 38369 4.30 - 4.90: 63750 Nonbonded interactions: 141099 Sorted by model distance: nonbonded pdb=" O2G GTP H1001 " pdb="MG MG H1002 " model vdw 1.906 2.170 nonbonded pdb=" O1G GTP C1001 " pdb="MG MG C1002 " model vdw 1.933 2.170 nonbonded pdb=" CG2 THR H 31 " pdb="MG MG H1002 " model vdw 2.015 2.590 nonbonded pdb=" O1B GTP C1001 " pdb="MG MG C1002 " model vdw 2.195 2.170 nonbonded pdb=" O2B GTP H1001 " pdb="MG MG H1002 " model vdw 2.209 2.170 ... (remaining 141094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 17 through 179 or resid 1001 through 1002)) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.670 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: 0.000 Extract box with map and model: 0.500 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 39.140 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 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 : 0.009 0.087 18007 Z= 0.568 Angle : 1.022 10.944 24368 Z= 0.539 Chirality : 0.059 0.285 2790 Planarity : 0.007 0.086 3085 Dihedral : 11.579 172.905 6810 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 0.26 % Allowed : 2.81 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.83 (0.14), residues: 2170 helix: -3.18 (0.10), residues: 1090 sheet: -4.03 (0.27), residues: 242 loop : -2.66 (0.19), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP M 343 HIS 0.016 0.003 HIS G 235 PHE 0.029 0.004 PHE M 95 TYR 0.034 0.003 TYR G 290 ARG 0.008 0.001 ARG M 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 561 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 155 LEU cc_start: 0.8426 (tp) cc_final: 0.8129 (tp) REVERT: B 204 ILE cc_start: 0.8980 (mt) cc_final: 0.8745 (mm) REVERT: B 212 ASN cc_start: 0.7890 (m-40) cc_final: 0.7624 (t0) REVERT: G 29 LYS cc_start: 0.8157 (ttmp) cc_final: 0.7900 (tttt) REVERT: G 183 LEU cc_start: 0.7994 (mm) cc_final: 0.7717 (mt) REVERT: G 201 MET cc_start: 0.7703 (mmm) cc_final: 0.7435 (mtp) REVERT: H 114 ASP cc_start: 0.7740 (t70) cc_final: 0.7384 (t0) REVERT: M 28 SER cc_start: 0.7237 (m) cc_final: 0.6634 (p) REVERT: M 58 MET cc_start: 0.8690 (mpp) cc_final: 0.8229 (mtt) REVERT: M 86 LYS cc_start: 0.8346 (tppp) cc_final: 0.7946 (mptt) REVERT: M 264 LEU cc_start: 0.8739 (tp) cc_final: 0.8532 (tp) REVERT: M 298 LYS cc_start: 0.8496 (ptpp) cc_final: 0.8216 (tttm) REVERT: M 324 LYS cc_start: 0.8430 (mttp) cc_final: 0.7761 (tttt) outliers start: 5 outliers final: 4 residues processed: 566 average time/residue: 0.3544 time to fit residues: 289.3151 Evaluate side-chains 328 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 324 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 378 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 0.7980 chunk 164 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 chunk 65 optimal weight: 0.0970 chunk 103 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 197 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 GLN B 152 ASN B 305 ASN B 386 GLN C 86 GLN C 150 HIS C 180 GLN G 184 ASN G 218 GLN G 273 GLN G 452 HIS G 474 GLN H 101 ASN H 128 GLN M 63 ASN M 169 ASN M 239 HIS M 300 GLN M 313 HIS M 414 GLN ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 HIS S 74 GLN N 104 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18007 Z= 0.197 Angle : 0.650 9.586 24368 Z= 0.332 Chirality : 0.044 0.179 2790 Planarity : 0.005 0.065 3085 Dihedral : 9.865 167.100 2423 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.35 % Allowed : 10.78 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.16 (0.16), residues: 2170 helix: -1.56 (0.14), residues: 1091 sheet: -3.80 (0.29), residues: 225 loop : -2.11 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 450 HIS 0.009 0.001 HIS N 116 PHE 0.015 0.002 PHE N 68 TYR 0.015 0.002 TYR G 61 ARG 0.008 0.001 ARG M 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 368 time to evaluate : 1.921 Fit side-chains REVERT: B 58 MET cc_start: 0.8411 (ttp) cc_final: 0.8025 (ttp) REVERT: B 212 ASN cc_start: 0.8014 (m-40) cc_final: 0.7392 (t0) REVERT: B 457 GLU cc_start: 0.7299 (mp0) cc_final: 0.6804 (mp0) REVERT: B 494 LYS cc_start: 0.7800 (mttm) cc_final: 0.7414 (mmtm) REVERT: G 183 LEU cc_start: 0.7938 (mm) cc_final: 0.7579 (mt) REVERT: G 201 MET cc_start: 0.7686 (mmm) cc_final: 0.7131 (mtp) REVERT: G 212 PHE cc_start: 0.7766 (m-10) cc_final: 0.7085 (m-10) REVERT: G 313 LEU cc_start: 0.8055 (mt) cc_final: 0.7801 (mt) REVERT: G 474 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8474 (mt0) REVERT: M 10 ASP cc_start: 0.6979 (p0) cc_final: 0.6692 (p0) REVERT: M 58 MET cc_start: 0.8754 (mpp) cc_final: 0.8311 (mtt) REVERT: M 86 LYS cc_start: 0.8474 (tppp) cc_final: 0.7868 (mptt) REVERT: M 98 LEU cc_start: 0.8266 (tp) cc_final: 0.8024 (tp) REVERT: M 264 LEU cc_start: 0.9013 (tp) cc_final: 0.8730 (tp) REVERT: M 298 LYS cc_start: 0.8297 (ptpp) cc_final: 0.8037 (tttm) REVERT: M 324 LYS cc_start: 0.8369 (mttp) cc_final: 0.7761 (tttt) REVERT: S 13 LYS cc_start: 0.8582 (mmtm) cc_final: 0.8294 (tttt) REVERT: N 77 ARG cc_start: 0.6344 (ptt180) cc_final: 0.5408 (mtt90) outliers start: 46 outliers final: 27 residues processed: 399 average time/residue: 0.3109 time to fit residues: 183.4078 Evaluate side-chains 334 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 306 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 208 MET Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 474 GLN Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 161 SER Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 322 SER Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain S residue 99 CYS Chi-restraints excluded: chain S residue 119 ILE Chi-restraints excluded: chain S residue 127 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 109 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 164 optimal weight: 6.9990 chunk 134 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 213 optimal weight: 8.9990 chunk 175 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 chunk 67 optimal weight: 20.0000 chunk 158 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS C 180 GLN G 100 HIS ** G 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 474 GLN G 491 GLN H 128 GLN ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18007 Z= 0.254 Angle : 0.633 11.619 24368 Z= 0.317 Chirality : 0.044 0.191 2790 Planarity : 0.005 0.049 3085 Dihedral : 9.614 169.965 2423 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.55 % Allowed : 12.67 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.41 (0.17), residues: 2170 helix: -0.83 (0.15), residues: 1097 sheet: -3.76 (0.29), residues: 220 loop : -1.84 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 450 HIS 0.006 0.001 HIS N 116 PHE 0.020 0.002 PHE M 107 TYR 0.017 0.002 TYR M 403 ARG 0.008 0.000 ARG M 246 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 338 time to evaluate : 2.164 Fit side-chains revert: symmetry clash REVERT: B 175 MET cc_start: 0.6628 (tpt) cc_final: 0.6386 (tpt) REVERT: B 212 ASN cc_start: 0.8153 (m-40) cc_final: 0.7717 (t0) REVERT: C 22 MET cc_start: 0.6698 (mtp) cc_final: 0.6462 (mtp) REVERT: C 26 ASP cc_start: 0.7445 (p0) cc_final: 0.7140 (p0) REVERT: G 123 LEU cc_start: 0.8951 (mt) cc_final: 0.8714 (mt) REVERT: G 183 LEU cc_start: 0.7895 (mm) cc_final: 0.7472 (mt) REVERT: G 201 MET cc_start: 0.7768 (mmm) cc_final: 0.7350 (mtp) REVERT: G 321 ASP cc_start: 0.6430 (OUTLIER) cc_final: 0.6139 (m-30) REVERT: G 474 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8521 (mt0) REVERT: H 49 ILE cc_start: 0.9092 (mm) cc_final: 0.8816 (mp) REVERT: M 10 ASP cc_start: 0.7024 (p0) cc_final: 0.6755 (p0) REVERT: M 58 MET cc_start: 0.8782 (mpp) cc_final: 0.8339 (mtt) REVERT: M 86 LYS cc_start: 0.8607 (tppp) cc_final: 0.8011 (mptt) REVERT: M 264 LEU cc_start: 0.8965 (tp) cc_final: 0.8711 (tp) REVERT: M 298 LYS cc_start: 0.8343 (ptpp) cc_final: 0.8024 (tttm) REVERT: M 324 LYS cc_start: 0.8392 (mttp) cc_final: 0.7697 (tttt) REVERT: S 23 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8523 (pt) REVERT: S 30 LYS cc_start: 0.8533 (mppt) cc_final: 0.8098 (mppt) REVERT: S 77 GLU cc_start: 0.7327 (mt-10) cc_final: 0.6889 (mp0) REVERT: S 142 GLN cc_start: 0.6635 (pm20) cc_final: 0.5725 (pm20) REVERT: N 77 ARG cc_start: 0.6373 (ptt180) cc_final: 0.5339 (mtt90) outliers start: 50 outliers final: 35 residues processed: 373 average time/residue: 0.3059 time to fit residues: 170.9871 Evaluate side-chains 340 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 302 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 392 CYS Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 474 GLN Chi-restraints excluded: chain G residue 502 GLU Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 127 ASP Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 99 CYS Chi-restraints excluded: chain S residue 119 ILE Chi-restraints excluded: chain S residue 127 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 195 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 chunk 102 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 132 optimal weight: 7.9990 chunk 198 optimal weight: 0.7980 chunk 209 optimal weight: 20.0000 chunk 103 optimal weight: 0.8980 chunk 187 optimal weight: 0.0770 chunk 56 optimal weight: 5.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 166 HIS B 56 ASN ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 474 GLN H 128 GLN M 64 ASN ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 74 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18007 Z= 0.173 Angle : 0.588 12.982 24368 Z= 0.291 Chirality : 0.042 0.165 2790 Planarity : 0.004 0.043 3085 Dihedral : 9.359 168.272 2423 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.35 % Allowed : 13.79 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.83 (0.18), residues: 2170 helix: -0.33 (0.16), residues: 1081 sheet: -3.59 (0.29), residues: 222 loop : -1.54 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 450 HIS 0.004 0.001 HIS N 116 PHE 0.021 0.001 PHE M 83 TYR 0.017 0.001 TYR B 524 ARG 0.009 0.000 ARG M 246 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 332 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 212 ASN cc_start: 0.8176 (m-40) cc_final: 0.7721 (t0) REVERT: C 22 MET cc_start: 0.6766 (mtp) cc_final: 0.6467 (mtp) REVERT: G 183 LEU cc_start: 0.7779 (mm) cc_final: 0.7554 (mt) REVERT: G 201 MET cc_start: 0.7692 (mmm) cc_final: 0.7250 (mtp) REVERT: G 427 THR cc_start: 0.7402 (p) cc_final: 0.7072 (t) REVERT: G 474 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8385 (mt0) REVERT: H 46 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7481 (mt) REVERT: H 49 ILE cc_start: 0.9138 (mm) cc_final: 0.8872 (mp) REVERT: M 10 ASP cc_start: 0.6905 (p0) cc_final: 0.6645 (p0) REVERT: M 58 MET cc_start: 0.8733 (mpp) cc_final: 0.8366 (mtt) REVERT: M 86 LYS cc_start: 0.8542 (tppp) cc_final: 0.7909 (mptt) REVERT: M 98 LEU cc_start: 0.8282 (tp) cc_final: 0.8063 (tp) REVERT: M 264 LEU cc_start: 0.9033 (tp) cc_final: 0.8742 (tp) REVERT: M 298 LYS cc_start: 0.8338 (ptpp) cc_final: 0.7947 (ttpp) REVERT: M 324 LYS cc_start: 0.8385 (mttp) cc_final: 0.7662 (tttt) REVERT: S 30 LYS cc_start: 0.8409 (mppt) cc_final: 0.8139 (mppt) REVERT: S 65 LEU cc_start: 0.8450 (tp) cc_final: 0.8249 (tp) REVERT: N 77 ARG cc_start: 0.6278 (ptt180) cc_final: 0.5179 (mtt90) outliers start: 46 outliers final: 29 residues processed: 362 average time/residue: 0.2940 time to fit residues: 159.1147 Evaluate side-chains 340 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 309 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 505 GLN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 474 GLN Chi-restraints excluded: chain G residue 502 GLU Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 128 GLN Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 127 ASP Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain S residue 99 CYS Chi-restraints excluded: chain S residue 119 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 174 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 156 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 178 optimal weight: 7.9990 chunk 144 optimal weight: 0.0060 chunk 0 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 474 GLN H 80 HIS H 128 GLN M 64 ASN ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 18007 Z= 0.325 Angle : 0.651 12.607 24368 Z= 0.323 Chirality : 0.045 0.167 2790 Planarity : 0.004 0.055 3085 Dihedral : 9.382 170.911 2423 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.58 % Allowed : 13.99 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.79 (0.18), residues: 2170 helix: -0.31 (0.15), residues: 1097 sheet: -3.67 (0.29), residues: 233 loop : -1.45 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 450 HIS 0.005 0.001 HIS M 62 PHE 0.018 0.002 PHE M 83 TYR 0.023 0.002 TYR B 524 ARG 0.011 0.001 ARG M 246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 309 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 212 ASN cc_start: 0.8236 (m-40) cc_final: 0.7803 (t0) REVERT: C 26 ASP cc_start: 0.7498 (p0) cc_final: 0.7221 (p0) REVERT: G 123 LEU cc_start: 0.8946 (mt) cc_final: 0.8719 (mt) REVERT: G 183 LEU cc_start: 0.7776 (mm) cc_final: 0.7533 (mt) REVERT: G 201 MET cc_start: 0.7845 (mmm) cc_final: 0.7511 (mtp) REVERT: G 333 LEU cc_start: 0.7579 (mt) cc_final: 0.7373 (mt) REVERT: H 46 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7535 (mt) REVERT: M 10 ASP cc_start: 0.7089 (p0) cc_final: 0.6884 (p0) REVERT: M 58 MET cc_start: 0.8827 (mpp) cc_final: 0.8369 (mtt) REVERT: M 86 LYS cc_start: 0.8581 (tppp) cc_final: 0.7985 (mptt) REVERT: M 298 LYS cc_start: 0.8380 (ptpp) cc_final: 0.8008 (ttpp) REVERT: S 65 LEU cc_start: 0.8625 (tp) cc_final: 0.8380 (tp) REVERT: S 100 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7392 (mm-30) REVERT: N 77 ARG cc_start: 0.6260 (ptt180) cc_final: 0.5163 (mtt90) outliers start: 70 outliers final: 53 residues processed: 358 average time/residue: 0.2922 time to fit residues: 157.0322 Evaluate side-chains 347 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 292 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 505 GLN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 381 MET Chi-restraints excluded: chain G residue 392 CYS Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 443 GLN Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 502 GLU Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 95 PHE Chi-restraints excluded: chain M residue 127 ASP Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 161 SER Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain S residue 71 ILE Chi-restraints excluded: chain S residue 99 CYS Chi-restraints excluded: chain S residue 100 GLU Chi-restraints excluded: chain S residue 119 ILE Chi-restraints excluded: chain S residue 127 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 70 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 209 optimal weight: 6.9990 chunk 174 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 GLN G 273 GLN H 128 GLN ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18007 Z= 0.312 Angle : 0.642 12.853 24368 Z= 0.318 Chirality : 0.045 0.167 2790 Planarity : 0.004 0.048 3085 Dihedral : 9.364 172.701 2423 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.78 % Allowed : 14.45 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.68 (0.18), residues: 2170 helix: -0.23 (0.15), residues: 1097 sheet: -3.60 (0.29), residues: 232 loop : -1.39 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 450 HIS 0.004 0.001 HIS M 62 PHE 0.017 0.002 PHE M 83 TYR 0.016 0.002 TYR G 61 ARG 0.010 0.000 ARG M 246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 308 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: T 13 MET cc_start: 0.7448 (mmm) cc_final: 0.7156 (tpp) REVERT: B 212 ASN cc_start: 0.8204 (m-40) cc_final: 0.7498 (t0) REVERT: C 26 ASP cc_start: 0.7552 (p0) cc_final: 0.7302 (p0) REVERT: G 23 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8303 (tm-30) REVERT: G 24 ARG cc_start: 0.8356 (ttp-110) cc_final: 0.8117 (tmm160) REVERT: G 94 ASP cc_start: 0.7061 (OUTLIER) cc_final: 0.6488 (p0) REVERT: G 183 LEU cc_start: 0.7701 (mm) cc_final: 0.7489 (mt) REVERT: G 201 MET cc_start: 0.7881 (mmm) cc_final: 0.7616 (mtp) REVERT: G 427 THR cc_start: 0.7289 (p) cc_final: 0.7008 (t) REVERT: H 46 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7480 (mt) REVERT: H 59 LYS cc_start: 0.7169 (mmmt) cc_final: 0.6906 (mmmt) REVERT: M 10 ASP cc_start: 0.7165 (p0) cc_final: 0.6902 (p0) REVERT: M 58 MET cc_start: 0.8803 (mpp) cc_final: 0.8407 (mtt) REVERT: M 86 LYS cc_start: 0.8594 (tppp) cc_final: 0.7984 (mptt) REVERT: M 298 LYS cc_start: 0.8418 (ptpp) cc_final: 0.8034 (ttpp) REVERT: S 65 LEU cc_start: 0.8554 (tp) cc_final: 0.8321 (tp) REVERT: S 100 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7340 (mm-30) REVERT: N 77 ARG cc_start: 0.6232 (ptt180) cc_final: 0.5163 (mtt90) outliers start: 74 outliers final: 59 residues processed: 360 average time/residue: 0.3004 time to fit residues: 162.2122 Evaluate side-chains 348 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 286 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 505 GLN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 381 MET Chi-restraints excluded: chain G residue 392 CYS Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 443 GLN Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 502 GLU Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 95 PHE Chi-restraints excluded: chain M residue 127 ASP Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain M residue 390 ILE Chi-restraints excluded: chain S residue 71 ILE Chi-restraints excluded: chain S residue 99 CYS Chi-restraints excluded: chain S residue 100 GLU Chi-restraints excluded: chain S residue 119 ILE Chi-restraints excluded: chain S residue 127 SER Chi-restraints excluded: chain S residue 138 SER Chi-restraints excluded: chain N residue 70 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 202 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 209 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 180 GLN G 105 ASN H 128 GLN M 64 ASN ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18007 Z= 0.302 Angle : 0.651 12.797 24368 Z= 0.320 Chirality : 0.044 0.165 2790 Planarity : 0.004 0.043 3085 Dihedral : 9.314 174.256 2423 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.19 % Allowed : 14.76 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.56 (0.18), residues: 2170 helix: -0.15 (0.15), residues: 1101 sheet: -3.64 (0.28), residues: 250 loop : -1.19 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 450 HIS 0.004 0.001 HIS M 62 PHE 0.018 0.002 PHE M 83 TYR 0.015 0.002 TYR G 61 ARG 0.007 0.000 ARG M 246 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 298 time to evaluate : 1.976 Fit side-chains revert: symmetry clash REVERT: B 212 ASN cc_start: 0.8200 (m-40) cc_final: 0.7523 (t0) REVERT: G 94 ASP cc_start: 0.7097 (OUTLIER) cc_final: 0.6527 (p0) REVERT: G 183 LEU cc_start: 0.7641 (mm) cc_final: 0.7440 (mt) REVERT: G 228 MET cc_start: 0.6759 (mmm) cc_final: 0.6351 (mmm) REVERT: G 427 THR cc_start: 0.7342 (p) cc_final: 0.7102 (t) REVERT: G 560 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7903 (tm130) REVERT: H 59 LYS cc_start: 0.7136 (mmmt) cc_final: 0.6903 (mmmt) REVERT: M 10 ASP cc_start: 0.7151 (p0) cc_final: 0.6889 (p0) REVERT: M 58 MET cc_start: 0.8768 (mpp) cc_final: 0.8371 (mtt) REVERT: M 86 LYS cc_start: 0.8626 (tppp) cc_final: 0.8035 (mptt) REVERT: M 298 LYS cc_start: 0.8398 (ptpp) cc_final: 0.8063 (ttpt) REVERT: S 65 LEU cc_start: 0.8570 (tp) cc_final: 0.8301 (tp) REVERT: S 100 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7291 (mm-30) REVERT: S 108 GLU cc_start: 0.7072 (pt0) cc_final: 0.6658 (tt0) REVERT: N 77 ARG cc_start: 0.6226 (ptt180) cc_final: 0.5158 (mtt90) outliers start: 82 outliers final: 65 residues processed: 356 average time/residue: 0.2944 time to fit residues: 156.7725 Evaluate side-chains 354 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 286 time to evaluate : 2.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 505 GLN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 381 MET Chi-restraints excluded: chain G residue 392 CYS Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 443 GLN Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 502 GLU Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain G residue 560 GLN Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 95 PHE Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain S residue 71 ILE Chi-restraints excluded: chain S residue 99 CYS Chi-restraints excluded: chain S residue 100 GLU Chi-restraints excluded: chain S residue 119 ILE Chi-restraints excluded: chain S residue 127 SER Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain N residue 70 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 129 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 63 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 132 optimal weight: 0.0870 chunk 142 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 ASN ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18007 Z= 0.185 Angle : 0.613 13.569 24368 Z= 0.300 Chirality : 0.043 0.200 2790 Planarity : 0.004 0.042 3085 Dihedral : 9.135 175.038 2423 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.96 % Allowed : 16.04 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.22 (0.18), residues: 2170 helix: 0.14 (0.16), residues: 1102 sheet: -3.45 (0.29), residues: 244 loop : -1.07 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 450 HIS 0.003 0.001 HIS M 62 PHE 0.017 0.001 PHE M 83 TYR 0.014 0.001 TYR S 20 ARG 0.007 0.000 ARG H 97 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 320 time to evaluate : 2.126 Fit side-chains REVERT: B 86 MET cc_start: 0.6459 (ptp) cc_final: 0.6223 (ptp) REVERT: B 212 ASN cc_start: 0.8212 (m-40) cc_final: 0.7511 (t0) REVERT: G 23 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8376 (tm-30) REVERT: G 94 ASP cc_start: 0.7062 (OUTLIER) cc_final: 0.6483 (p0) REVERT: G 324 ILE cc_start: 0.7628 (mm) cc_final: 0.7349 (mm) REVERT: G 427 THR cc_start: 0.7320 (p) cc_final: 0.6958 (t) REVERT: G 560 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7885 (tm130) REVERT: M 10 ASP cc_start: 0.6946 (p0) cc_final: 0.6691 (p0) REVERT: M 58 MET cc_start: 0.8576 (mpp) cc_final: 0.8282 (mtt) REVERT: M 86 LYS cc_start: 0.8535 (tppp) cc_final: 0.7951 (mptt) REVERT: M 298 LYS cc_start: 0.8386 (ptpp) cc_final: 0.8015 (ttpp) REVERT: M 366 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7030 (mm-30) REVERT: S 65 LEU cc_start: 0.8436 (tp) cc_final: 0.7959 (tp) REVERT: S 100 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.6792 (mm-30) REVERT: N 77 ARG cc_start: 0.6212 (ptt180) cc_final: 0.5121 (mtt90) outliers start: 58 outliers final: 42 residues processed: 357 average time/residue: 0.3072 time to fit residues: 163.3180 Evaluate side-chains 337 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 292 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 505 GLN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 174 MET Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 381 MET Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain G residue 560 GLN Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain S residue 99 CYS Chi-restraints excluded: chain S residue 100 GLU Chi-restraints excluded: chain S residue 119 ILE Chi-restraints excluded: chain S residue 127 SER Chi-restraints excluded: chain N residue 20 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 190 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 194 optimal weight: 0.1980 chunk 117 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 176 optimal weight: 0.7980 chunk 184 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 GLN M 64 ASN ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18007 Z= 0.257 Angle : 0.644 12.016 24368 Z= 0.318 Chirality : 0.044 0.196 2790 Planarity : 0.004 0.071 3085 Dihedral : 9.172 178.829 2423 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.06 % Allowed : 16.24 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.20 (0.18), residues: 2170 helix: 0.15 (0.16), residues: 1100 sheet: -3.46 (0.29), residues: 244 loop : -1.06 (0.23), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 172 HIS 0.004 0.001 HIS M 62 PHE 0.015 0.001 PHE M 83 TYR 0.017 0.001 TYR H 58 ARG 0.013 0.001 ARG H 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 297 time to evaluate : 1.862 Fit side-chains REVERT: B 85 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8585 (mp) REVERT: B 212 ASN cc_start: 0.8225 (m-40) cc_final: 0.7541 (t0) REVERT: B 458 ARG cc_start: 0.6659 (mmp-170) cc_final: 0.6328 (ttm-80) REVERT: G 23 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8306 (tm-30) REVERT: G 94 ASP cc_start: 0.7061 (OUTLIER) cc_final: 0.6486 (p0) REVERT: G 228 MET cc_start: 0.6942 (mmm) cc_final: 0.6432 (mmm) REVERT: G 324 ILE cc_start: 0.7699 (mm) cc_final: 0.7412 (mm) REVERT: G 427 THR cc_start: 0.7335 (p) cc_final: 0.6935 (t) REVERT: G 560 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7873 (tm130) REVERT: H 134 MET cc_start: 0.6074 (mmt) cc_final: 0.5489 (mmt) REVERT: M 10 ASP cc_start: 0.7001 (p0) cc_final: 0.6717 (p0) REVERT: M 58 MET cc_start: 0.8615 (mpp) cc_final: 0.8247 (mtt) REVERT: M 86 LYS cc_start: 0.8593 (tppp) cc_final: 0.7989 (mptt) REVERT: M 264 LEU cc_start: 0.8952 (tp) cc_final: 0.8575 (tp) REVERT: M 296 LYS cc_start: 0.8522 (pttt) cc_final: 0.8245 (pttt) REVERT: M 298 LYS cc_start: 0.8388 (ptpp) cc_final: 0.8020 (ttpp) REVERT: M 366 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7180 (mm-30) REVERT: M 395 LEU cc_start: 0.8437 (tt) cc_final: 0.8198 (tt) REVERT: N 77 ARG cc_start: 0.6109 (ptt180) cc_final: 0.5089 (mtt90) outliers start: 60 outliers final: 48 residues processed: 336 average time/residue: 0.3138 time to fit residues: 157.6285 Evaluate side-chains 342 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 291 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 505 GLN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 174 MET Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 381 MET Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 443 GLN Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain G residue 560 GLN Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 127 ASP Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain S residue 99 CYS Chi-restraints excluded: chain S residue 119 ILE Chi-restraints excluded: chain S residue 127 SER Chi-restraints excluded: chain N residue 20 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 206 optimal weight: 8.9990 chunk 125 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 216 optimal weight: 6.9990 chunk 198 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 17 optimal weight: 0.0980 chunk 132 optimal weight: 8.9990 chunk 105 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 ASN G 218 GLN M 64 ASN ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18007 Z= 0.199 Angle : 0.636 12.956 24368 Z= 0.310 Chirality : 0.043 0.192 2790 Planarity : 0.004 0.043 3085 Dihedral : 9.080 178.996 2423 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.86 % Allowed : 16.39 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.07 (0.18), residues: 2170 helix: 0.26 (0.16), residues: 1102 sheet: -3.27 (0.30), residues: 241 loop : -1.06 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 172 HIS 0.003 0.001 HIS M 62 PHE 0.016 0.001 PHE M 83 TYR 0.020 0.001 TYR H 58 ARG 0.009 0.000 ARG H 117 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 302 time to evaluate : 2.108 Fit side-chains REVERT: B 212 ASN cc_start: 0.8209 (m-40) cc_final: 0.7507 (t0) REVERT: G 23 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8216 (tm-30) REVERT: G 94 ASP cc_start: 0.7032 (OUTLIER) cc_final: 0.6546 (p0) REVERT: G 228 MET cc_start: 0.6897 (mmm) cc_final: 0.6410 (mmm) REVERT: G 324 ILE cc_start: 0.7691 (mm) cc_final: 0.7363 (mm) REVERT: G 427 THR cc_start: 0.7307 (p) cc_final: 0.6874 (t) REVERT: G 560 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.7915 (tm130) REVERT: M 10 ASP cc_start: 0.6855 (p0) cc_final: 0.6575 (p0) REVERT: M 58 MET cc_start: 0.8570 (mpp) cc_final: 0.8274 (mtt) REVERT: M 86 LYS cc_start: 0.8541 (tppp) cc_final: 0.7927 (mptt) REVERT: M 264 LEU cc_start: 0.8925 (tp) cc_final: 0.8571 (tp) REVERT: M 298 LYS cc_start: 0.8393 (ptpp) cc_final: 0.8036 (ttpp) REVERT: M 366 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7151 (mm-30) REVERT: N 77 ARG cc_start: 0.6098 (ptt180) cc_final: 0.4995 (mtt90) outliers start: 56 outliers final: 43 residues processed: 338 average time/residue: 0.3082 time to fit residues: 155.4557 Evaluate side-chains 334 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 289 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 505 GLN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 381 MET Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain G residue 560 GLN Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain S residue 99 CYS Chi-restraints excluded: chain S residue 119 ILE Chi-restraints excluded: chain S residue 127 SER Chi-restraints excluded: chain N residue 20 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 172 optimal weight: 0.7980 chunk 72 optimal weight: 20.0000 chunk 177 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 ASN ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.171555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.137674 restraints weight = 23342.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.135643 restraints weight = 28268.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.137636 restraints weight = 27658.954| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18007 Z= 0.190 Angle : 0.627 13.244 24368 Z= 0.305 Chirality : 0.043 0.190 2790 Planarity : 0.004 0.042 3085 Dihedral : 9.022 178.600 2423 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.45 % Allowed : 17.11 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.96 (0.18), residues: 2170 helix: 0.34 (0.16), residues: 1116 sheet: -3.20 (0.30), residues: 242 loop : -1.01 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 172 HIS 0.003 0.001 HIS M 62 PHE 0.015 0.001 PHE M 83 TYR 0.022 0.001 TYR H 58 ARG 0.006 0.000 ARG M 246 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3893.45 seconds wall clock time: 70 minutes 18.41 seconds (4218.41 seconds total)