Starting phenix.real_space_refine on Mon Feb 19 13:07:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjj_25927/02_2024/7tjj_25927_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjj_25927/02_2024/7tjj_25927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjj_25927/02_2024/7tjj_25927.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjj_25927/02_2024/7tjj_25927.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjj_25927/02_2024/7tjj_25927_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjj_25927/02_2024/7tjj_25927_updated.pdb" } resolution = 2.7 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= 0.000 sd= 0.002 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 93 5.49 5 Mg 4 5.21 5 S 105 5.16 5 C 15519 2.51 5 N 4112 2.21 5 O 4899 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24732 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3889 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 475} Chain breaks: 4 Chain: "B" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2081 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 11, 'TRANS': 239} Chain breaks: 1 Chain: "C" Number of atoms: 4504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4504 Classifications: {'peptide': 544} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 528} Chain breaks: 5 Chain: "D" Number of atoms: 3536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3536 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 420} Chain breaks: 3 Chain: "E" Number of atoms: 3596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3596 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 21, 'TRANS': 416} Chain breaks: 3 Chain: "F" Number of atoms: 2141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2141 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 7, 'TRANS': 252} Chain breaks: 2 Chain: "G" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 832 Classifications: {'DNA': 41} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 40} Chain: "H" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 846 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "I" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3019 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 14, 'TRANS': 365} Chain breaks: 5 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "H" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "I" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 12.98, per 1000 atoms: 0.52 Number of scatterers: 24732 At special positions: 0 Unit cell: (117.82, 141.9, 179.74, 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 105 16.00 P 93 15.00 Mg 4 11.99 O 4899 8.00 N 4112 7.00 C 15519 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.86 Conformation dependent library (CDL) restraints added in 3.9 seconds 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5414 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 146 helices and 12 sheets defined 52.2% alpha, 7.5% beta 41 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 10.51 Creating SS restraints... Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 424 through 429 Processing helix chain 'A' and resid 454 through 468 Processing helix chain 'A' and resid 485 through 501 Processing helix chain 'A' and resid 515 through 517 No H-bonds generated for 'chain 'A' and resid 515 through 517' Processing helix chain 'A' and resid 521 through 533 removed outlier: 3.684A pdb=" N CYS A 524 " --> pdb=" O PRO A 521 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A 528 " --> pdb=" O TYR A 525 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TRP A 529 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER A 533 " --> pdb=" O ASN A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 551 Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 568 through 571 Processing helix chain 'A' and resid 577 through 587 removed outlier: 4.081A pdb=" N THR A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 607 No H-bonds generated for 'chain 'A' and resid 604 through 607' Processing helix chain 'A' and resid 611 through 617 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 686 through 699 Processing helix chain 'A' and resid 703 through 725 Processing helix chain 'A' and resid 775 through 783 Processing helix chain 'A' and resid 789 through 795 Processing helix chain 'A' and resid 799 through 814 Processing helix chain 'A' and resid 822 through 835 Processing helix chain 'A' and resid 840 through 851 removed outlier: 5.242A pdb=" N LYS A 847 " --> pdb=" O MET A 843 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N THR A 848 " --> pdb=" O GLU A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 875 Processing helix chain 'A' and resid 898 through 907 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 271 through 284 Processing helix chain 'B' and resid 287 through 309 removed outlier: 4.440A pdb=" N LYS B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N MET B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE B 301 " --> pdb=" O GLN B 297 " (cutoff:3.500A) Proline residue: B 302 - end of helix Processing helix chain 'B' and resid 323 through 332 Processing helix chain 'B' and resid 334 through 342 Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 391 through 393 No H-bonds generated for 'chain 'B' and resid 391 through 393' Processing helix chain 'B' and resid 399 through 411 Processing helix chain 'B' and resid 435 through 446 Processing helix chain 'B' and resid 461 through 464 Processing helix chain 'B' and resid 467 through 473 Processing helix chain 'B' and resid 489 through 492 Processing helix chain 'C' and resid 17 through 19 No H-bonds generated for 'chain 'C' and resid 17 through 19' Processing helix chain 'C' and resid 51 through 91 removed outlier: 3.841A pdb=" N GLN C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 157 Processing helix chain 'C' and resid 185 through 189 Processing helix chain 'C' and resid 191 through 195 Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 213 through 228 removed outlier: 3.782A pdb=" N SER C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LYS C 228 " --> pdb=" O LYS C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 248 Processing helix chain 'C' and resid 253 through 261 removed outlier: 4.031A pdb=" N ARG C 261 " --> pdb=" O ARG C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 285 removed outlier: 3.612A pdb=" N ILE C 280 " --> pdb=" O TYR C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 306 Processing helix chain 'C' and resid 314 through 331 Processing helix chain 'C' and resid 333 through 336 removed outlier: 3.860A pdb=" N VAL C 336 " --> pdb=" O ALA C 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 333 through 336' Processing helix chain 'C' and resid 348 through 354 Processing helix chain 'C' and resid 358 through 370 Processing helix chain 'C' and resid 389 through 394 Processing helix chain 'C' and resid 402 through 413 Processing helix chain 'C' and resid 424 through 432 Processing helix chain 'C' and resid 436 through 440 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 475 through 478 No H-bonds generated for 'chain 'C' and resid 475 through 478' Processing helix chain 'C' and resid 483 through 492 Processing helix chain 'C' and resid 494 through 496 No H-bonds generated for 'chain 'C' and resid 494 through 496' Processing helix chain 'C' and resid 511 through 514 No H-bonds generated for 'chain 'C' and resid 511 through 514' Processing helix chain 'C' and resid 520 through 529 Processing helix chain 'C' and resid 537 through 547 removed outlier: 3.754A pdb=" N THR C 547 " --> pdb=" O ALA C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 558 removed outlier: 3.763A pdb=" N ARG C 558 " --> pdb=" O LEU C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 570 Processing helix chain 'C' and resid 575 through 594 Processing helix chain 'D' and resid 47 through 61 Processing helix chain 'D' and resid 66 through 68 No H-bonds generated for 'chain 'D' and resid 66 through 68' Processing helix chain 'D' and resid 73 through 90 removed outlier: 5.116A pdb=" N ASP D 77 " --> pdb=" O TYR D 74 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N CYS D 78 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN D 80 " --> pdb=" O ASP D 77 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE D 86 " --> pdb=" O ASP D 83 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE D 90 " --> pdb=" O LYS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 120 Processing helix chain 'D' and resid 141 through 157 removed outlier: 3.544A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 188 Processing helix chain 'D' and resid 229 through 240 Processing helix chain 'D' and resid 257 through 259 No H-bonds generated for 'chain 'D' and resid 257 through 259' Processing helix chain 'D' and resid 262 through 267 Processing helix chain 'D' and resid 281 through 292 Processing helix chain 'D' and resid 302 through 314 Processing helix chain 'D' and resid 319 through 330 Processing helix chain 'D' and resid 334 through 346 removed outlier: 3.630A pdb=" N SER D 340 " --> pdb=" O THR D 336 " (cutoff:3.500A) Proline residue: D 343 - end of helix Processing helix chain 'D' and resid 351 through 360 Processing helix chain 'D' and resid 362 through 371 removed outlier: 3.518A pdb=" N ILE D 366 " --> pdb=" O SER D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 381 Processing helix chain 'D' and resid 385 through 400 Processing helix chain 'D' and resid 408 through 423 Processing helix chain 'D' and resid 453 through 465 removed outlier: 3.590A pdb=" N LYS D 457 " --> pdb=" O LYS D 453 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASN D 458 " --> pdb=" O LYS D 454 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL D 459 " --> pdb=" O ASP D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 488 Processing helix chain 'D' and resid 493 through 495 No H-bonds generated for 'chain 'D' and resid 493 through 495' Processing helix chain 'D' and resid 499 through 501 No H-bonds generated for 'chain 'D' and resid 499 through 501' Processing helix chain 'D' and resid 510 through 516 Processing helix chain 'D' and resid 524 through 527 Processing helix chain 'E' and resid 12 through 21 Processing helix chain 'E' and resid 43 through 53 Processing helix chain 'E' and resid 64 through 67 No H-bonds generated for 'chain 'E' and resid 64 through 67' Processing helix chain 'E' and resid 70 through 88 Processing helix chain 'E' and resid 99 through 101 No H-bonds generated for 'chain 'E' and resid 99 through 101' Processing helix chain 'E' and resid 105 through 118 removed outlier: 4.048A pdb=" N GLN E 118 " --> pdb=" O ASN E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 137 No H-bonds generated for 'chain 'E' and resid 135 through 137' Processing helix chain 'E' and resid 145 through 154 removed outlier: 3.568A pdb=" N TYR E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASN E 153 " --> pdb=" O TYR E 149 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLU E 154 " --> pdb=" O ILE E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 182 removed outlier: 4.207A pdb=" N TYR E 179 " --> pdb=" O PHE E 175 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER E 180 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N THR E 181 " --> pdb=" O GLN E 177 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N HIS E 182 " --> pdb=" O ARG E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 210 removed outlier: 5.864A pdb=" N GLY E 207 " --> pdb=" O MET E 203 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLU E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 221 removed outlier: 3.832A pdb=" N ILE E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 251 removed outlier: 5.808A pdb=" N SER E 249 " --> pdb=" O GLN E 245 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N TYR E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 272 Proline residue: E 267 - end of helix removed outlier: 3.826A pdb=" N ARG E 272 " --> pdb=" O LYS E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 287 Processing helix chain 'E' and resid 289 through 292 Processing helix chain 'E' and resid 326 through 340 Processing helix chain 'E' and resid 343 through 345 No H-bonds generated for 'chain 'E' and resid 343 through 345' Processing helix chain 'E' and resid 373 through 375 No H-bonds generated for 'chain 'E' and resid 373 through 375' Processing helix chain 'E' and resid 383 through 393 Processing helix chain 'E' and resid 418 through 429 Processing helix chain 'E' and resid 456 through 465 removed outlier: 3.666A pdb=" N GLU E 461 " --> pdb=" O GLU E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 473 No H-bonds generated for 'chain 'E' and resid 471 through 473' Processing helix chain 'F' and resid 3 through 14 Processing helix chain 'F' and resid 28 through 46 removed outlier: 3.806A pdb=" N ASN F 45 " --> pdb=" O ASN F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 72 removed outlier: 5.362A pdb=" N CYS F 58 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS F 59 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE F 60 " --> pdb=" O ARG F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 102 Processing helix chain 'F' and resid 107 through 109 No H-bonds generated for 'chain 'F' and resid 107 through 109' Processing helix chain 'F' and resid 282 through 292 removed outlier: 4.129A pdb=" N PHE F 292 " --> pdb=" O LEU F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 312 removed outlier: 3.692A pdb=" N ILE F 308 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N SER F 311 " --> pdb=" O ASN F 307 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ARG F 312 " --> pdb=" O ILE F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 331 removed outlier: 4.319A pdb=" N ILE F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 338 removed outlier: 3.651A pdb=" N LYS F 338 " --> pdb=" O GLU F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 342 No H-bonds generated for 'chain 'F' and resid 340 through 342' Processing helix chain 'F' and resid 347 through 351 removed outlier: 3.691A pdb=" N CYS F 351 " --> pdb=" O SER F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 373 removed outlier: 4.106A pdb=" N GLU F 371 " --> pdb=" O LYS F 367 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 385 Processing helix chain 'F' and resid 394 through 401 removed outlier: 3.941A pdb=" N PHE F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 425 Processing helix chain 'I' and resid 54 through 61 Processing helix chain 'I' and resid 82 through 96 Processing helix chain 'I' and resid 114 through 125 Processing helix chain 'I' and resid 178 through 189 removed outlier: 3.886A pdb=" N ILE I 181 " --> pdb=" O PRO I 178 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N PHE I 182 " --> pdb=" O SER I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 208 Processing helix chain 'I' and resid 225 through 228 Processing helix chain 'I' and resid 235 through 238 No H-bonds generated for 'chain 'I' and resid 235 through 238' Processing helix chain 'I' and resid 242 through 248 Processing helix chain 'I' and resid 293 through 306 removed outlier: 4.579A pdb=" N SER I 306 " --> pdb=" O GLN I 302 " (cutoff:3.500A) Processing helix chain 'I' and resid 314 through 323 Processing helix chain 'I' and resid 331 through 347 Processing helix chain 'I' and resid 387 through 396 removed outlier: 3.525A pdb=" N ALA I 391 " --> pdb=" O LEU I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 403 through 409 Processing helix chain 'I' and resid 412 through 427 Processing helix chain 'I' and resid 433 through 447 Processing helix chain 'I' and resid 455 through 468 Processing helix chain 'I' and resid 495 through 503 Processing helix chain 'I' and resid 509 through 511 No H-bonds generated for 'chain 'I' and resid 509 through 511' Processing sheet with id= A, first strand: chain 'A' and resid 622 through 624 removed outlier: 6.484A pdb=" N ILE A 561 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE A 596 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL A 563 " --> pdb=" O ILE A 596 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL A 598 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU A 565 " --> pdb=" O VAL A 598 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 657 through 659 removed outlier: 3.515A pdb=" N SER A 646 " --> pdb=" O LEU A 682 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 819 through 821 Processing sheet with id= D, first strand: chain 'B' and resid 475 through 479 removed outlier: 6.432A pdb=" N SER B 313 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N HIS B 478 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU B 315 " --> pdb=" O HIS B 478 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU B 420 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL B 453 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU B 422 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N SER B 455 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL B 424 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL B 423 " --> pdb=" O PRO B 359 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU B 361 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N HIS B 425 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU B 363 " --> pdb=" O HIS B 425 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 263 through 267 removed outlier: 6.558A pdb=" N THR C 104 " --> pdb=" O HIS C 264 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N LEU C 266 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE C 106 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU C 199 " --> pdb=" O LYS C 233 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N SER C 235 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N MET C 201 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ILE C 237 " --> pdb=" O MET C 201 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE C 203 " --> pdb=" O ILE C 237 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ASN C 239 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N PHE C 205 " --> pdb=" O ASN C 239 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 534 through 536 Processing sheet with id= G, first strand: chain 'D' and resid 272 through 274 removed outlier: 8.058A pdb=" N ILE D 273 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE D 99 " --> pdb=" O ILE D 273 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL D 212 " --> pdb=" O CYS D 246 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N PHE D 248 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N PHE D 214 " --> pdb=" O PHE D 248 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N CYS D 250 " --> pdb=" O PHE D 214 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N PHE D 216 " --> pdb=" O CYS D 250 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 469 through 471 Processing sheet with id= I, first strand: chain 'E' and resid 185 through 189 removed outlier: 9.177A pdb=" N LEU E 33 " --> pdb=" O ILE E 164 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N PHE E 166 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N LEU E 35 " --> pdb=" O PHE E 166 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N TYR E 168 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N GLY E 37 " --> pdb=" O TYR E 168 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N MET E 170 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR E 126 " --> pdb=" O ASN E 163 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LYS E 165 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LEU E 128 " --> pdb=" O LYS E 165 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE E 167 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU E 130 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N THR E 169 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU E 132 " --> pdb=" O THR E 169 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 433 through 435 Processing sheet with id= K, first strand: chain 'I' and resid 284 through 287 removed outlier: 8.359A pdb=" N LEU I 104 " --> pdb=" O PHE I 256 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU I 258 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ILE I 106 " --> pdb=" O LEU I 258 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLY I 260 " --> pdb=" O ILE I 106 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N GLY I 108 " --> pdb=" O GLY I 260 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA I 262 " --> pdb=" O GLY I 108 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE I 218 " --> pdb=" O VAL I 257 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE I 259 " --> pdb=" O PHE I 218 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL I 220 " --> pdb=" O ILE I 259 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N MET I 261 " --> pdb=" O VAL I 220 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU I 222 " --> pdb=" O MET I 261 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N ASN I 263 " --> pdb=" O LEU I 222 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'I' and resid 471 through 477 925 hydrogen bonds defined for protein. 2613 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 8.71 Time building geometry restraints manager: 10.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3844 1.31 - 1.44: 7026 1.44 - 1.57: 13990 1.57 - 1.70: 183 1.70 - 1.83: 172 Bond restraints: 25215 Sorted by residual: bond pdb=" C PHE F 98 " pdb=" N ARG F 99 " ideal model delta sigma weight residual 1.334 1.455 -0.120 1.33e-02 5.65e+03 8.18e+01 bond pdb=" C ARG F 99 " pdb=" N GLN F 100 " ideal model delta sigma weight residual 1.335 1.219 0.116 1.38e-02 5.25e+03 7.03e+01 bond pdb=" C ILE I 407 " pdb=" N ALA I 408 " ideal model delta sigma weight residual 1.334 1.242 0.092 1.49e-02 4.50e+03 3.81e+01 bond pdb=" CA ALA A 599 " pdb=" CB ALA A 599 " ideal model delta sigma weight residual 1.534 1.466 0.068 1.60e-02 3.91e+03 1.83e+01 bond pdb=" C THR D 527 " pdb=" O THR D 527 " ideal model delta sigma weight residual 1.235 1.181 0.054 1.33e-02 5.65e+03 1.67e+01 ... (remaining 25210 not shown) Histogram of bond angle deviations from ideal: 96.87 - 105.51: 752 105.51 - 114.16: 14638 114.16 - 122.80: 16761 122.80 - 131.44: 2193 131.44 - 140.08: 77 Bond angle restraints: 34421 Sorted by residual: angle pdb=" PA ATP I1001 " pdb=" O3A ATP I1001 " pdb=" PB ATP I1001 " ideal model delta sigma weight residual 136.83 130.02 6.81 1.00e+00 1.00e+00 4.64e+01 angle pdb=" N ARG I 227 " pdb=" CA ARG I 227 " pdb=" C ARG I 227 " ideal model delta sigma weight residual 112.93 106.46 6.47 1.12e+00 7.97e-01 3.33e+01 angle pdb=" N LEU F 29 " pdb=" CA LEU F 29 " pdb=" C LEU F 29 " ideal model delta sigma weight residual 111.82 105.36 6.46 1.16e+00 7.43e-01 3.10e+01 angle pdb=" CA THR A 601 " pdb=" C THR A 601 " pdb=" O THR A 601 " ideal model delta sigma weight residual 121.44 115.22 6.22 1.17e+00 7.31e-01 2.83e+01 angle pdb=" N MET I 225 " pdb=" CA MET I 225 " pdb=" C MET I 225 " ideal model delta sigma weight residual 112.54 106.24 6.30 1.22e+00 6.72e-01 2.67e+01 ... (remaining 34416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 13114 17.90 - 35.79: 1426 35.79 - 53.69: 505 53.69 - 71.59: 123 71.59 - 89.48: 28 Dihedral angle restraints: 15196 sinusoidal: 6910 harmonic: 8286 Sorted by residual: dihedral pdb=" CA ASP C 111 " pdb=" C ASP C 111 " pdb=" N SER C 112 " pdb=" CA SER C 112 " ideal model delta harmonic sigma weight residual -180.00 -150.55 -29.45 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA PHE B 475 " pdb=" C PHE B 475 " pdb=" N VAL B 476 " pdb=" CA VAL B 476 " ideal model delta harmonic sigma weight residual 180.00 155.32 24.68 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA LYS E 431 " pdb=" C LYS E 431 " pdb=" N LEU E 432 " pdb=" CA LEU E 432 " ideal model delta harmonic sigma weight residual 180.00 155.81 24.19 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 15193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3413 0.080 - 0.161: 458 0.161 - 0.241: 43 0.241 - 0.322: 4 0.322 - 0.402: 1 Chirality restraints: 3919 Sorted by residual: chirality pdb=" CB ILE A 422 " pdb=" CA ILE A 422 " pdb=" CG1 ILE A 422 " pdb=" CG2 ILE A 422 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" CA TYR D 524 " pdb=" N TYR D 524 " pdb=" C TYR D 524 " pdb=" CB TYR D 524 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CB ILE E 326 " pdb=" CA ILE E 326 " pdb=" CG1 ILE E 326 " pdb=" CG2 ILE E 326 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 3916 not shown) Planarity restraints: 4023 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU I 222 " 0.019 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C LEU I 222 " -0.064 2.00e-02 2.50e+03 pdb=" O LEU I 222 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP I 223 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 473 " -0.013 2.00e-02 2.50e+03 2.25e-02 1.01e+01 pdb=" CG TYR B 473 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR B 473 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR B 473 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR B 473 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR B 473 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 473 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 473 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP D 526 " 0.015 2.00e-02 2.50e+03 3.15e-02 9.92e+00 pdb=" C TRP D 526 " -0.054 2.00e-02 2.50e+03 pdb=" O TRP D 526 " 0.020 2.00e-02 2.50e+03 pdb=" N THR D 527 " 0.019 2.00e-02 2.50e+03 ... (remaining 4020 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 239 2.58 - 3.16: 18968 3.16 - 3.74: 41092 3.74 - 4.32: 58193 4.32 - 4.90: 90319 Nonbonded interactions: 208811 Sorted by model distance: nonbonded pdb=" O3G ATP I1001 " pdb="MG MG I1002 " model vdw 2.003 2.170 nonbonded pdb=" OG1 THR D 109 " pdb="MG MG D1002 " model vdw 2.070 2.170 nonbonded pdb=" O3G ATP D1001 " pdb="MG MG D1002 " model vdw 2.079 2.170 nonbonded pdb="MG MG A1002 " pdb=" O HOH A1124 " model vdw 2.080 2.170 nonbonded pdb=" OG1 THR I 115 " pdb="MG MG I1002 " model vdw 2.084 2.170 ... (remaining 208806 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.080 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 69.960 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.080 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:13.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 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 : 0.006 0.120 25215 Z= 0.351 Angle : 0.942 17.750 34421 Z= 0.522 Chirality : 0.055 0.402 3919 Planarity : 0.007 0.117 4023 Dihedral : 17.517 89.483 9782 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.47 % Allowed : 0.62 % Favored : 98.91 % 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: -1.54 (0.14), residues: 2731 helix: -1.13 (0.11), residues: 1520 sheet: 0.26 (0.30), residues: 250 loop : -0.88 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 494 HIS 0.016 0.001 HIS C 74 PHE 0.044 0.003 PHE B 437 TYR 0.047 0.003 TYR B 473 ARG 0.021 0.001 ARG A 705 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 544 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 603 ASP cc_start: 0.7879 (p0) cc_final: 0.7451 (p0) REVERT: C 340 PRO cc_start: 0.7755 (Cg_exo) cc_final: 0.7530 (Cg_endo) REVERT: C 449 TYR cc_start: 0.7853 (m-80) cc_final: 0.7393 (m-80) REVERT: C 559 LYS cc_start: 0.7558 (tttm) cc_final: 0.7131 (tttt) REVERT: F 96 ASN cc_start: 0.8715 (t0) cc_final: 0.8305 (t0) REVERT: F 300 TYR cc_start: 0.7379 (m-10) cc_final: 0.6684 (m-10) REVERT: F 307 ASN cc_start: 0.8661 (m110) cc_final: 0.8405 (m-40) REVERT: F 318 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7599 (mm110) REVERT: F 358 LYS cc_start: 0.7780 (mtmm) cc_final: 0.7555 (mtpp) REVERT: F 416 ASP cc_start: 0.7547 (t0) cc_final: 0.7168 (t0) REVERT: I 159 ASP cc_start: 0.8363 (m-30) cc_final: 0.8095 (p0) REVERT: I 404 ARG cc_start: 0.7817 (mmt180) cc_final: 0.7333 (mmt180) REVERT: I 488 LYS cc_start: 0.7664 (tttp) cc_final: 0.7422 (mtpp) REVERT: I 503 THR cc_start: 0.9152 (m) cc_final: 0.8907 (p) outliers start: 12 outliers final: 5 residues processed: 553 average time/residue: 1.6098 time to fit residues: 1005.4883 Evaluate side-chains 302 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 297 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 525 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 4.9990 chunk 216 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 145 optimal weight: 0.7980 chunk 115 optimal weight: 7.9990 chunk 223 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 258 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN A 774 HIS B 399 HIS C 69 HIS C 190 ASN C 418 ASN C 490 ASN D 76 GLN D 491 GLN F 5 GLN F 41 ASN F 51 GLN F 100 GLN F 333 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 25215 Z= 0.262 Angle : 0.569 9.741 34421 Z= 0.305 Chirality : 0.041 0.146 3919 Planarity : 0.004 0.063 4023 Dihedral : 17.677 87.640 4085 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.10 % Allowed : 11.69 % Favored : 86.20 % 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: -0.17 (0.15), residues: 2731 helix: 0.25 (0.13), residues: 1508 sheet: 0.37 (0.29), residues: 257 loop : -0.62 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 305 HIS 0.007 0.001 HIS F 8 PHE 0.017 0.001 PHE F 345 TYR 0.022 0.002 TYR A 721 ARG 0.011 0.001 ARG C 193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 300 time to evaluate : 2.825 Fit side-chains REVERT: A 705 ARG cc_start: 0.8157 (mmm-85) cc_final: 0.7834 (mmm160) REVERT: B 407 MET cc_start: 0.8730 (mtp) cc_final: 0.8528 (mtp) REVERT: C 286 ASP cc_start: 0.7530 (t0) cc_final: 0.7263 (t0) REVERT: C 361 MET cc_start: 0.5616 (mmm) cc_final: 0.4942 (mmm) REVERT: C 448 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7886 (pt0) REVERT: C 559 LYS cc_start: 0.7617 (tttm) cc_final: 0.7155 (tttt) REVERT: E 275 LYS cc_start: 0.7358 (mmtt) cc_final: 0.6886 (mmtm) REVERT: E 439 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8144 (pttt) REVERT: E 461 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6554 (tm-30) REVERT: F 71 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7909 (mt-10) REVERT: F 95 MET cc_start: 0.8283 (pp-130) cc_final: 0.7998 (tmm) REVERT: F 287 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7404 (pmt170) REVERT: F 358 LYS cc_start: 0.7771 (mtmm) cc_final: 0.7537 (mtpp) REVERT: F 417 GLN cc_start: 0.7961 (mp10) cc_final: 0.7761 (mp10) REVERT: I 86 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: I 503 THR cc_start: 0.9225 (m) cc_final: 0.8912 (p) outliers start: 54 outliers final: 18 residues processed: 336 average time/residue: 1.5672 time to fit residues: 596.5500 Evaluate side-chains 275 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 252 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain E residue 461 GLU Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 52 ASP Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 449 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 143 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 215 optimal weight: 6.9990 chunk 176 optimal weight: 0.7980 chunk 71 optimal weight: 8.9990 chunk 259 optimal weight: 9.9990 chunk 280 optimal weight: 6.9990 chunk 230 optimal weight: 8.9990 chunk 257 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 208 optimal weight: 0.7980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN A 774 HIS A 787 ASN C 418 ASN D 270 GLN E 248 HIS F 8 HIS F 51 GLN F 100 GLN F 407 GLN I 171 ASN I 230 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 25215 Z= 0.302 Angle : 0.565 10.760 34421 Z= 0.301 Chirality : 0.042 0.147 3919 Planarity : 0.004 0.063 4023 Dihedral : 17.705 86.596 4079 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.49 % Allowed : 13.45 % Favored : 84.06 % 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: 0.37 (0.16), residues: 2731 helix: 0.76 (0.13), residues: 1505 sheet: 0.36 (0.29), residues: 260 loop : -0.45 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 443 HIS 0.012 0.001 HIS F 8 PHE 0.022 0.001 PHE C 408 TYR 0.020 0.002 TYR C 276 ARG 0.008 0.001 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 268 time to evaluate : 2.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 603 ASP cc_start: 0.7947 (p0) cc_final: 0.7615 (p0) REVERT: A 705 ARG cc_start: 0.8211 (mmm-85) cc_final: 0.7838 (mmm160) REVERT: A 844 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: C 361 MET cc_start: 0.5704 (mmm) cc_final: 0.5162 (mmm) REVERT: C 448 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7787 (pt0) REVERT: C 559 LYS cc_start: 0.7600 (tttm) cc_final: 0.7152 (tttt) REVERT: E 139 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8057 (mp10) REVERT: E 439 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8225 (pttt) REVERT: E 461 GLU cc_start: 0.6719 (OUTLIER) cc_final: 0.6444 (tm-30) REVERT: F 38 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8287 (pp) REVERT: F 71 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7959 (mt-10) REVERT: F 283 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7437 (tp30) REVERT: F 287 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7331 (pmt170) REVERT: F 358 LYS cc_start: 0.7728 (mtmm) cc_final: 0.7467 (mmmm) REVERT: I 86 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7463 (mp0) REVERT: I 503 THR cc_start: 0.9307 (m) cc_final: 0.9046 (p) outliers start: 64 outliers final: 27 residues processed: 305 average time/residue: 1.5338 time to fit residues: 533.2938 Evaluate side-chains 272 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 237 time to evaluate : 2.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 286 LYS Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain E residue 461 GLU Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 52 ASP Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 415 ASP Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 449 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 256 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 260 optimal weight: 10.0000 chunk 275 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 246 optimal weight: 6.9990 chunk 74 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 ASN C 490 ASN D 270 GLN F 8 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25215 Z= 0.266 Angle : 0.545 10.774 34421 Z= 0.290 Chirality : 0.041 0.143 3919 Planarity : 0.004 0.061 4023 Dihedral : 17.638 89.356 4077 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.77 % Allowed : 14.69 % Favored : 82.54 % 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: 0.62 (0.16), residues: 2731 helix: 1.00 (0.14), residues: 1512 sheet: 0.25 (0.29), residues: 258 loop : -0.34 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 539 HIS 0.012 0.001 HIS F 8 PHE 0.023 0.001 PHE C 408 TYR 0.017 0.001 TYR A 721 ARG 0.009 0.000 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 256 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 518 MET cc_start: 0.8729 (mmp) cc_final: 0.8227 (mmt) REVERT: A 603 ASP cc_start: 0.8046 (p0) cc_final: 0.7784 (p0) REVERT: A 705 ARG cc_start: 0.8183 (mmm-85) cc_final: 0.7940 (mmm160) REVERT: A 844 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7447 (mp0) REVERT: C 286 ASP cc_start: 0.7893 (t0) cc_final: 0.7455 (t0) REVERT: C 342 ASN cc_start: 0.8470 (m-40) cc_final: 0.8231 (m110) REVERT: C 361 MET cc_start: 0.5652 (mmm) cc_final: 0.5202 (mmm) REVERT: C 448 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7907 (pt0) REVERT: C 559 LYS cc_start: 0.7640 (tttm) cc_final: 0.7166 (pttp) REVERT: D 151 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7519 (mm-30) REVERT: E 139 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8017 (mp10) REVERT: E 234 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8499 (m-40) REVERT: E 414 MET cc_start: 0.7060 (OUTLIER) cc_final: 0.6793 (ttt) REVERT: E 439 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8195 (pttt) REVERT: E 461 GLU cc_start: 0.6676 (OUTLIER) cc_final: 0.6414 (tm-30) REVERT: E 469 ASN cc_start: 0.6287 (p0) cc_final: 0.5919 (t0) REVERT: F 71 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7878 (mt-10) REVERT: F 287 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7316 (pmt170) REVERT: F 358 LYS cc_start: 0.7730 (mtmm) cc_final: 0.7503 (mmmt) REVERT: I 100 ARG cc_start: 0.6975 (ttp-110) cc_final: 0.6683 (tmm160) REVERT: I 503 THR cc_start: 0.9345 (m) cc_final: 0.9109 (p) outliers start: 71 outliers final: 33 residues processed: 303 average time/residue: 1.5280 time to fit residues: 529.5836 Evaluate side-chains 285 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 244 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 286 LYS Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain E residue 461 GLU Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 8 HIS Chi-restraints excluded: chain F residue 52 ASP Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 104 ASN Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 345 PHE Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 395 ASP Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 202 MET Chi-restraints excluded: chain I residue 449 THR Chi-restraints excluded: chain I residue 478 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 205 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 235 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 247 optimal weight: 0.0470 chunk 69 optimal weight: 6.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 ASN D 155 GLN D 270 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 25215 Z= 0.307 Angle : 0.559 10.183 34421 Z= 0.297 Chirality : 0.042 0.146 3919 Planarity : 0.004 0.061 4023 Dihedral : 17.673 89.218 4077 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.73 % Allowed : 15.86 % Favored : 81.41 % 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: 0.68 (0.16), residues: 2731 helix: 1.06 (0.14), residues: 1512 sheet: 0.22 (0.29), residues: 258 loop : -0.33 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 539 HIS 0.021 0.001 HIS F 8 PHE 0.022 0.001 PHE C 408 TYR 0.018 0.002 TYR C 483 ARG 0.011 0.000 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 249 time to evaluate : 2.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 603 ASP cc_start: 0.8114 (p0) cc_final: 0.7907 (p0) REVERT: A 705 ARG cc_start: 0.8185 (mmm-85) cc_final: 0.7832 (mmm160) REVERT: A 844 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7438 (mp0) REVERT: A 867 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7569 (p0) REVERT: C 286 ASP cc_start: 0.7942 (t0) cc_final: 0.7607 (t0) REVERT: C 361 MET cc_start: 0.5865 (mmm) cc_final: 0.5397 (mmm) REVERT: C 448 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.8030 (pt0) REVERT: C 559 LYS cc_start: 0.7772 (tttm) cc_final: 0.7270 (pttp) REVERT: E 139 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8018 (mp10) REVERT: E 209 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8634 (mp) REVERT: E 414 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.6802 (ttt) REVERT: E 439 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8105 (pttt) REVERT: E 461 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.6425 (tm-30) REVERT: F 71 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7887 (mt-10) REVERT: F 287 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7398 (pmt170) REVERT: F 358 LYS cc_start: 0.7679 (mtmm) cc_final: 0.7395 (mmmm) REVERT: I 100 ARG cc_start: 0.7011 (ttp-110) cc_final: 0.6762 (tmm160) REVERT: I 488 LYS cc_start: 0.7719 (mtpt) cc_final: 0.7375 (mtpm) REVERT: I 503 THR cc_start: 0.9380 (m) cc_final: 0.9165 (p) outliers start: 70 outliers final: 35 residues processed: 297 average time/residue: 1.5740 time to fit residues: 532.1662 Evaluate side-chains 279 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 235 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 286 LYS Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain E residue 461 GLU Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 52 ASP Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 104 ASN Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 395 ASP Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 202 MET Chi-restraints excluded: chain I residue 449 THR Chi-restraints excluded: chain I residue 478 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 275 optimal weight: 0.9990 chunk 228 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 ASN D 155 GLN D 270 GLN F 5 GLN F 8 HIS F 45 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 25215 Z= 0.272 Angle : 0.546 10.767 34421 Z= 0.291 Chirality : 0.041 0.143 3919 Planarity : 0.003 0.060 4023 Dihedral : 17.634 86.018 4077 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.92 % Allowed : 16.06 % Favored : 81.02 % 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: 0.78 (0.16), residues: 2731 helix: 1.16 (0.14), residues: 1511 sheet: 0.20 (0.29), residues: 260 loop : -0.28 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 539 HIS 0.012 0.001 HIS F 8 PHE 0.030 0.001 PHE F 345 TYR 0.021 0.001 TYR C 528 ARG 0.007 0.000 ARG D 425 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 251 time to evaluate : 2.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 518 MET cc_start: 0.8764 (mmp) cc_final: 0.8557 (mmt) REVERT: A 603 ASP cc_start: 0.8164 (p0) cc_final: 0.7928 (p0) REVERT: A 705 ARG cc_start: 0.8152 (mmm-85) cc_final: 0.7904 (mmm160) REVERT: A 844 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: A 867 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7620 (p0) REVERT: C 286 ASP cc_start: 0.7839 (t0) cc_final: 0.7603 (t0) REVERT: C 361 MET cc_start: 0.5863 (mmm) cc_final: 0.5334 (mmm) REVERT: C 559 LYS cc_start: 0.7725 (tttm) cc_final: 0.7265 (pttp) REVERT: E 139 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8011 (mp10) REVERT: E 209 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8627 (mp) REVERT: E 414 MET cc_start: 0.7034 (OUTLIER) cc_final: 0.6753 (ttt) REVERT: F 71 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7859 (mt-10) REVERT: F 287 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7208 (ppt170) REVERT: F 358 LYS cc_start: 0.7668 (mtmm) cc_final: 0.7316 (mmmm) outliers start: 75 outliers final: 41 residues processed: 298 average time/residue: 1.4892 time to fit residues: 507.9896 Evaluate side-chains 285 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 238 time to evaluate : 2.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 286 LYS Chi-restraints excluded: chain E residue 290 LYS Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 8 HIS Chi-restraints excluded: chain F residue 52 ASP Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 104 ASN Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 395 ASP Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 202 MET Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 449 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 265 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 chunk 201 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 232 optimal weight: 10.0000 chunk 153 optimal weight: 0.9980 chunk 274 optimal weight: 0.0570 chunk 171 optimal weight: 0.8980 chunk 167 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 overall best weight: 0.7898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 GLN ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 ASN E 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25215 Z= 0.148 Angle : 0.510 11.858 34421 Z= 0.270 Chirality : 0.039 0.161 3919 Planarity : 0.003 0.058 4023 Dihedral : 17.347 80.380 4077 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.95 % Allowed : 17.73 % Favored : 80.32 % 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: 1.03 (0.16), residues: 2731 helix: 1.34 (0.14), residues: 1514 sheet: 0.27 (0.30), residues: 258 loop : -0.14 (0.20), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 539 HIS 0.031 0.001 HIS F 8 PHE 0.018 0.001 PHE C 412 TYR 0.021 0.001 TYR C 528 ARG 0.008 0.000 ARG D 425 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 266 time to evaluate : 2.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 518 MET cc_start: 0.8711 (mmp) cc_final: 0.8341 (mmt) REVERT: A 603 ASP cc_start: 0.8149 (p0) cc_final: 0.7877 (p0) REVERT: C 286 ASP cc_start: 0.7818 (t0) cc_final: 0.7605 (t0) REVERT: C 361 MET cc_start: 0.5829 (mmm) cc_final: 0.5369 (mmm) REVERT: C 533 MET cc_start: 0.7584 (ttp) cc_final: 0.7347 (ttp) REVERT: C 559 LYS cc_start: 0.7693 (tttm) cc_final: 0.7240 (pttp) REVERT: E 414 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6636 (ttt) REVERT: F 71 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7905 (mt-10) REVERT: F 279 LYS cc_start: 0.8015 (mmpt) cc_final: 0.7340 (mmtt) REVERT: F 287 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7280 (ppt170) REVERT: F 358 LYS cc_start: 0.7683 (mtmm) cc_final: 0.7293 (mmmm) outliers start: 50 outliers final: 23 residues processed: 297 average time/residue: 1.5221 time to fit residues: 517.6795 Evaluate side-chains 263 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 238 time to evaluate : 2.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 290 LYS Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 52 ASP Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 202 MET Chi-restraints excluded: chain I residue 261 MET Chi-restraints excluded: chain I residue 387 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 0.0060 chunk 109 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 chunk 249 optimal weight: 4.9990 overall best weight: 3.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 ASN D 155 GLN E 123 GLN F 8 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 25215 Z= 0.360 Angle : 0.592 11.228 34421 Z= 0.312 Chirality : 0.043 0.287 3919 Planarity : 0.004 0.060 4023 Dihedral : 17.642 84.753 4077 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.18 % Allowed : 17.85 % Favored : 79.97 % 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: 0.88 (0.16), residues: 2731 helix: 1.20 (0.14), residues: 1518 sheet: 0.20 (0.29), residues: 260 loop : -0.18 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 443 HIS 0.013 0.001 HIS F 8 PHE 0.031 0.002 PHE F 345 TYR 0.025 0.002 TYR C 528 ARG 0.014 0.001 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 237 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 603 ASP cc_start: 0.8165 (p0) cc_final: 0.7906 (p0) REVERT: A 844 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7377 (mp0) REVERT: C 361 MET cc_start: 0.6009 (mmm) cc_final: 0.5562 (mmm) REVERT: C 559 LYS cc_start: 0.7734 (tttm) cc_final: 0.7301 (pttp) REVERT: D 317 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7865 (mtp85) REVERT: E 209 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8646 (mp) REVERT: E 414 MET cc_start: 0.7089 (OUTLIER) cc_final: 0.6806 (ttt) REVERT: F 71 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7866 (mt-10) REVERT: F 287 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7228 (ppt170) REVERT: F 358 LYS cc_start: 0.7691 (mtmm) cc_final: 0.7295 (mmmm) REVERT: I 488 LYS cc_start: 0.7726 (mtpt) cc_final: 0.7416 (mtpt) outliers start: 56 outliers final: 34 residues processed: 273 average time/residue: 1.5757 time to fit residues: 490.5420 Evaluate side-chains 262 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 223 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 550 LYS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 317 ARG Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 290 LYS Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 8 HIS Chi-restraints excluded: chain F residue 12 GLU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 52 ASP Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 395 ASP Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 202 MET Chi-restraints excluded: chain I residue 385 ILE Chi-restraints excluded: chain I residue 387 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 263 optimal weight: 2.9990 chunk 240 optimal weight: 4.9990 chunk 255 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 chunk 111 optimal weight: 0.5980 chunk 201 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 231 optimal weight: 7.9990 chunk 242 optimal weight: 10.0000 chunk 168 optimal weight: 1.9990 chunk 270 optimal weight: 0.9980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 ASN D 155 GLN E 123 GLN F 8 HIS F 45 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25215 Z= 0.256 Angle : 0.558 11.159 34421 Z= 0.295 Chirality : 0.041 0.244 3919 Planarity : 0.004 0.062 4023 Dihedral : 17.568 83.608 4077 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.87 % Allowed : 18.32 % Favored : 79.81 % 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: 0.94 (0.16), residues: 2731 helix: 1.26 (0.14), residues: 1519 sheet: 0.21 (0.29), residues: 260 loop : -0.16 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 539 HIS 0.011 0.001 HIS F 8 PHE 0.022 0.001 PHE A 648 TYR 0.027 0.001 TYR C 528 ARG 0.014 0.000 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 236 time to evaluate : 2.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 603 ASP cc_start: 0.8146 (p0) cc_final: 0.7895 (p0) REVERT: A 678 ARG cc_start: 0.7829 (mtp180) cc_final: 0.7473 (ttt180) REVERT: A 844 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7385 (mp0) REVERT: A 867 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7505 (p0) REVERT: C 361 MET cc_start: 0.6104 (mmm) cc_final: 0.5667 (mmm) REVERT: C 559 LYS cc_start: 0.7750 (tttm) cc_final: 0.7317 (pttp) REVERT: E 414 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6777 (ttt) REVERT: F 71 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7896 (mt-10) REVERT: F 279 LYS cc_start: 0.8161 (mmpt) cc_final: 0.7475 (mmtt) REVERT: F 287 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7211 (ppt170) REVERT: F 358 LYS cc_start: 0.7609 (mtmm) cc_final: 0.7252 (mmmm) REVERT: I 488 LYS cc_start: 0.7698 (mtpt) cc_final: 0.7377 (mtpt) outliers start: 48 outliers final: 35 residues processed: 269 average time/residue: 1.6007 time to fit residues: 494.8644 Evaluate side-chains 266 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 227 time to evaluate : 3.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 528 TYR Chi-restraints excluded: chain C residue 550 LYS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 290 LYS Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 8 HIS Chi-restraints excluded: chain F residue 12 GLU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 52 ASP Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 202 MET Chi-restraints excluded: chain I residue 385 ILE Chi-restraints excluded: chain I residue 387 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 165 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 188 optimal weight: 1.9990 chunk 283 optimal weight: 6.9990 chunk 261 optimal weight: 9.9990 chunk 226 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 174 optimal weight: 0.8980 chunk 138 optimal weight: 0.0570 chunk 179 optimal weight: 1.9990 chunk 240 optimal weight: 4.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN E 123 GLN F 8 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25215 Z= 0.160 Angle : 0.526 12.418 34421 Z= 0.279 Chirality : 0.039 0.172 3919 Planarity : 0.003 0.063 4023 Dihedral : 17.335 80.284 4077 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.52 % Allowed : 18.78 % Favored : 79.70 % 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: 1.08 (0.16), residues: 2731 helix: 1.37 (0.14), residues: 1526 sheet: 0.26 (0.30), residues: 256 loop : -0.10 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 539 HIS 0.026 0.001 HIS F 8 PHE 0.034 0.001 PHE F 345 TYR 0.025 0.001 TYR C 528 ARG 0.015 0.000 ARG A 683 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 238 time to evaluate : 3.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 518 MET cc_start: 0.8706 (mmp) cc_final: 0.8461 (mmt) REVERT: A 603 ASP cc_start: 0.8106 (p0) cc_final: 0.7830 (p0) REVERT: A 678 ARG cc_start: 0.7839 (mtp180) cc_final: 0.7483 (ttt180) REVERT: A 844 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: C 361 MET cc_start: 0.6036 (mmm) cc_final: 0.5603 (mmm) REVERT: C 559 LYS cc_start: 0.7737 (tttm) cc_final: 0.7307 (pttp) REVERT: E 211 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7536 (tp30) REVERT: E 414 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.6686 (ttt) REVERT: F 71 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7886 (mt-10) REVERT: F 279 LYS cc_start: 0.8154 (mmpt) cc_final: 0.7480 (mmtt) REVERT: F 287 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7201 (ppt170) REVERT: F 358 LYS cc_start: 0.7563 (mtmm) cc_final: 0.7261 (mmmm) outliers start: 39 outliers final: 27 residues processed: 263 average time/residue: 1.5326 time to fit residues: 460.1395 Evaluate side-chains 261 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 231 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 550 LYS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 290 LYS Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 52 ASP Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 202 MET Chi-restraints excluded: chain I residue 385 ILE Chi-restraints excluded: chain I residue 387 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 69 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 226 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 232 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 198 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 HIS ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN ** E 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.104556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.071793 restraints weight = 41853.977| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.06 r_work: 0.2772 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 25215 Z= 0.479 Angle : 0.657 11.627 34421 Z= 0.343 Chirality : 0.046 0.159 3919 Planarity : 0.004 0.062 4023 Dihedral : 17.826 86.526 4077 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.22 % Favored : 96.74 % Rotamer: Outliers : 1.91 % Allowed : 18.47 % Favored : 79.62 % 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: 0.77 (0.16), residues: 2731 helix: 1.11 (0.13), residues: 1517 sheet: 0.28 (0.30), residues: 251 loop : -0.23 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 443 HIS 0.015 0.001 HIS F 8 PHE 0.026 0.002 PHE C 412 TYR 0.026 0.002 TYR C 528 ARG 0.009 0.001 ARG A 683 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9379.29 seconds wall clock time: 167 minutes 57.78 seconds (10077.78 seconds total)