Starting phenix.real_space_refine on Fri Mar 15 05:59:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrb_0258/03_2024/6hrb_0258_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrb_0258/03_2024/6hrb_0258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrb_0258/03_2024/6hrb_0258.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrb_0258/03_2024/6hrb_0258.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrb_0258/03_2024/6hrb_0258_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrb_0258/03_2024/6hrb_0258_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 K 1 8.98 5 P 1 5.49 5 S 61 5.16 5 C 6947 2.51 5 N 1818 2.21 5 O 1959 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B ARG 461": "NH1" <-> "NH2" Residue "B ARG 572": "NH1" <-> "NH2" Residue "C ARG 106": "NH1" <-> "NH2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10787 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4155 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "B" Number of atoms: 5008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5008 Classifications: {'peptide': 674} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 646} Chain: "C" Number of atoms: 1423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1423 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 13, 'TRANS': 175} Chain: "D" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 200 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.99, per 1000 atoms: 0.56 Number of scatterers: 10787 At special positions: 0 Unit cell: (88.044, 114.356, 161.92, 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) K 1 19.00 S 61 16.00 P 1 15.00 O 1959 8.00 N 1818 7.00 C 6947 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: 4.27 Conformation dependent library (CDL) restraints added in 2.1 seconds 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2632 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 7 sheets defined 52.7% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'A' and resid 2 through 31 removed outlier: 3.548A pdb=" N ILE A 9 " --> pdb=" O GLY A 5 " (cutoff:3.500A) Proline residue: A 22 - end of helix removed outlier: 4.116A pdb=" N ARG A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 50 removed outlier: 3.734A pdb=" N LEU A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG A 48 " --> pdb=" O ARG A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 80 removed outlier: 3.597A pdb=" N CYS A 64 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 86 Processing helix chain 'A' and resid 99 through 110 removed outlier: 3.853A pdb=" N VAL A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 123 No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 134 through 156 removed outlier: 3.866A pdb=" N PHE A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 142 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 178 through 191 removed outlier: 3.529A pdb=" N ALA A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 228 removed outlier: 3.603A pdb=" N ALA A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 259 Processing helix chain 'A' and resid 261 through 273 removed outlier: 3.755A pdb=" N ALA A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N CYS A 267 " --> pdb=" O PRO A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 4.021A pdb=" N MET A 282 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 304 removed outlier: 3.613A pdb=" N VAL A 289 " --> pdb=" O TRP A 285 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 298 " --> pdb=" O CYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 329 through 341 removed outlier: 3.556A pdb=" N VAL A 337 " --> pdb=" O SER A 333 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 356 through 367 Proline residue: A 362 - end of helix removed outlier: 3.546A pdb=" N GLN A 367 " --> pdb=" O MET A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 398 removed outlier: 3.893A pdb=" N PHE A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 429 removed outlier: 4.027A pdb=" N LEU A 416 " --> pdb=" O ARG A 412 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N THR A 417 " --> pdb=" O GLU A 413 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix removed outlier: 4.009A pdb=" N VAL A 428 " --> pdb=" O THR A 424 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU A 429 " --> pdb=" O PRO A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 437 Processing helix chain 'A' and resid 442 through 444 No H-bonds generated for 'chain 'A' and resid 442 through 444' Processing helix chain 'A' and resid 450 through 461 removed outlier: 3.528A pdb=" N SER A 454 " --> pdb=" O PRO A 450 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 456 " --> pdb=" O GLY A 452 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A 459 " --> pdb=" O GLU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 494 removed outlier: 3.856A pdb=" N ALA A 486 " --> pdb=" O ASN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 506 Processing helix chain 'A' and resid 525 through 548 removed outlier: 3.729A pdb=" N GLY A 529 " --> pdb=" O PRO A 525 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY A 533 " --> pdb=" O GLY A 529 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU A 537 " --> pdb=" O GLY A 533 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY A 539 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 544 " --> pdb=" O ALA A 540 " (cutoff:3.500A) Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'B' and resid 12 through 23 removed outlier: 3.558A pdb=" N ALA B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS B 19 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLU B 20 " --> pdb=" O GLN B 16 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 55 removed outlier: 3.843A pdb=" N ILE B 38 " --> pdb=" O PRO B 34 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 86 removed outlier: 3.604A pdb=" N ALA B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TRP B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU B 72 " --> pdb=" O ILE B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 102 removed outlier: 3.618A pdb=" N VAL B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LYS B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 207 removed outlier: 4.033A pdb=" N MET B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 237 removed outlier: 3.578A pdb=" N LEU B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE B 223 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 234 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 243 Processing helix chain 'B' and resid 252 through 262 removed outlier: 3.672A pdb=" N ALA B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 273 No H-bonds generated for 'chain 'B' and resid 270 through 273' Processing helix chain 'B' and resid 275 through 285 removed outlier: 4.070A pdb=" N LEU B 283 " --> pdb=" O MET B 279 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 299 removed outlier: 3.707A pdb=" N GLU B 296 " --> pdb=" O GLY B 292 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLY B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 341 Processing helix chain 'B' and resid 347 through 356 removed outlier: 4.023A pdb=" N ILE B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 408 removed outlier: 3.590A pdb=" N HIS B 404 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU B 406 " --> pdb=" O ARG B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 423 Processing helix chain 'B' and resid 454 through 462 removed outlier: 3.600A pdb=" N GLN B 459 " --> pdb=" O GLU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 483 removed outlier: 4.472A pdb=" N ALA B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE B 481 " --> pdb=" O THR B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 508 removed outlier: 3.665A pdb=" N LEU B 500 " --> pdb=" O PRO B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 525 No H-bonds generated for 'chain 'B' and resid 522 through 525' Processing helix chain 'B' and resid 540 through 545 removed outlier: 3.726A pdb=" N GLU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 590 removed outlier: 3.791A pdb=" N GLN B 567 " --> pdb=" O HIS B 563 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER B 574 " --> pdb=" O MET B 570 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA B 581 " --> pdb=" O THR B 577 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL B 584 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE B 588 " --> pdb=" O VAL B 584 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 595 removed outlier: 3.677A pdb=" N PHE B 595 " --> pdb=" O PRO B 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 592 through 595' Processing helix chain 'B' and resid 600 through 605 removed outlier: 3.917A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 636 removed outlier: 3.706A pdb=" N ILE B 617 " --> pdb=" O PRO B 613 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 618 " --> pdb=" O ASP B 614 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE B 632 " --> pdb=" O ILE B 628 " (cutoff:3.500A) Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 647 through 656 removed outlier: 3.581A pdb=" N TRP B 655 " --> pdb=" O ARG B 651 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B 656 " --> pdb=" O ARG B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 678 removed outlier: 3.546A pdb=" N LEU B 662 " --> pdb=" O GLY B 658 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 663 " --> pdb=" O LEU B 659 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 664 " --> pdb=" O GLY B 660 " (cutoff:3.500A) Proline residue: B 665 - end of helix removed outlier: 3.868A pdb=" N LYS B 670 " --> pdb=" O PHE B 666 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B 674 " --> pdb=" O LYS B 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 18 removed outlier: 3.789A pdb=" N THR C 10 " --> pdb=" O PRO C 6 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 33 Processing helix chain 'C' and resid 35 through 39 removed outlier: 3.549A pdb=" N ASN C 39 " --> pdb=" O PRO C 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 35 through 39' Processing helix chain 'C' and resid 92 through 108 removed outlier: 3.507A pdb=" N ALA C 103 " --> pdb=" O ALA C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 121 No H-bonds generated for 'chain 'C' and resid 118 through 121' Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 141 through 147 Processing helix chain 'C' and resid 152 through 162 Processing helix chain 'C' and resid 179 through 189 Processing helix chain 'D' and resid 7 through 24 removed outlier: 4.126A pdb=" N TYR D 21 " --> pdb=" O GLY D 17 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 203 through 205 removed outlier: 3.527A pdb=" N GLN A 212 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 106 through 109 Processing sheet with id= C, first strand: chain 'B' and resid 131 through 134 removed outlier: 6.735A pdb=" N GLU B 190 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N VAL B 146 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 150 through 154 Processing sheet with id= E, first strand: chain 'B' and resid 287 through 289 Processing sheet with id= F, first strand: chain 'B' and resid 513 through 516 removed outlier: 7.286A pdb=" N VAL B 303 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N THR B 516 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU B 305 " --> pdb=" O THR B 516 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYS B 466 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N LEU B 306 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL B 468 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASP B 489 " --> pdb=" O MET B 469 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 373 through 375 removed outlier: 3.810A pdb=" N GLY B 441 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLU B 435 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N VAL B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1239 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.71 Time building geometry restraints manager: 4.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3441 1.34 - 1.46: 1833 1.46 - 1.57: 5598 1.57 - 1.69: 4 1.69 - 1.81: 110 Bond restraints: 10986 Sorted by residual: bond pdb=" N ARG B 89 " pdb=" CA ARG B 89 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.90e-02 2.77e+03 5.25e+00 bond pdb=" CB VAL A 428 " pdb=" CG2 VAL A 428 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.70e+00 bond pdb=" C LEU A 213 " pdb=" N LEU A 214 " ideal model delta sigma weight residual 1.331 1.368 -0.037 2.07e-02 2.33e+03 3.19e+00 bond pdb=" CA ARG B 89 " pdb=" CB ARG B 89 " ideal model delta sigma weight residual 1.530 1.565 -0.035 2.00e-02 2.50e+03 3.05e+00 bond pdb=" C GLN C 164 " pdb=" N GLN C 165 " ideal model delta sigma weight residual 1.331 1.283 0.048 2.83e-02 1.25e+03 2.92e+00 ... (remaining 10981 not shown) Histogram of bond angle deviations from ideal: 97.31 - 105.00: 243 105.00 - 112.69: 5982 112.69 - 120.39: 4756 120.39 - 128.08: 3883 128.08 - 135.78: 90 Bond angle restraints: 14954 Sorted by residual: angle pdb=" C GLY B 88 " pdb=" N ARG B 89 " pdb=" CA ARG B 89 " ideal model delta sigma weight residual 121.70 135.78 -14.08 1.80e+00 3.09e-01 6.12e+01 angle pdb=" C MET A 360 " pdb=" N VAL A 361 " pdb=" CA VAL A 361 " ideal model delta sigma weight residual 120.24 124.03 -3.79 6.30e-01 2.52e+00 3.61e+01 angle pdb=" N ASN B 26 " pdb=" CA ASN B 26 " pdb=" C ASN B 26 " ideal model delta sigma weight residual 109.81 119.59 -9.78 2.21e+00 2.05e-01 1.96e+01 angle pdb=" C ALA B 319 " pdb=" N SER B 320 " pdb=" CA SER B 320 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 angle pdb=" CB LEU A 133 " pdb=" CG LEU A 133 " pdb=" CD2 LEU A 133 " ideal model delta sigma weight residual 110.70 98.39 12.31 3.00e+00 1.11e-01 1.68e+01 ... (remaining 14949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.50: 6245 15.50 - 31.01: 244 31.01 - 46.51: 36 46.51 - 62.01: 5 62.01 - 77.51: 3 Dihedral angle restraints: 6533 sinusoidal: 2436 harmonic: 4097 Sorted by residual: dihedral pdb=" CA ASN A 239 " pdb=" C ASN A 239 " pdb=" N SER A 240 " pdb=" CA SER A 240 " ideal model delta harmonic sigma weight residual 180.00 148.70 31.30 0 5.00e+00 4.00e-02 3.92e+01 dihedral pdb=" CA ALA B 319 " pdb=" C ALA B 319 " pdb=" N SER B 320 " pdb=" CA SER B 320 " ideal model delta harmonic sigma weight residual 180.00 150.18 29.82 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA ALA A 238 " pdb=" C ALA A 238 " pdb=" N ASN A 239 " pdb=" CA ASN A 239 " ideal model delta harmonic sigma weight residual 180.00 -151.31 -28.69 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 6530 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1144 0.046 - 0.092: 499 0.092 - 0.138: 138 0.138 - 0.185: 16 0.185 - 0.231: 6 Chirality restraints: 1803 Sorted by residual: chirality pdb=" CA ARG B 89 " pdb=" N ARG B 89 " pdb=" C ARG B 89 " pdb=" CB ARG B 89 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB ILE B 388 " pdb=" CA ILE B 388 " pdb=" CG1 ILE B 388 " pdb=" CG2 ILE B 388 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB VAL B 449 " pdb=" CA VAL B 449 " pdb=" CG1 VAL B 449 " pdb=" CG2 VAL B 449 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1800 not shown) Planarity restraints: 1898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 424 " -0.058 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO A 425 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 425 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 425 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 240 " -0.041 5.00e-02 4.00e+02 6.09e-02 5.93e+00 pdb=" N PRO B 241 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 241 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 241 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 523 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.81e+00 pdb=" N PRO B 524 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 524 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 524 " -0.034 5.00e-02 4.00e+02 ... (remaining 1895 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.78: 2681 2.78 - 3.37: 12233 3.37 - 3.96: 20841 3.96 - 4.55: 29259 4.55 - 5.14: 41926 Nonbonded interactions: 106940 Sorted by model distance: nonbonded pdb=" O ASP B 307 " pdb=" OG1 THR B 311 " model vdw 2.186 2.440 nonbonded pdb=" OG1 THR C 72 " pdb=" O MET C 75 " model vdw 2.246 2.440 nonbonded pdb=" O VAL A 107 " pdb=" OG1 THR A 111 " model vdw 2.248 2.440 nonbonded pdb=" OG SER A 343 " pdb=" O ASN A 466 " model vdw 2.262 2.440 nonbonded pdb=" O MET A 130 " pdb=" OG1 THR A 134 " model vdw 2.264 2.440 ... (remaining 106935 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.740 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 31.380 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 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 : 0.008 0.085 10986 Z= 0.513 Angle : 0.963 14.078 14954 Z= 0.499 Chirality : 0.054 0.231 1803 Planarity : 0.007 0.087 1898 Dihedral : 9.280 77.514 3901 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.26 % Allowed : 1.50 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.97 (0.16), residues: 1436 helix: -3.80 (0.10), residues: 765 sheet: -2.20 (0.46), residues: 91 loop : -2.48 (0.22), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 245 HIS 0.012 0.002 HIS A 451 PHE 0.025 0.003 PHE A 471 TYR 0.015 0.003 TYR A 201 ARG 0.019 0.001 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 240 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.8870 (p0) cc_final: 0.8537 (p0) REVERT: A 167 TRP cc_start: 0.8897 (m100) cc_final: 0.8258 (m100) REVERT: A 175 LEU cc_start: 0.9369 (mt) cc_final: 0.8536 (tp) REVERT: A 227 MET cc_start: 0.8998 (mmm) cc_final: 0.8195 (mmt) REVERT: A 287 MET cc_start: 0.9044 (mtm) cc_final: 0.8481 (mtp) REVERT: A 320 MET cc_start: 0.8796 (mmm) cc_final: 0.8336 (tpp) REVERT: A 366 MET cc_start: 0.9280 (mtm) cc_final: 0.8999 (mtm) REVERT: A 392 PHE cc_start: 0.8360 (t80) cc_final: 0.7865 (t80) REVERT: A 469 SER cc_start: 0.9426 (m) cc_final: 0.8875 (p) REVERT: A 510 LYS cc_start: 0.8642 (mttm) cc_final: 0.8434 (mtpt) REVERT: A 537 LEU cc_start: 0.8895 (tp) cc_final: 0.8646 (tp) REVERT: A 541 LEU cc_start: 0.9595 (mt) cc_final: 0.9295 (mp) REVERT: B 371 HIS cc_start: 0.8348 (m-70) cc_final: 0.8106 (m-70) REVERT: C 22 TYR cc_start: 0.9150 (t80) cc_final: 0.8749 (t80) REVERT: C 48 THR cc_start: 0.9290 (p) cc_final: 0.8427 (p) REVERT: D 14 LEU cc_start: 0.9444 (mt) cc_final: 0.9117 (tt) REVERT: D 21 TYR cc_start: 0.9335 (t80) cc_final: 0.8894 (t80) outliers start: 3 outliers final: 1 residues processed: 242 average time/residue: 0.2221 time to fit residues: 76.2887 Evaluate side-chains 126 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 36 optimal weight: 0.2980 chunk 72 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 128 optimal weight: 9.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 HIS ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 ASN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 ASN B 326 GLN B 338 GLN B 404 HIS ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 ASN B 567 GLN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN C 154 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10986 Z= 0.347 Angle : 0.740 11.254 14954 Z= 0.372 Chirality : 0.044 0.203 1803 Planarity : 0.005 0.052 1898 Dihedral : 5.802 33.927 1525 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.65 % Allowed : 9.71 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.19), residues: 1436 helix: -1.93 (0.15), residues: 822 sheet: -1.97 (0.45), residues: 104 loop : -2.17 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 176 HIS 0.004 0.001 HIS A 451 PHE 0.019 0.002 PHE C 13 TYR 0.019 0.002 TYR A 381 ARG 0.004 0.001 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 140 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.8958 (p0) cc_final: 0.8527 (p0) REVERT: A 167 TRP cc_start: 0.8847 (m100) cc_final: 0.8063 (m100) REVERT: A 175 LEU cc_start: 0.9244 (mt) cc_final: 0.8973 (tp) REVERT: A 176 TRP cc_start: 0.8227 (m100) cc_final: 0.7288 (m100) REVERT: A 227 MET cc_start: 0.8640 (mmm) cc_final: 0.8245 (mmm) REVERT: A 392 PHE cc_start: 0.8448 (t80) cc_final: 0.7821 (t80) REVERT: A 537 LEU cc_start: 0.9023 (tp) cc_final: 0.8756 (tp) REVERT: A 541 LEU cc_start: 0.9593 (mt) cc_final: 0.9324 (mp) REVERT: B 371 HIS cc_start: 0.8315 (m-70) cc_final: 0.8047 (m-70) REVERT: C 10 THR cc_start: 0.9521 (m) cc_final: 0.8928 (m) outliers start: 30 outliers final: 15 residues processed: 160 average time/residue: 0.1926 time to fit residues: 47.0158 Evaluate side-chains 125 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain D residue 9 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 4.9990 chunk 40 optimal weight: 0.1980 chunk 107 optimal weight: 0.9980 chunk 87 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 115 optimal weight: 0.0970 chunk 128 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 overall best weight: 1.2380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10986 Z= 0.194 Angle : 0.617 9.289 14954 Z= 0.304 Chirality : 0.041 0.241 1803 Planarity : 0.003 0.043 1898 Dihedral : 5.142 28.508 1525 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.03 % Allowed : 10.94 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.21), residues: 1436 helix: -0.90 (0.17), residues: 812 sheet: -1.59 (0.47), residues: 104 loop : -1.89 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 167 HIS 0.003 0.001 HIS A 451 PHE 0.017 0.001 PHE A 253 TYR 0.018 0.002 TYR A 381 ARG 0.002 0.000 ARG C 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 150 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.9028 (p0) cc_final: 0.8433 (p0) REVERT: A 256 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8952 (mtt) REVERT: A 392 PHE cc_start: 0.8413 (t80) cc_final: 0.7976 (t80) REVERT: A 489 MET cc_start: 0.9270 (mtm) cc_final: 0.9002 (mtm) REVERT: A 537 LEU cc_start: 0.8965 (tp) cc_final: 0.8633 (tp) REVERT: A 541 LEU cc_start: 0.9580 (mt) cc_final: 0.9361 (mp) REVERT: B 371 HIS cc_start: 0.8459 (m-70) cc_final: 0.8141 (m-70) outliers start: 23 outliers final: 11 residues processed: 164 average time/residue: 0.1874 time to fit residues: 47.6437 Evaluate side-chains 132 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 383 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 129 optimal weight: 0.3980 chunk 137 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 GLN ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 ASN ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10986 Z= 0.271 Angle : 0.631 9.007 14954 Z= 0.312 Chirality : 0.041 0.169 1803 Planarity : 0.003 0.043 1898 Dihedral : 4.959 31.210 1525 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.56 % Allowed : 12.09 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -1.50 (0.21), residues: 1436 helix: -0.33 (0.18), residues: 823 sheet: -1.48 (0.46), residues: 107 loop : -1.87 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 176 HIS 0.004 0.001 HIS A 451 PHE 0.024 0.002 PHE A 235 TYR 0.020 0.002 TYR A 458 ARG 0.002 0.000 ARG B 425 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 120 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.9089 (p0) cc_final: 0.8515 (p0) REVERT: A 176 TRP cc_start: 0.8235 (m100) cc_final: 0.8011 (m100) REVERT: A 256 MET cc_start: 0.9214 (mtm) cc_final: 0.8955 (mtt) REVERT: A 392 PHE cc_start: 0.8406 (t80) cc_final: 0.7936 (t80) REVERT: A 537 LEU cc_start: 0.9022 (tp) cc_final: 0.8649 (tp) REVERT: A 541 LEU cc_start: 0.9563 (mt) cc_final: 0.9316 (mp) REVERT: B 271 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8935 (mt) REVERT: B 371 HIS cc_start: 0.8447 (m-70) cc_final: 0.8113 (m-70) REVERT: B 383 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7462 (mtm) REVERT: B 515 MET cc_start: 0.8952 (tmm) cc_final: 0.8367 (tmm) REVERT: C 22 TYR cc_start: 0.8898 (t80) cc_final: 0.8585 (t80) outliers start: 29 outliers final: 18 residues processed: 136 average time/residue: 0.1894 time to fit residues: 40.1135 Evaluate side-chains 127 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 19 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 102 optimal weight: 0.0870 chunk 56 optimal weight: 0.2980 chunk 117 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 0 optimal weight: 0.9990 chunk 70 optimal weight: 0.0050 chunk 123 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.4172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10986 Z= 0.156 Angle : 0.578 9.208 14954 Z= 0.281 Chirality : 0.040 0.201 1803 Planarity : 0.003 0.043 1898 Dihedral : 4.609 27.130 1525 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.12 % Allowed : 13.15 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.22), residues: 1436 helix: 0.17 (0.18), residues: 823 sheet: -1.30 (0.48), residues: 106 loop : -1.72 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 71 HIS 0.002 0.001 HIS B 404 PHE 0.015 0.001 PHE A 260 TYR 0.023 0.002 TYR B 641 ARG 0.002 0.000 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 1.213 Fit side-chains revert: symmetry clash REVERT: A 100 ASP cc_start: 0.9062 (p0) cc_final: 0.8365 (p0) REVERT: A 367 GLN cc_start: 0.8745 (mt0) cc_final: 0.8334 (mp10) REVERT: A 380 LEU cc_start: 0.9398 (tp) cc_final: 0.9031 (tp) REVERT: A 383 MET cc_start: 0.9237 (tpp) cc_final: 0.8971 (tpp) REVERT: A 537 LEU cc_start: 0.8975 (tp) cc_final: 0.8601 (tp) REVERT: A 541 LEU cc_start: 0.9538 (mt) cc_final: 0.9336 (mp) REVERT: B 221 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9195 (tt) REVERT: B 371 HIS cc_start: 0.8506 (m-70) cc_final: 0.8158 (m-70) REVERT: B 515 MET cc_start: 0.8799 (tmm) cc_final: 0.8382 (tmm) REVERT: C 22 TYR cc_start: 0.8956 (t80) cc_final: 0.8579 (t80) outliers start: 24 outliers final: 12 residues processed: 150 average time/residue: 0.1883 time to fit residues: 42.9258 Evaluate side-chains 128 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 383 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 GLN C 39 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10986 Z= 0.209 Angle : 0.580 8.963 14954 Z= 0.285 Chirality : 0.040 0.156 1803 Planarity : 0.003 0.042 1898 Dihedral : 4.510 32.940 1525 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.03 % Allowed : 13.24 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -0.65 (0.22), residues: 1436 helix: 0.44 (0.19), residues: 822 sheet: -1.13 (0.48), residues: 106 loop : -1.64 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 176 HIS 0.003 0.001 HIS A 451 PHE 0.017 0.001 PHE A 138 TYR 0.025 0.002 TYR B 641 ARG 0.001 0.000 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.9120 (p0) cc_final: 0.8444 (p0) REVERT: A 320 MET cc_start: 0.8680 (mmt) cc_final: 0.7990 (mmm) REVERT: A 367 GLN cc_start: 0.8870 (mt0) cc_final: 0.8361 (mp10) REVERT: A 537 LEU cc_start: 0.8991 (tp) cc_final: 0.8615 (tp) REVERT: A 541 LEU cc_start: 0.9556 (mt) cc_final: 0.9347 (mp) REVERT: B 221 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9201 (tt) REVERT: B 371 HIS cc_start: 0.8516 (m-70) cc_final: 0.8207 (m-70) REVERT: B 383 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7407 (mtm) REVERT: C 22 TYR cc_start: 0.8970 (t80) cc_final: 0.8596 (t80) outliers start: 23 outliers final: 15 residues processed: 134 average time/residue: 0.1751 time to fit residues: 36.5931 Evaluate side-chains 125 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain D residue 12 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 77 optimal weight: 0.0000 chunk 115 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 63 optimal weight: 0.0980 chunk 84 optimal weight: 0.1980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10986 Z= 0.167 Angle : 0.587 9.050 14954 Z= 0.282 Chirality : 0.040 0.180 1803 Planarity : 0.003 0.042 1898 Dihedral : 4.440 30.915 1525 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.77 % Allowed : 13.24 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -0.43 (0.22), residues: 1436 helix: 0.63 (0.19), residues: 813 sheet: -0.98 (0.49), residues: 106 loop : -1.54 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 176 HIS 0.003 0.001 HIS B 563 PHE 0.013 0.001 PHE A 471 TYR 0.027 0.002 TYR B 641 ARG 0.002 0.000 ARG A 412 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.9123 (p0) cc_final: 0.8379 (p0) REVERT: A 256 MET cc_start: 0.9078 (mmm) cc_final: 0.8744 (mtt) REVERT: A 367 GLN cc_start: 0.8779 (mt0) cc_final: 0.8300 (mp10) REVERT: A 380 LEU cc_start: 0.9277 (tp) cc_final: 0.8749 (tt) REVERT: A 537 LEU cc_start: 0.8942 (tp) cc_final: 0.8585 (tp) REVERT: B 203 MET cc_start: 0.9423 (tpt) cc_final: 0.9143 (tpp) REVERT: B 221 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9194 (tt) REVERT: B 371 HIS cc_start: 0.8476 (m-70) cc_final: 0.8169 (m-70) REVERT: B 383 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7403 (mtm) REVERT: C 22 TYR cc_start: 0.8937 (t80) cc_final: 0.8587 (t80) REVERT: C 48 THR cc_start: 0.9195 (p) cc_final: 0.8927 (t) REVERT: C 75 MET cc_start: 0.8200 (ptt) cc_final: 0.7639 (ppp) outliers start: 20 outliers final: 13 residues processed: 147 average time/residue: 0.1774 time to fit residues: 40.4444 Evaluate side-chains 133 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 618 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.3980 chunk 81 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 87 optimal weight: 20.0000 chunk 93 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10986 Z= 0.241 Angle : 0.621 9.756 14954 Z= 0.302 Chirality : 0.041 0.160 1803 Planarity : 0.003 0.041 1898 Dihedral : 4.474 32.022 1525 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.03 % Allowed : 13.77 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.23), residues: 1436 helix: 0.71 (0.19), residues: 818 sheet: -0.93 (0.49), residues: 106 loop : -1.52 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 176 HIS 0.003 0.001 HIS A 451 PHE 0.021 0.001 PHE A 138 TYR 0.028 0.002 TYR B 641 ARG 0.004 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.9167 (p0) cc_final: 0.8480 (p0) REVERT: A 256 MET cc_start: 0.9069 (mmm) cc_final: 0.8829 (mtt) REVERT: A 320 MET cc_start: 0.8690 (mmt) cc_final: 0.8013 (mmm) REVERT: A 471 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.8177 (m-80) REVERT: A 489 MET cc_start: 0.9173 (mtm) cc_final: 0.8779 (mtm) REVERT: B 203 MET cc_start: 0.9433 (tpt) cc_final: 0.9162 (tpp) REVERT: B 371 HIS cc_start: 0.8478 (m-70) cc_final: 0.8162 (m-70) REVERT: B 383 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7422 (mtm) REVERT: B 515 MET cc_start: 0.8786 (tmm) cc_final: 0.8452 (tmm) REVERT: C 22 TYR cc_start: 0.8952 (t80) cc_final: 0.8642 (t80) outliers start: 23 outliers final: 17 residues processed: 136 average time/residue: 0.1716 time to fit residues: 36.4407 Evaluate side-chains 125 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 73 TRP Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 618 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 115 optimal weight: 0.2980 chunk 120 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 GLN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10986 Z= 0.177 Angle : 0.621 10.315 14954 Z= 0.295 Chirality : 0.040 0.182 1803 Planarity : 0.003 0.041 1898 Dihedral : 4.381 30.312 1525 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.94 % Allowed : 14.74 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -0.18 (0.23), residues: 1436 helix: 0.82 (0.19), residues: 816 sheet: -0.92 (0.49), residues: 106 loop : -1.43 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 176 HIS 0.002 0.001 HIS B 563 PHE 0.025 0.001 PHE A 471 TYR 0.027 0.002 TYR B 641 ARG 0.002 0.000 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.9127 (p0) cc_final: 0.8347 (p0) REVERT: A 225 ILE cc_start: 0.8058 (mt) cc_final: 0.7856 (mt) REVERT: A 367 GLN cc_start: 0.8829 (mt0) cc_final: 0.8322 (mp10) REVERT: A 380 LEU cc_start: 0.9235 (tp) cc_final: 0.8798 (tp) REVERT: A 489 MET cc_start: 0.9026 (mtm) cc_final: 0.8641 (mtm) REVERT: B 203 MET cc_start: 0.9402 (tpt) cc_final: 0.9123 (tpp) REVERT: B 240 TRP cc_start: 0.8564 (t60) cc_final: 0.8315 (t60) REVERT: B 371 HIS cc_start: 0.8415 (m-70) cc_final: 0.8163 (m-70) REVERT: C 22 TYR cc_start: 0.8871 (t80) cc_final: 0.8525 (t80) REVERT: C 48 THR cc_start: 0.9266 (p) cc_final: 0.9026 (t) REVERT: C 75 MET cc_start: 0.8226 (ptt) cc_final: 0.7676 (ppp) outliers start: 22 outliers final: 17 residues processed: 141 average time/residue: 0.1718 time to fit residues: 38.3414 Evaluate side-chains 127 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 73 TRP Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 618 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 0.0970 chunk 63 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 11 optimal weight: 0.0000 chunk 87 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 89 optimal weight: 7.9990 chunk 120 optimal weight: 0.6980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 GLN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10986 Z= 0.186 Angle : 0.627 9.976 14954 Z= 0.298 Chirality : 0.041 0.211 1803 Planarity : 0.003 0.038 1898 Dihedral : 4.329 33.330 1525 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.77 % Allowed : 15.27 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.23), residues: 1436 helix: 0.92 (0.19), residues: 819 sheet: -0.84 (0.49), residues: 106 loop : -1.33 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 176 HIS 0.002 0.001 HIS B 563 PHE 0.019 0.001 PHE A 392 TYR 0.035 0.002 TYR A 458 ARG 0.001 0.000 ARG A 157 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 1.184 Fit side-chains revert: symmetry clash REVERT: A 100 ASP cc_start: 0.9116 (p0) cc_final: 0.8332 (p0) REVERT: A 227 MET cc_start: 0.7288 (mtp) cc_final: 0.7052 (mtp) REVERT: A 287 MET cc_start: 0.8637 (mtt) cc_final: 0.8415 (mtt) REVERT: A 350 MET cc_start: 0.8646 (mmm) cc_final: 0.8441 (mmm) REVERT: A 380 LEU cc_start: 0.9195 (tp) cc_final: 0.8786 (tp) REVERT: A 489 MET cc_start: 0.9062 (mtm) cc_final: 0.8814 (mtm) REVERT: A 542 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8947 (p) REVERT: B 203 MET cc_start: 0.9403 (tpt) cc_final: 0.9126 (tpp) REVERT: B 240 TRP cc_start: 0.8563 (t60) cc_final: 0.8297 (t60) REVERT: B 371 HIS cc_start: 0.8511 (m-70) cc_final: 0.8237 (m-70) REVERT: B 515 MET cc_start: 0.8797 (tmm) cc_final: 0.8469 (tmm) REVERT: C 22 TYR cc_start: 0.8856 (t80) cc_final: 0.8555 (t80) REVERT: C 48 THR cc_start: 0.9289 (p) cc_final: 0.9051 (t) REVERT: C 75 MET cc_start: 0.8207 (ptt) cc_final: 0.7629 (ppp) outliers start: 20 outliers final: 15 residues processed: 133 average time/residue: 0.1946 time to fit residues: 39.4962 Evaluate side-chains 127 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 73 TRP Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain C residue 15 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 115 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.057630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.047053 restraints weight = 50574.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.048438 restraints weight = 24927.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.049250 restraints weight = 15004.755| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10986 Z= 0.249 Angle : 0.652 10.738 14954 Z= 0.312 Chirality : 0.041 0.145 1803 Planarity : 0.003 0.037 1898 Dihedral : 4.415 38.502 1525 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.59 % Allowed : 15.53 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: 0.00 (0.23), residues: 1436 helix: 0.90 (0.19), residues: 836 sheet: -0.86 (0.49), residues: 106 loop : -1.28 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 176 HIS 0.002 0.001 HIS A 451 PHE 0.020 0.001 PHE A 392 TYR 0.029 0.002 TYR B 641 ARG 0.009 0.000 ARG B 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2000.82 seconds wall clock time: 37 minutes 9.64 seconds (2229.64 seconds total)