Starting phenix.real_space_refine (version: 1.21rc1) on Sat Jul 8 07:29:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gsa_0051/07_2023/6gsa_0051.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gsa_0051/07_2023/6gsa_0051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gsa_0051/07_2023/6gsa_0051.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gsa_0051/07_2023/6gsa_0051.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gsa_0051/07_2023/6gsa_0051.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gsa_0051/07_2023/6gsa_0051.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.004 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: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 10593 2.51 5 N 2674 2.21 5 O 2940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 307": "NH1" <-> "NH2" Residue "D ARG 341": "NH1" <-> "NH2" Residue "D ARG 456": "NH1" <-> "NH2" Residue "D ARG 463": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 16272 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4320 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 17, 'TRANS': 506} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 4249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4249 Classifications: {'peptide': 512} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 495} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1137 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 66 Chain: "D" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2773 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 6, 'TRANS': 354} Chain breaks: 3 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 314 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 12, 'ASP:plan': 10, 'GLU:plan': 16, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 175 Chain: "E" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3793 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 32, 'TRANS': 419} Chain breaks: 5 Time building chain proxies: 8.10, per 1000 atoms: 0.50 Number of scatterers: 16272 At special positions: 0 Unit cell: (101.76, 129.32, 174.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 2940 8.00 N 2674 7.00 C 10593 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 215 " distance=2.04 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 215 " distance=2.04 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: 6.28 Conformation dependent library (CDL) restraints added in 2.3 seconds 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3886 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 8 sheets defined 64.5% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 57 through 72 removed outlier: 3.778A pdb=" N GLN A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.818A pdb=" N TYR A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 105 Processing helix chain 'A' and resid 107 through 121 Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.855A pdb=" N TYR A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 135 through 147 removed outlier: 4.045A pdb=" N ARG A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 173 Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 185 through 193 removed outlier: 3.684A pdb=" N HIS A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY A 193 " --> pdb=" O HIS A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.685A pdb=" N GLY A 203 " --> pdb=" O TRP A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 222 Processing helix chain 'A' and resid 230 through 241 removed outlier: 4.483A pdb=" N VAL A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 249 through 266 Processing helix chain 'A' and resid 279 through 302 Processing helix chain 'A' and resid 340 through 356 Processing helix chain 'A' and resid 366 through 386 Processing helix chain 'A' and resid 394 through 421 removed outlier: 3.517A pdb=" N PHE A 398 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 444 Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 450 through 456 removed outlier: 3.838A pdb=" N HIS A 456 " --> pdb=" O PHE A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 477 removed outlier: 3.870A pdb=" N ILE A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 468 " --> pdb=" O THR A 464 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A 471 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE A 476 " --> pdb=" O PHE A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 495 removed outlier: 3.894A pdb=" N LYS A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA A 494 " --> pdb=" O THR A 490 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 500 through 524 removed outlier: 3.795A pdb=" N LEU A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 551 removed outlier: 3.535A pdb=" N LYS A 539 " --> pdb=" O HIS A 535 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE A 545 " --> pdb=" O LEU A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 563 Processing helix chain 'A' and resid 589 through 601 Processing helix chain 'A' and resid 602 through 607 removed outlier: 3.609A pdb=" N ASP A 605 " --> pdb=" O ASN A 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 72 removed outlier: 4.462A pdb=" N ASP B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.576A pdb=" N TYR B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 105 removed outlier: 3.822A pdb=" N PHE B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 122 Processing helix chain 'B' and resid 122 through 127 removed outlier: 3.665A pdb=" N TYR B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 147 Processing helix chain 'B' and resid 153 through 173 removed outlier: 3.520A pdb=" N TYR B 173 " --> pdb=" O MET B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 183 Processing helix chain 'B' and resid 185 through 193 removed outlier: 3.580A pdb=" N HIS B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 223 Processing helix chain 'B' and resid 231 through 241 removed outlier: 3.572A pdb=" N LEU B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 249 removed outlier: 3.687A pdb=" N GLU B 249 " --> pdb=" O PHE B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 266 Processing helix chain 'B' and resid 279 through 302 Processing helix chain 'B' and resid 340 through 357 Processing helix chain 'B' and resid 366 through 387 Processing helix chain 'B' and resid 393 through 421 removed outlier: 3.798A pdb=" N ARG B 397 " --> pdb=" O SER B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 444 Processing helix chain 'B' and resid 450 through 455 removed outlier: 3.571A pdb=" N PHE B 453 " --> pdb=" O SER B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 477 removed outlier: 3.902A pdb=" N MET B 460 " --> pdb=" O HIS B 456 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 476 " --> pdb=" O PHE B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 495 removed outlier: 3.629A pdb=" N ALA B 494 " --> pdb=" O THR B 490 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 524 Processing helix chain 'B' and resid 535 through 552 removed outlier: 3.730A pdb=" N ILE B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 563 Processing helix chain 'B' and resid 589 through 601 Processing helix chain 'B' and resid 603 through 607 removed outlier: 3.617A pdb=" N LEU B 607 " --> pdb=" O SER B 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 24 Processing helix chain 'C' and resid 28 through 33 Processing helix chain 'C' and resid 83 through 97 Processing helix chain 'C' and resid 107 through 113 removed outlier: 3.709A pdb=" N LYS C 112 " --> pdb=" O ASP C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 124 Processing helix chain 'C' and resid 127 through 141 Processing helix chain 'C' and resid 143 through 160 Processing helix chain 'C' and resid 177 through 188 Processing helix chain 'D' and resid 7 through 12 removed outlier: 3.663A pdb=" N GLU D 11 " --> pdb=" O VAL D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 23 removed outlier: 3.893A pdb=" N HIS D 23 " --> pdb=" O GLU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 111 removed outlier: 3.622A pdb=" N LEU D 101 " --> pdb=" O ASP D 97 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP D 111 " --> pdb=" O ASN D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 156 Processing helix chain 'D' and resid 176 through 190 removed outlier: 4.070A pdb=" N LYS D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 267 removed outlier: 3.756A pdb=" N SER D 266 " --> pdb=" O ARG D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 288 removed outlier: 3.902A pdb=" N TYR D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU D 285 " --> pdb=" O GLU D 281 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU D 286 " --> pdb=" O LYS D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 381 removed outlier: 3.645A pdb=" N LYS D 381 " --> pdb=" O LEU D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 389 Processing helix chain 'D' and resid 419 through 432 Processing helix chain 'D' and resid 457 through 459 No H-bonds generated for 'chain 'D' and resid 457 through 459' Processing helix chain 'E' and resid 45 through 59 removed outlier: 3.825A pdb=" N LYS E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR E 52 " --> pdb=" O TYR E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 92 Processing helix chain 'E' and resid 108 through 139 Processing helix chain 'E' and resid 147 through 168 Processing helix chain 'E' and resid 183 through 194 Processing helix chain 'E' and resid 207 through 225 Processing helix chain 'E' and resid 227 through 232 Processing helix chain 'E' and resid 233 through 234 No H-bonds generated for 'chain 'E' and resid 233 through 234' Processing helix chain 'E' and resid 235 through 237 No H-bonds generated for 'chain 'E' and resid 235 through 237' Processing helix chain 'E' and resid 277 through 280 Processing helix chain 'E' and resid 281 through 296 Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 317 through 321 Processing helix chain 'E' and resid 334 through 349 Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 371 through 378 removed outlier: 3.571A pdb=" N PHE E 378 " --> pdb=" O PHE E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 384 removed outlier: 4.138A pdb=" N GLY E 384 " --> pdb=" O GLU E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 removed outlier: 3.730A pdb=" N PHE E 393 " --> pdb=" O PRO E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 399 Processing helix chain 'E' and resid 400 through 408 Processing helix chain 'E' and resid 428 through 433 Processing helix chain 'E' and resid 434 through 436 No H-bonds generated for 'chain 'E' and resid 434 through 436' Processing helix chain 'E' and resid 437 through 445 Processing helix chain 'E' and resid 446 through 450 Processing helix chain 'E' and resid 451 through 479 Proline residue: E 473 - end of helix Processing helix chain 'E' and resid 482 through 491 removed outlier: 4.098A pdb=" N ASP E 487 " --> pdb=" O ILE E 484 " (cutoff:3.500A) Proline residue: E 488 - end of helix Processing helix chain 'E' and resid 492 through 504 removed outlier: 3.793A pdb=" N THR E 503 " --> pdb=" O PHE E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 507 No H-bonds generated for 'chain 'E' and resid 505 through 507' Processing helix chain 'E' and resid 520 through 525 Processing helix chain 'E' and resid 526 through 532 Processing sheet with id=AA1, first strand: chain 'A' and resid 315 through 316 Processing sheet with id=AA2, first strand: chain 'A' and resid 527 through 528 removed outlier: 4.006A pdb=" N TYR A 534 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 527 through 528 Processing sheet with id=AA4, first strand: chain 'C' and resid 15 through 19 removed outlier: 8.686A pdb=" N MET C 77 " --> pdb=" O ASN C 5 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL C 7 " --> pdb=" O MET C 77 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 118 through 123 removed outlier: 6.517A pdb=" N LEU D 129 " --> pdb=" O TRP D 141 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TRP D 141 " --> pdb=" O LEU D 129 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TYR D 131 " --> pdb=" O GLU D 139 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 198 through 200 removed outlier: 6.616A pdb=" N VAL D 199 " --> pdb=" O THR D 277 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE D 276 " --> pdb=" O ARG D 313 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE D 312 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU D 337 " --> pdb=" O SER D 358 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE D 440 " --> pdb=" O GLU D 465 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 391 through 392 removed outlier: 6.096A pdb=" N ARG D 409 " --> pdb=" O VAL D 475 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N VAL D 477 " --> pdb=" O ARG D 409 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LYS D 411 " --> pdb=" O VAL D 477 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE D 452 " --> pdb=" O GLN D 474 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 239 through 241 860 hydrogen bonds defined for protein. 2493 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: 4.79 Time building geometry restraints manager: 6.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2685 1.32 - 1.45: 4816 1.45 - 1.59: 9067 1.59 - 1.72: 6 1.72 - 1.85: 100 Bond restraints: 16674 Sorted by residual: bond pdb=" CA LYS E 240 " pdb=" C LYS E 240 " ideal model delta sigma weight residual 1.521 1.431 0.090 1.20e-02 6.94e+03 5.68e+01 bond pdb=" N VAL E 138 " pdb=" CA VAL E 138 " ideal model delta sigma weight residual 1.461 1.542 -0.080 1.17e-02 7.31e+03 4.71e+01 bond pdb=" ND1 HIS E 139 " pdb=" CE1 HIS E 139 " ideal model delta sigma weight residual 1.321 1.386 -0.065 1.00e-02 1.00e+04 4.24e+01 bond pdb=" CG HIS E 139 " pdb=" CD2 HIS E 139 " ideal model delta sigma weight residual 1.354 1.419 -0.065 1.10e-02 8.26e+03 3.52e+01 bond pdb=" N LEU E 464 " pdb=" CA LEU E 464 " ideal model delta sigma weight residual 1.459 1.526 -0.067 1.23e-02 6.61e+03 2.98e+01 ... (remaining 16669 not shown) Histogram of bond angle deviations from ideal: 76.26 - 87.98: 1 87.98 - 99.70: 4 99.70 - 111.42: 6830 111.42 - 123.14: 14890 123.14 - 134.85: 887 Bond angle restraints: 22612 Sorted by residual: angle pdb=" CG MET E 407 " pdb=" SD MET E 407 " pdb=" CE MET E 407 " ideal model delta sigma weight residual 100.90 76.26 24.64 2.20e+00 2.07e-01 1.25e+02 angle pdb=" C CYS E 182 " pdb=" N PRO E 183 " pdb=" CA PRO E 183 " ideal model delta sigma weight residual 119.66 114.00 5.66 7.30e-01 1.88e+00 6.00e+01 angle pdb=" N ILE E 523 " pdb=" CA ILE E 523 " pdb=" C ILE E 523 " ideal model delta sigma weight residual 110.23 118.07 -7.84 1.04e+00 9.25e-01 5.68e+01 angle pdb=" C ILE E 484 " pdb=" CA ILE E 484 " pdb=" CB ILE E 484 " ideal model delta sigma weight residual 112.05 101.78 10.27 1.46e+00 4.69e-01 4.95e+01 angle pdb=" N LEU E 93 " pdb=" CA LEU E 93 " pdb=" C LEU E 93 " ideal model delta sigma weight residual 111.07 117.29 -6.22 1.07e+00 8.73e-01 3.38e+01 ... (remaining 22607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 9285 16.82 - 33.65: 503 33.65 - 50.47: 116 50.47 - 67.30: 18 67.30 - 84.12: 15 Dihedral angle restraints: 9937 sinusoidal: 3972 harmonic: 5965 Sorted by residual: dihedral pdb=" CA ASN D 450 " pdb=" C ASN D 450 " pdb=" N ASN D 451 " pdb=" CA ASN D 451 " ideal model delta harmonic sigma weight residual 180.00 147.91 32.09 0 5.00e+00 4.00e-02 4.12e+01 dihedral pdb=" C HIS E 256 " pdb=" N HIS E 256 " pdb=" CA HIS E 256 " pdb=" CB HIS E 256 " ideal model delta harmonic sigma weight residual -122.60 -136.30 13.70 0 2.50e+00 1.60e-01 3.00e+01 dihedral pdb=" CA PHE C 170 " pdb=" C PHE C 170 " pdb=" N ASN C 171 " pdb=" CA ASN C 171 " ideal model delta harmonic sigma weight residual -180.00 -153.06 -26.94 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 9934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.251: 2473 0.251 - 0.502: 50 0.502 - 0.752: 1 0.752 - 1.003: 0 1.003 - 1.254: 1 Chirality restraints: 2525 Sorted by residual: chirality pdb=" CG LEU E 239 " pdb=" CB LEU E 239 " pdb=" CD1 LEU E 239 " pdb=" CD2 LEU E 239 " both_signs ideal model delta sigma weight residual False -2.59 -1.34 -1.25 2.00e-01 2.50e+01 3.93e+01 chirality pdb=" CA HIS E 256 " pdb=" N HIS E 256 " pdb=" C HIS E 256 " pdb=" CB HIS E 256 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.21e+00 chirality pdb=" CA LYS E 253 " pdb=" N LYS E 253 " pdb=" C LYS E 253 " pdb=" CB LYS E 253 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.33e+00 ... (remaining 2522 not shown) Planarity restraints: 2839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 214 " 0.064 2.00e-02 2.50e+03 4.17e-02 3.04e+01 pdb=" CG PHE E 214 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE E 214 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE E 214 " -0.059 2.00e-02 2.50e+03 pdb=" CE1 PHE E 214 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE E 214 " 0.025 2.00e-02 2.50e+03 pdb=" CZ PHE E 214 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 92 " -0.021 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C THR E 92 " 0.071 2.00e-02 2.50e+03 pdb=" O THR E 92 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU E 93 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 332 " 0.036 2.00e-02 2.50e+03 2.50e-02 1.25e+01 pdb=" CG TYR E 332 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR E 332 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR E 332 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR E 332 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR E 332 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR E 332 " -0.016 2.00e-02 2.50e+03 pdb=" OH TYR E 332 " 0.047 2.00e-02 2.50e+03 ... (remaining 2836 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 932 2.73 - 3.27: 16174 3.27 - 3.82: 26414 3.82 - 4.36: 32764 4.36 - 4.90: 54127 Nonbonded interactions: 130411 Sorted by model distance: nonbonded pdb=" O PRO E 264 " pdb=" O GLY E 265 " model vdw 2.189 3.040 nonbonded pdb=" O PRO B 365 " pdb=" OH TYR B 422 " model vdw 2.284 2.440 nonbonded pdb=" O LYS B 108 " pdb=" OG SER B 111 " model vdw 2.307 2.440 nonbonded pdb=" OH TYR B 158 " pdb=" O HIS B 228 " model vdw 2.316 2.440 nonbonded pdb=" O GLU A 512 " pdb=" OG SER A 515 " model vdw 2.323 2.440 ... (remaining 130406 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 54 through 316 or (resid 317 and (name N or name CA or nam \ e C or name O or name CB )) or resid 339 through 608)) selection = (chain 'B' and (resid 54 through 388 or (resid 389 and (name N or name CA or nam \ e C or name O or name CB )) or resid 390 or (resid 391 through 392 and (name N o \ r name CA or name C or name O or name CB )) or resid 393 through 608)) } 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=0.00 max=1.00 mean=0.99 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: 1.050 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: 5.190 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 40.640 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4740 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 : 0.011 0.090 16674 Z= 0.694 Angle : 1.237 24.642 22612 Z= 0.731 Chirality : 0.085 1.254 2525 Planarity : 0.008 0.102 2839 Dihedral : 11.996 84.123 6045 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.15 % Favored : 94.65 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.92 (0.15), residues: 1963 helix: -1.51 (0.12), residues: 1172 sheet: -1.49 (0.54), residues: 83 loop : -2.53 (0.19), residues: 708 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 455 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 4 residues processed: 482 average time/residue: 0.3322 time to fit residues: 224.7650 Evaluate side-chains 218 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 214 time to evaluate : 2.005 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.2900 time to fit residues: 4.3225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 168 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 180 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 116 ASN ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 GLN A 474 GLN ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 GLN B 82 GLN B 104 ASN B 121 ASN B 205 GLN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 HIS B 360 ASN B 406 GLN B 461 GLN B 474 GLN B 543 ASN B 552 ASN C 128 GLN E 44 GLN ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 453 ASN ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5120 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 16674 Z= 0.258 Angle : 0.721 9.248 22612 Z= 0.381 Chirality : 0.045 0.258 2525 Planarity : 0.005 0.048 2839 Dihedral : 5.409 32.242 2170 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.17 (0.18), residues: 1963 helix: -0.10 (0.14), residues: 1224 sheet: -0.93 (0.58), residues: 80 loop : -1.92 (0.22), residues: 659 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 273 time to evaluate : 2.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 276 average time/residue: 0.3089 time to fit residues: 124.6469 Evaluate side-chains 180 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 2.048 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 100 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 123 optimal weight: 0.0040 chunk 49 optimal weight: 2.9990 chunk 181 optimal weight: 6.9990 chunk 195 optimal weight: 40.0000 chunk 161 optimal weight: 20.0000 chunk 179 optimal weight: 50.0000 chunk 61 optimal weight: 20.0000 chunk 145 optimal weight: 9.9990 overall best weight: 4.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN B 121 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 433 HIS ** D 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 GLN ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5284 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.123 16674 Z= 0.283 Angle : 0.705 11.399 22612 Z= 0.372 Chirality : 0.044 0.266 2525 Planarity : 0.005 0.047 2839 Dihedral : 5.192 31.162 2170 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.19), residues: 1963 helix: 0.29 (0.15), residues: 1230 sheet: -0.58 (0.59), residues: 82 loop : -1.79 (0.23), residues: 651 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 248 time to evaluate : 1.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 252 average time/residue: 0.3013 time to fit residues: 112.2599 Evaluate side-chains 157 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 2.122 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1469 time to fit residues: 3.0096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 178 optimal weight: 20.0000 chunk 136 optimal weight: 20.0000 chunk 93 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 181 optimal weight: 30.0000 chunk 192 optimal weight: 30.0000 chunk 94 optimal weight: 1.9990 chunk 172 optimal weight: 40.0000 chunk 51 optimal weight: 9.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 495 ASN ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 ASN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN B 495 ASN C 81 ASN D 407 HIS D 427 GLN ** D 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 HIS ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 HIS E 283 GLN E 453 ASN ** E 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5525 moved from start: 0.6032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.098 16674 Z= 0.386 Angle : 0.824 13.296 22612 Z= 0.435 Chirality : 0.046 0.315 2525 Planarity : 0.006 0.073 2839 Dihedral : 5.447 28.788 2170 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 27.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer Outliers : 0.23 % 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: -0.90 (0.18), residues: 1963 helix: 0.02 (0.14), residues: 1219 sheet: -0.58 (0.56), residues: 96 loop : -1.64 (0.24), residues: 648 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 216 time to evaluate : 2.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 219 average time/residue: 0.2917 time to fit residues: 95.7027 Evaluate side-chains 137 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 135 time to evaluate : 1.969 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1574 time to fit residues: 3.1919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 160 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 164 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 172 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 GLN ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN B 228 HIS ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 HIS B 461 GLN B 543 ASN D 474 GLN ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5516 moved from start: 0.6533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 16674 Z= 0.293 Angle : 0.715 11.002 22612 Z= 0.378 Chirality : 0.044 0.226 2525 Planarity : 0.005 0.065 2839 Dihedral : 5.301 31.412 2170 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 23.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.85 (0.18), residues: 1963 helix: 0.10 (0.14), residues: 1222 sheet: -0.69 (0.54), residues: 96 loop : -1.71 (0.24), residues: 645 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 218 time to evaluate : 2.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 219 average time/residue: 0.3060 time to fit residues: 99.4874 Evaluate side-chains 140 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 2.144 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1508 time to fit residues: 3.1131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 64 optimal weight: 4.9990 chunk 173 optimal weight: 40.0000 chunk 38 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 192 optimal weight: 30.0000 chunk 159 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 GLN ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 HIS ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN C 31 ASN D 443 GLN E 86 HIS ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN E 389 GLN ** E 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5559 moved from start: 0.7025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.076 16674 Z= 0.302 Angle : 0.725 15.111 22612 Z= 0.381 Chirality : 0.044 0.290 2525 Planarity : 0.005 0.063 2839 Dihedral : 5.276 32.754 2170 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 25.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.85 (0.18), residues: 1963 helix: 0.08 (0.14), residues: 1225 sheet: -0.58 (0.56), residues: 86 loop : -1.68 (0.24), residues: 652 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 208 time to evaluate : 1.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 209 average time/residue: 0.2855 time to fit residues: 89.4707 Evaluate side-chains 138 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 1.885 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1352 time to fit residues: 2.7506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 185 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 140 optimal weight: 9.9990 chunk 108 optimal weight: 0.8980 chunk 162 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 191 optimal weight: 20.0000 chunk 120 optimal weight: 0.0040 chunk 116 optimal weight: 7.9990 chunk 88 optimal weight: 7.9990 overall best weight: 3.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 GLN ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 427 GLN E 86 HIS ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN E 319 GLN ** E 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5517 moved from start: 0.7221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 16674 Z= 0.229 Angle : 0.674 13.379 22612 Z= 0.349 Chirality : 0.043 0.214 2525 Planarity : 0.005 0.066 2839 Dihedral : 5.116 31.444 2170 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.52 (0.19), residues: 1963 helix: 0.33 (0.14), residues: 1227 sheet: -0.56 (0.56), residues: 86 loop : -1.50 (0.24), residues: 650 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2835 time to fit residues: 88.7023 Evaluate side-chains 140 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 2.131 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 118 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 57 optimal weight: 0.0020 chunk 37 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 chunk 130 optimal weight: 0.5980 chunk 94 optimal weight: 9.9990 chunk 17 optimal weight: 0.1980 chunk 150 optimal weight: 0.0770 chunk 174 optimal weight: 30.0000 overall best weight: 0.9748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 HIS ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 HIS ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN E 283 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5429 moved from start: 0.7266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 16674 Z= 0.181 Angle : 0.659 12.107 22612 Z= 0.335 Chirality : 0.043 0.251 2525 Planarity : 0.004 0.058 2839 Dihedral : 4.919 31.764 2170 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.19), residues: 1963 helix: 0.63 (0.15), residues: 1225 sheet: -0.45 (0.57), residues: 86 loop : -1.40 (0.24), residues: 652 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.2977 time to fit residues: 96.8175 Evaluate side-chains 144 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.997 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 183 optimal weight: 10.0000 chunk 167 optimal weight: 7.9990 chunk 178 optimal weight: 20.0000 chunk 107 optimal weight: 0.7980 chunk 77 optimal weight: 20.0000 chunk 140 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 169 optimal weight: 40.0000 chunk 117 optimal weight: 9.9990 chunk 189 optimal weight: 0.7980 overall best weight: 4.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN E 86 HIS ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN ** E 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5550 moved from start: 0.7614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.092 16674 Z= 0.260 Angle : 0.695 13.961 22612 Z= 0.361 Chirality : 0.044 0.278 2525 Planarity : 0.005 0.056 2839 Dihedral : 5.016 32.831 2170 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 22.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.19), residues: 1963 helix: 0.51 (0.15), residues: 1225 sheet: -0.40 (0.55), residues: 87 loop : -1.34 (0.25), residues: 651 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.2831 time to fit residues: 84.9574 Evaluate side-chains 134 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 2.025 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 115 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 131 optimal weight: 4.9990 chunk 198 optimal weight: 40.0000 chunk 182 optimal weight: 50.0000 chunk 157 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 96 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 268 GLN E 283 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5532 moved from start: 0.7761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 16674 Z= 0.227 Angle : 0.687 13.516 22612 Z= 0.352 Chirality : 0.044 0.255 2525 Planarity : 0.005 0.055 2839 Dihedral : 5.004 33.071 2170 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.20 (0.19), residues: 1963 helix: 0.56 (0.15), residues: 1219 sheet: -0.34 (0.55), residues: 87 loop : -1.32 (0.25), residues: 657 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 2.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.2750 time to fit residues: 80.7830 Evaluate side-chains 137 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 2.057 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 48 optimal weight: 0.1980 chunk 145 optimal weight: 20.0000 chunk 23 optimal weight: 0.0050 chunk 43 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 162 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 overall best weight: 2.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.083958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.062026 restraints weight = 131122.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.062731 restraints weight = 90768.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.063551 restraints weight = 67660.286| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.7909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 16674 Z= 0.194 Angle : 0.658 12.595 22612 Z= 0.334 Chirality : 0.043 0.243 2525 Planarity : 0.004 0.054 2839 Dihedral : 4.900 32.581 2170 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.19), residues: 1963 helix: 0.72 (0.15), residues: 1221 sheet: -0.22 (0.57), residues: 87 loop : -1.31 (0.25), residues: 655 =============================================================================== Job complete usr+sys time: 3082.75 seconds wall clock time: 57 minutes 37.00 seconds (3457.00 seconds total)