Starting phenix.real_space_refine (version: dev) on Sat May 14 02:48:33 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gsa_0051/05_2022/6gsa_0051.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gsa_0051/05_2022/6gsa_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_0051/05_2022/6gsa_0051.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gsa_0051/05_2022/6gsa_0051.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gsa_0051/05_2022/6gsa_0051.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gsa_0051/05_2022/6gsa_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 Convert atoms to be neutral 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: 9.16, per 1000 atoms: 0.56 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: 5.95 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: 0.84 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: 4.67 Time building geometry restraints manager: 6.33 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 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. 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 5.100 Check model and map are aligned: 0.230 Convert atoms to be neutral: 0.140 Process input model: 40.720 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.680 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: 0.4431 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 : 4.82 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 : 2.219 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: 0.3203 time to fit residues: 217.7003 Evaluate side-chains 218 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 214 time to evaluate : 2.130 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.2876 time to fit residues: 4.4454 ------------------------------------------------------------------------------- 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: 0.4795 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 : 16.81 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 : 2.146 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: 0.2903 time to fit residues: 118.0467 Evaluate side-chains 180 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 2.200 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7208 ------------------------------------------------------------------------------- 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: 5.9990 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: 5.0000 ------------------------------------------------------------------------------- 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 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 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 433 HIS ** D 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN 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: 0.5005 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 16674 Z= 0.297 Angle : 0.735 9.668 22612 Z= 0.389 Chirality : 0.044 0.291 2525 Planarity : 0.005 0.048 2839 Dihedral : 5.255 31.090 2170 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 20.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % 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: -0.73 (0.19), residues: 1963 helix: 0.21 (0.14), residues: 1234 sheet: -0.50 (0.58), residues: 87 loop : -1.74 (0.24), residues: 642 *********************** 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 251 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 246 time to evaluate : 2.228 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: 5 outliers final: 1 residues processed: 250 average time/residue: 0.3074 time to fit residues: 113.9388 Evaluate side-chains 158 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 2.078 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2459 time to fit residues: 3.1552 ------------------------------------------------------------------------------- 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: 0.2980 chunk 136 optimal weight: 0.0670 chunk 93 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 chunk 181 optimal weight: 40.0000 chunk 192 optimal weight: 30.0000 chunk 94 optimal weight: 0.0670 chunk 172 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 overall best weight: 1.8860 ------------------------------------------------------------------------------- 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** A 474 GLN ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN B 121 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 HIS B 461 GLN B 495 ASN ** D 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4930 moved from start: 0.5248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 16674 Z= 0.196 Angle : 0.635 9.711 22612 Z= 0.326 Chirality : 0.043 0.221 2525 Planarity : 0.005 0.101 2839 Dihedral : 5.044 29.514 2170 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % 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: -0.33 (0.19), residues: 1963 helix: 0.53 (0.15), residues: 1233 sheet: -0.36 (0.64), residues: 79 loop : -1.58 (0.24), residues: 651 *********************** 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 246 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 242 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: 4 outliers final: 1 residues processed: 245 average time/residue: 0.3050 time to fit residues: 113.4225 Evaluate side-chains 154 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 2.455 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1765 time to fit residues: 3.4283 ------------------------------------------------------------------------------- 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: 5.9990 chunk 109 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 164 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 172 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 313 HIS A 495 ASN ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 ASN B 116 ASN B 121 ASN B 205 GLN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN B 433 HIS ** D 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN E 266 HIS E 268 GLN ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5076 moved from start: 0.5973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 16674 Z= 0.274 Angle : 0.686 9.316 22612 Z= 0.363 Chirality : 0.043 0.334 2525 Planarity : 0.005 0.061 2839 Dihedral : 5.027 30.330 2170 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 22.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % 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: -0.41 (0.19), residues: 1963 helix: 0.43 (0.15), residues: 1226 sheet: -0.30 (0.58), residues: 89 loop : -1.53 (0.24), residues: 648 *********************** 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 225 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 223 time to evaluate : 2.076 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: 2 outliers final: 1 residues processed: 224 average time/residue: 0.2845 time to fit residues: 95.7577 Evaluate side-chains 149 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 2.102 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1542 time to fit residues: 3.1221 ------------------------------------------------------------------------------- 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: 2.9990 chunk 173 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 192 optimal weight: 50.0000 chunk 159 optimal weight: 5.9990 chunk 89 optimal weight: 0.0870 chunk 16 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 overall best weight: 2.8166 ------------------------------------------------------------------------------- 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** ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN B 121 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN C 81 ASN E 86 HIS ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5045 moved from start: 0.6217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 16674 Z= 0.216 Angle : 0.644 10.502 22612 Z= 0.336 Chirality : 0.043 0.200 2525 Planarity : 0.004 0.050 2839 Dihedral : 4.962 32.869 2170 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % 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: -0.30 (0.19), residues: 1963 helix: 0.54 (0.15), residues: 1233 sheet: -0.56 (0.59), residues: 87 loop : -1.52 (0.24), residues: 643 *********************** 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 222 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 221 time to evaluate : 2.063 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: 1 outliers final: 1 residues processed: 222 average time/residue: 0.2804 time to fit residues: 93.9826 Evaluate side-chains 151 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 2.077 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1427 time to fit residues: 3.3170 ------------------------------------------------------------------------------- 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: 30.0000 chunk 21 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 116 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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** ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 ASN B 116 ASN B 121 ASN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN B 543 ASN D 443 GLN E 86 HIS ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 GLN E 389 GLN E 471 ASN ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5084 moved from start: 0.6598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 16674 Z= 0.225 Angle : 0.645 9.313 22612 Z= 0.340 Chirality : 0.042 0.220 2525 Planarity : 0.004 0.056 2839 Dihedral : 4.922 31.166 2170 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 19.89 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: -0.23 (0.19), residues: 1963 helix: 0.61 (0.15), residues: 1224 sheet: -0.70 (0.58), residues: 87 loop : -1.45 (0.24), residues: 652 *********************** 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 213 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 2.081 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 outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.2787 time to fit residues: 90.2642 Evaluate side-chains 145 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 2.056 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7319 ------------------------------------------------------------------------------- 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: 5.9990 chunk 76 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 121 optimal weight: 0.2980 chunk 130 optimal weight: 1.9990 chunk 94 optimal weight: 20.0000 chunk 17 optimal weight: 0.7980 chunk 150 optimal weight: 0.8980 chunk 174 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN B 121 ASN E 86 HIS ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 471 ASN ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5003 moved from start: 0.6659 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= 0.178 Angle : 0.626 9.291 22612 Z= 0.323 Chirality : 0.043 0.240 2525 Planarity : 0.004 0.071 2839 Dihedral : 4.807 30.813 2170 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % 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: 0.83 (0.15), residues: 1217 sheet: -0.52 (0.59), residues: 87 loop : -1.38 (0.25), residues: 659 *********************** 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 219 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 2.110 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: 219 average time/residue: 0.2687 time to fit residues: 88.8435 Evaluate side-chains 152 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 2.100 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6871 ------------------------------------------------------------------------------- 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: 6.9990 chunk 178 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 77 optimal weight: 20.0000 chunk 140 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 161 optimal weight: 8.9990 chunk 169 optimal weight: 50.0000 chunk 117 optimal weight: 8.9990 chunk 189 optimal weight: 0.0470 overall best weight: 3.9284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 407 HIS E 86 HIS ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 471 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5137 moved from start: 0.7167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.087 16674 Z= 0.251 Angle : 0.676 10.303 22612 Z= 0.357 Chirality : 0.043 0.248 2525 Planarity : 0.005 0.065 2839 Dihedral : 4.900 30.407 2170 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 21.03 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: -0.13 (0.19), residues: 1963 helix: 0.66 (0.15), residues: 1218 sheet: -0.63 (0.57), residues: 87 loop : -1.35 (0.25), residues: 658 *********************** 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 209 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 2.147 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 outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.2737 time to fit residues: 87.3619 Evaluate side-chains 137 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.978 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7849 ------------------------------------------------------------------------------- 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: 0.0980 chunk 131 optimal weight: 8.9990 chunk 198 optimal weight: 7.9990 chunk 182 optimal weight: 6.9990 chunk 157 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 168 optimal weight: 0.2980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN B 121 ASN B 259 GLN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 471 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5076 moved from start: 0.7241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 16674 Z= 0.187 Angle : 0.643 11.681 22612 Z= 0.330 Chirality : 0.043 0.263 2525 Planarity : 0.004 0.061 2839 Dihedral : 4.804 30.250 2170 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % 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: -0.01 (0.19), residues: 1963 helix: 0.76 (0.15), residues: 1217 sheet: -0.43 (0.58), residues: 87 loop : -1.31 (0.25), residues: 659 ********************** 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 208 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 2.092 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: 208 average time/residue: 0.2788 time to fit residues: 87.8833 Evaluate side-chains 144 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 2.228 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9153 ------------------------------------------------------------------------------- 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: 10.0000 chunk 145 optimal weight: 0.1980 chunk 23 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 162 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 303 GLN ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 471 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.086418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.063908 restraints weight = 125618.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.064810 restraints weight = 87472.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.065802 restraints weight = 65419.571| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.7329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 16674 Z= 0.171 Angle : 0.639 10.018 22612 Z= 0.328 Chirality : 0.043 0.259 2525 Planarity : 0.005 0.108 2839 Dihedral : 4.756 29.803 2170 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.19), residues: 1963 helix: 0.80 (0.15), residues: 1219 sheet: -0.33 (0.59), residues: 87 loop : -1.34 (0.25), residues: 657 =============================================================================== Job complete usr+sys time: 3105.00 seconds wall clock time: 57 minutes 56.01 seconds (3476.01 seconds total)