Starting phenix.real_space_refine on Sun Mar 17 01:14:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gsa_0051/03_2024/6gsa_0051.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gsa_0051/03_2024/6gsa_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_0051/03_2024/6gsa_0051.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gsa_0051/03_2024/6gsa_0051.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gsa_0051/03_2024/6gsa_0051.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gsa_0051/03_2024/6gsa_0051.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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-dev-5265/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: 8.71, per 1000 atoms: 0.54 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: 5.78 Conformation dependent library (CDL) restraints added in 2.7 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: 1.62 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: 4.83 Time building geometry restraints manager: 6.37 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.470 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 42.330 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.480 ------------------------------------------------------------------------------- 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 % Allowed : 4.07 % Favored : 94.18 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.006 TRP E 386 HIS 0.027 0.003 HIS E 158 PHE 0.064 0.005 PHE E 214 TYR 0.049 0.005 TYR E 291 ARG 0.042 0.002 ARG E 221 *********************** 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 : 1.868 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 REVERT: A 239 ILE cc_start: 0.6493 (mm) cc_final: 0.6234 (mm) REVERT: A 317 SER cc_start: 0.6500 (t) cc_final: 0.6017 (m) REVERT: C 29 LEU cc_start: 0.7804 (mm) cc_final: 0.7527 (mm) REVERT: C 153 VAL cc_start: 0.8131 (t) cc_final: 0.7851 (t) REVERT: D 24 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6741 (tm) outliers start: 31 outliers final: 4 residues processed: 482 average time/residue: 0.3191 time to fit residues: 215.8394 Evaluate side-chains 220 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 215 time to evaluate : 1.875 ------------------------------------------------------------------------------- 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 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 360 ASN B 399 GLN B 406 GLN B 461 GLN B 474 GLN B 543 ASN B 552 ASN C 128 GLN E 44 GLN E 453 ASN ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5131 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16674 Z= 0.271 Angle : 0.727 9.460 22612 Z= 0.383 Chirality : 0.046 0.269 2525 Planarity : 0.006 0.057 2839 Dihedral : 5.398 32.434 2170 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.17 % Allowed : 2.71 % Favored : 97.12 % 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: -1.13 (0.18), residues: 1963 helix: -0.06 (0.14), residues: 1224 sheet: -1.06 (0.57), residues: 82 loop : -1.91 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 412 HIS 0.011 0.002 HIS B 189 PHE 0.026 0.002 PHE B 415 TYR 0.033 0.002 TYR B 70 ARG 0.006 0.001 ARG C 185 *********************** 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 : 1.949 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: A 60 ASP cc_start: 0.6804 (p0) cc_final: 0.6496 (p0) REVERT: A 260 CYS cc_start: 0.7280 (m) cc_final: 0.6991 (m) REVERT: B 140 VAL cc_start: 0.8084 (t) cc_final: 0.7877 (t) REVERT: E 154 VAL cc_start: 0.3450 (t) cc_final: 0.2640 (t) outliers start: 3 outliers final: 0 residues processed: 276 average time/residue: 0.2980 time to fit residues: 119.9510 Evaluate side-chains 179 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.838 ------------------------------------------------------------------------------- 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: 10.0000 chunk 56 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 181 optimal weight: 20.0000 chunk 195 optimal weight: 40.0000 chunk 161 optimal weight: 9.9990 chunk 179 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** 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 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 399 GLN B 433 HIS ** D 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 HIS ** 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: 0.5329 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 16674 Z= 0.282 Angle : 0.718 11.093 22612 Z= 0.380 Chirality : 0.043 0.263 2525 Planarity : 0.005 0.050 2839 Dihedral : 5.175 31.040 2170 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 20.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.28 % Allowed : 3.22 % Favored : 96.50 % 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: -0.62 (0.19), residues: 1963 helix: 0.30 (0.15), residues: 1230 sheet: -0.57 (0.57), residues: 94 loop : -1.67 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 119 HIS 0.010 0.002 HIS A 228 PHE 0.021 0.002 PHE B 398 TYR 0.026 0.002 TYR B 137 ARG 0.008 0.001 ARG D 265 *********************** 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 252 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 247 time to evaluate : 2.039 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: A 60 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.7202 (p0) REVERT: A 103 MET cc_start: 0.6959 (mmt) cc_final: 0.6697 (mmp) REVERT: A 260 CYS cc_start: 0.7275 (m) cc_final: 0.6984 (m) REVERT: A 464 THR cc_start: 0.7045 (m) cc_final: 0.6726 (m) REVERT: A 606 ILE cc_start: 0.7719 (pt) cc_final: 0.7476 (pt) REVERT: E 154 VAL cc_start: 0.3196 (t) cc_final: 0.2391 (t) outliers start: 5 outliers final: 1 residues processed: 250 average time/residue: 0.2974 time to fit residues: 108.5403 Evaluate side-chains 156 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 1.700 ------------------------------------------------------------------------------- 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: 7.9990 chunk 136 optimal weight: 20.0000 chunk 93 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 121 optimal weight: 0.9990 chunk 181 optimal weight: 9.9990 chunk 192 optimal weight: 40.0000 chunk 94 optimal weight: 40.0000 chunk 172 optimal weight: 40.0000 chunk 51 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 GLN ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS A 474 GLN ** 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 433 HIS B 461 GLN B 495 ASN ** D 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN E 283 GLN ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5416 moved from start: 0.5735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 16674 Z= 0.296 Angle : 0.704 10.269 22612 Z= 0.370 Chirality : 0.044 0.240 2525 Planarity : 0.005 0.072 2839 Dihedral : 5.172 33.627 2170 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 21.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.11 % Allowed : 2.99 % Favored : 96.89 % 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: -0.51 (0.19), residues: 1963 helix: 0.33 (0.14), residues: 1228 sheet: -0.34 (0.58), residues: 94 loop : -1.52 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 164 HIS 0.008 0.002 HIS A 189 PHE 0.026 0.002 PHE D 434 TYR 0.047 0.002 TYR B 345 ARG 0.009 0.001 ARG D 265 *********************** 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 231 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 229 time to evaluate : 1.947 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: A 464 THR cc_start: 0.6999 (m) cc_final: 0.6720 (m) REVERT: D 437 LEU cc_start: 0.6330 (mt) cc_final: 0.6116 (mp) outliers start: 2 outliers final: 1 residues processed: 230 average time/residue: 0.2815 time to fit residues: 96.0897 Evaluate side-chains 145 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 1.916 ------------------------------------------------------------------------------- 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: 3.9990 chunk 2 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 98 optimal weight: 0.9990 chunk 172 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 GLN ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN B 116 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN B 433 HIS B 543 ASN C 81 ASN ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 268 GLN ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5436 moved from start: 0.6265 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= 0.242 Angle : 0.666 10.410 22612 Z= 0.350 Chirality : 0.043 0.326 2525 Planarity : 0.005 0.062 2839 Dihedral : 5.013 32.110 2170 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.11 % Allowed : 2.49 % Favored : 97.40 % 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: -0.46 (0.19), residues: 1963 helix: 0.38 (0.14), residues: 1233 sheet: -0.22 (0.58), residues: 89 loop : -1.55 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 164 HIS 0.007 0.001 HIS A 189 PHE 0.022 0.002 PHE D 434 TYR 0.023 0.002 TYR B 126 ARG 0.029 0.001 ARG E 246 *********************** 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 224 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 222 time to evaluate : 2.164 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: A 464 THR cc_start: 0.7027 (m) cc_final: 0.6722 (m) REVERT: B 420 ILE cc_start: 0.7801 (pt) cc_final: 0.7537 (pt) REVERT: B 484 GLN cc_start: 0.8125 (tp-100) cc_final: 0.7859 (tp-100) REVERT: D 320 ILE cc_start: 0.6764 (mp) cc_final: 0.6364 (mp) outliers start: 2 outliers final: 1 residues processed: 223 average time/residue: 0.2770 time to fit residues: 93.5121 Evaluate side-chains 142 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 1.944 ------------------------------------------------------------------------------- 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: 10.0000 chunk 38 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 192 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN 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 205 GLN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN D 443 GLN ** E 165 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: 0.5364 moved from start: 0.6404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 16674 Z= 0.177 Angle : 0.626 9.258 22612 Z= 0.322 Chirality : 0.042 0.240 2525 Planarity : 0.004 0.055 2839 Dihedral : 4.865 31.907 2170 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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: -0.06 (0.19), residues: 1963 helix: 0.72 (0.15), residues: 1218 sheet: -0.21 (0.58), residues: 89 loop : -1.40 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 412 HIS 0.006 0.001 HIS A 189 PHE 0.028 0.002 PHE A 167 TYR 0.036 0.002 TYR B 418 ARG 0.004 0.000 ARG E 334 *********************** 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: 0 poor density : 222 time to evaluate : 1.997 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: A 247 TYR cc_start: 0.5886 (m-80) cc_final: 0.5657 (m-80) REVERT: A 260 CYS cc_start: 0.7431 (m) cc_final: 0.7222 (m) REVERT: A 464 THR cc_start: 0.6763 (m) cc_final: 0.6500 (m) REVERT: B 484 GLN cc_start: 0.8025 (tp-100) cc_final: 0.7689 (tp-100) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.2793 time to fit residues: 92.9986 Evaluate side-chains 146 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.822 ------------------------------------------------------------------------------- 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: 2.9990 chunk 21 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 140 optimal weight: 20.0000 chunk 108 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 191 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 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 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 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 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 389 GLN ** 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: 0.5458 moved from start: 0.6807 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= 0.241 Angle : 0.647 9.708 22612 Z= 0.341 Chirality : 0.042 0.255 2525 Planarity : 0.005 0.071 2839 Dihedral : 4.884 33.191 2170 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: 0.64 (0.15), residues: 1218 sheet: -0.38 (0.56), residues: 89 loop : -1.41 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP E 87 HIS 0.006 0.001 HIS A 189 PHE 0.033 0.002 PHE B 476 TYR 0.043 0.002 TYR B 418 ARG 0.005 0.001 ARG B 374 *********************** 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 216 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.968 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: A 260 CYS cc_start: 0.7451 (m) cc_final: 0.7218 (m) REVERT: A 354 ASP cc_start: 0.6508 (p0) cc_final: 0.6247 (m-30) REVERT: A 464 THR cc_start: 0.6904 (m) cc_final: 0.6648 (m) REVERT: D 320 ILE cc_start: 0.6940 (mp) cc_final: 0.6657 (mp) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.2735 time to fit residues: 88.3751 Evaluate side-chains 149 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.980 ------------------------------------------------------------------------------- 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: 2.9990 chunk 76 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 121 optimal weight: 0.0870 chunk 130 optimal weight: 9.9990 chunk 94 optimal weight: 30.0000 chunk 17 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 174 optimal weight: 20.0000 overall best weight: 2.4164 ------------------------------------------------------------------------------- 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 121 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 GLN E 86 HIS ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5427 moved from start: 0.6981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 16674 Z= 0.196 Angle : 0.637 10.834 22612 Z= 0.329 Chirality : 0.042 0.242 2525 Planarity : 0.005 0.060 2839 Dihedral : 4.847 32.422 2170 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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: -0.09 (0.19), residues: 1963 helix: 0.68 (0.15), residues: 1222 sheet: -0.38 (0.56), residues: 89 loop : -1.35 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 87 HIS 0.006 0.001 HIS A 189 PHE 0.030 0.002 PHE D 434 TYR 0.036 0.002 TYR B 247 ARG 0.006 0.000 ARG B 374 *********************** 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 210 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.957 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: A 174 MET cc_start: 0.6561 (tpp) cc_final: 0.6276 (tpp) REVERT: A 260 CYS cc_start: 0.7333 (m) cc_final: 0.7067 (m) REVERT: B 417 MET cc_start: 0.6606 (ptp) cc_final: 0.5196 (ptp) REVERT: B 484 GLN cc_start: 0.8035 (tp-100) cc_final: 0.7616 (tp-100) REVERT: D 317 MET cc_start: 0.5452 (ttt) cc_final: 0.5137 (ttt) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.2650 time to fit residues: 84.8147 Evaluate side-chains 144 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.914 ------------------------------------------------------------------------------- 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: 1.9990 chunk 167 optimal weight: 40.0000 chunk 178 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 77 optimal weight: 0.5980 chunk 140 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 169 optimal weight: 50.0000 chunk 117 optimal weight: 10.0000 chunk 189 optimal weight: 8.9990 overall best weight: 5.1188 ------------------------------------------------------------------------------- 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** ** 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 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 407 HIS D 427 GLN E 86 HIS ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 GLN ** E 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5557 moved from start: 0.7524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 16674 Z= 0.286 Angle : 0.707 11.345 22612 Z= 0.372 Chirality : 0.043 0.285 2525 Planarity : 0.005 0.057 2839 Dihedral : 5.054 30.962 2170 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 23.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: -0.34 (0.19), residues: 1963 helix: 0.45 (0.14), residues: 1216 sheet: -0.43 (0.54), residues: 89 loop : -1.38 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 412 HIS 0.008 0.002 HIS A 189 PHE 0.029 0.002 PHE D 434 TYR 0.042 0.002 TYR E 48 ARG 0.005 0.001 ARG B 374 *********************** 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 198 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.883 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: A 91 ASN cc_start: 0.6350 (t0) cc_final: 0.6002 (t0) REVERT: A 174 MET cc_start: 0.6826 (tpp) cc_final: 0.6587 (tpp) REVERT: B 268 HIS cc_start: 0.7200 (m90) cc_final: 0.6968 (m90) REVERT: B 417 MET cc_start: 0.6873 (ptp) cc_final: 0.5595 (ptp) REVERT: B 484 GLN cc_start: 0.8051 (tp-100) cc_final: 0.7773 (tp-100) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2652 time to fit residues: 80.9490 Evaluate side-chains 134 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.930 ------------------------------------------------------------------------------- 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: 20.0000 chunk 89 optimal weight: 9.9990 chunk 131 optimal weight: 7.9990 chunk 198 optimal weight: 5.9990 chunk 182 optimal weight: 0.3980 chunk 157 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 168 optimal weight: 50.0000 overall best weight: 5.2788 ------------------------------------------------------------------------------- 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** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** 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 86 HIS ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5598 moved from start: 0.7987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 16674 Z= 0.290 Angle : 0.714 9.666 22612 Z= 0.380 Chirality : 0.044 0.248 2525 Planarity : 0.005 0.059 2839 Dihedral : 5.153 30.630 2170 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 24.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: -0.53 (0.19), residues: 1963 helix: 0.29 (0.14), residues: 1212 sheet: -0.53 (0.54), residues: 90 loop : -1.40 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP E 87 HIS 0.007 0.001 HIS A 189 PHE 0.029 0.002 PHE D 434 TYR 0.037 0.002 TYR A 345 ARG 0.010 0.001 ARG A 214 ********************** 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 194 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.536 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: A 174 MET cc_start: 0.7046 (tpp) cc_final: 0.6728 (tpp) REVERT: B 226 MET cc_start: 0.7384 (mmm) cc_final: 0.7105 (mmm) REVERT: B 268 HIS cc_start: 0.7251 (m90) cc_final: 0.6958 (m90) REVERT: B 417 MET cc_start: 0.7203 (ptp) cc_final: 0.5861 (ptp) REVERT: B 484 GLN cc_start: 0.8069 (tp-100) cc_final: 0.7798 (tp-100) REVERT: B 541 LEU cc_start: 0.8250 (mm) cc_final: 0.7994 (mm) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.2640 time to fit residues: 78.3540 Evaluate side-chains 121 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 2.066 ------------------------------------------------------------------------------- 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: 5.9990 chunk 145 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 158 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 162 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 HIS ** 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 445 ASN ** 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 86 HIS ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 268 GLN E 283 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.081893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.059983 restraints weight = 132104.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.060526 restraints weight = 92695.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.061320 restraints weight = 68714.855| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.8228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 16674 Z= 0.257 Angle : 0.687 13.265 22612 Z= 0.360 Chirality : 0.043 0.274 2525 Planarity : 0.005 0.058 2839 Dihedral : 5.133 30.263 2170 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 23.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: 0.39 (0.14), residues: 1214 sheet: -0.60 (0.53), residues: 90 loop : -1.37 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 412 HIS 0.006 0.001 HIS A 189 PHE 0.029 0.002 PHE D 434 TYR 0.033 0.002 TYR A 78 ARG 0.005 0.001 ARG D 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3072.32 seconds wall clock time: 57 minutes 0.07 seconds (3420.07 seconds total)