Starting phenix.real_space_refine on Sat Jun 14 12:48:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gsa_0051/06_2025/6gsa_0051.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gsa_0051/06_2025/6gsa_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/cci-nas-00/data/ceres_data/6gsa_0051/06_2025/6gsa_0051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gsa_0051/06_2025/6gsa_0051.map" model { file = "/net/cci-nas-00/data/ceres_data/6gsa_0051/06_2025/6gsa_0051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gsa_0051/06_2025/6gsa_0051.cif" } 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. Time to flip 6 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.65, per 1000 atoms: 0.59 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 - 3.00 Amino acid : True - 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: 3.87 Conformation dependent library (CDL) restraints added in 2.1 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: 1.91 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: 5.70 Time building geometry restraints manager: 4.63 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: 0.00 - 4.93: 22398 4.93 - 9.86: 206 9.86 - 14.79: 7 14.79 - 19.71: 0 19.71 - 24.64: 1 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 3.040 nonbonded pdb=" O LYS B 108 " pdb=" OG SER B 111 " model vdw 2.307 3.040 nonbonded pdb=" OH TYR B 158 " pdb=" O HIS B 228 " model vdw 2.316 3.040 nonbonded pdb=" O GLU A 512 " pdb=" OG SER A 515 " model vdw 2.323 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 61.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 38.160 Find NCS groups from input model: 0.470 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:3.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.310 ------------------------------------------------------------------------------- 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 16676 Z= 0.666 Angle : 1.237 24.642 22616 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 Details of bonding type rmsd hydrogen bonds : bond 0.15253 ( 860) hydrogen bonds : angle 6.43366 ( 2493) SS BOND : bond 0.00483 ( 2) SS BOND : angle 2.10597 ( 4) covalent geometry : bond 0.01063 (16674) covalent geometry : angle 1.23676 (22612) *********************** 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 to be fit. rotamer outliers: 31 poor density : 455 time to evaluate : 2.690 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: 0.3888 time to fit residues: 266.4243 Evaluate side-chains 220 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 215 time to evaluate : 1.953 ------------------------------------------------------------------------------- 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: 7.9990 chunk 150 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 94 optimal weight: 20.0000 chunk 116 optimal weight: 5.9990 chunk 180 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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** 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 474 GLN B 543 ASN B 552 ASN C 128 GLN E 44 GLN E 60 GLN E 453 ASN ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.094665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.073875 restraints weight = 116251.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.075645 restraints weight = 79198.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.076970 restraints weight = 58742.718| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16676 Z= 0.186 Angle : 0.714 9.887 22616 Z= 0.377 Chirality : 0.045 0.265 2525 Planarity : 0.005 0.051 2839 Dihedral : 5.374 32.524 2170 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.17 % Allowed : 2.37 % Favored : 97.46 % 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: -1.16 (0.18), residues: 1963 helix: -0.08 (0.14), residues: 1222 sheet: -0.81 (0.60), residues: 76 loop : -1.96 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 102 HIS 0.009 0.001 HIS B 189 PHE 0.026 0.002 PHE B 398 TYR 0.029 0.002 TYR E 150 ARG 0.005 0.001 ARG A 397 Details of bonding type rmsd hydrogen bonds : bond 0.05182 ( 860) hydrogen bonds : angle 4.96200 ( 2493) SS BOND : bond 0.00559 ( 2) SS BOND : angle 5.28858 ( 4) covalent geometry : bond 0.00393 (16674) covalent geometry : angle 0.71067 (22612) *********************** 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 281 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 278 time to evaluate : 1.891 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: A 65 TRP cc_start: 0.9148 (t-100) cc_final: 0.8888 (t-100) REVERT: A 204 MET cc_start: 0.9491 (mmp) cc_final: 0.9067 (mmm) REVERT: A 312 LEU cc_start: 0.9049 (tt) cc_final: 0.8819 (tp) REVERT: A 345 TYR cc_start: 0.8320 (m-80) cc_final: 0.7986 (m-80) REVERT: A 349 ILE cc_start: 0.9707 (mm) cc_final: 0.9343 (tp) REVERT: A 352 ASP cc_start: 0.9300 (t70) cc_final: 0.8968 (t70) REVERT: A 364 LYS cc_start: 0.9657 (mttp) cc_final: 0.9413 (pptt) REVERT: A 378 ASP cc_start: 0.9286 (m-30) cc_final: 0.9031 (m-30) REVERT: A 417 MET cc_start: 0.9653 (mpp) cc_final: 0.9370 (mmt) REVERT: A 460 MET cc_start: 0.9550 (tpt) cc_final: 0.9253 (tpp) REVERT: A 464 THR cc_start: 0.9485 (m) cc_final: 0.9167 (m) REVERT: B 103 MET cc_start: 0.8509 (ptp) cc_final: 0.8034 (ptp) REVERT: B 119 MET cc_start: 0.9252 (mtp) cc_final: 0.9028 (mtt) REVERT: B 129 SER cc_start: 0.8465 (t) cc_final: 0.8238 (p) REVERT: B 312 LEU cc_start: 0.8211 (tp) cc_final: 0.7976 (tp) REVERT: B 510 LEU cc_start: 0.9646 (tp) cc_final: 0.9362 (pp) REVERT: D 434 PHE cc_start: 0.8620 (t80) cc_final: 0.7920 (t80) REVERT: D 437 LEU cc_start: 0.9422 (mt) cc_final: 0.9198 (mt) REVERT: E 251 TYR cc_start: 0.9110 (t80) cc_final: 0.8742 (t80) REVERT: E 342 TYR cc_start: 0.9128 (m-10) cc_final: 0.8925 (m-10) outliers start: 3 outliers final: 0 residues processed: 281 average time/residue: 0.3575 time to fit residues: 147.6995 Evaluate side-chains 193 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 22 optimal weight: 0.3980 chunk 155 optimal weight: 0.0470 chunk 152 optimal weight: 4.9990 chunk 7 optimal weight: 0.0770 chunk 37 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 145 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 171 optimal weight: 20.0000 overall best weight: 1.5040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 433 HIS E 44 GLN ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 HIS ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.093764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.073437 restraints weight = 116862.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.075162 restraints weight = 80032.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.076434 restraints weight = 59532.594| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 16676 Z= 0.135 Angle : 0.646 11.168 22616 Z= 0.336 Chirality : 0.043 0.326 2525 Planarity : 0.004 0.046 2839 Dihedral : 5.051 30.852 2170 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.28 % Allowed : 2.94 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.18), residues: 1963 helix: 0.34 (0.15), residues: 1215 sheet: -0.24 (0.58), residues: 85 loop : -1.85 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 164 HIS 0.009 0.001 HIS E 86 PHE 0.023 0.002 PHE B 398 TYR 0.022 0.002 TYR B 237 ARG 0.007 0.000 ARG E 537 Details of bonding type rmsd hydrogen bonds : bond 0.04634 ( 860) hydrogen bonds : angle 4.75915 ( 2493) SS BOND : bond 0.00205 ( 2) SS BOND : angle 7.39252 ( 4) covalent geometry : bond 0.00290 (16674) covalent geometry : angle 0.63818 (22612) *********************** 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 270 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 265 time to evaluate : 2.116 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: A 204 MET cc_start: 0.9327 (mmp) cc_final: 0.8902 (mmm) REVERT: A 226 MET cc_start: 0.8499 (mpp) cc_final: 0.8167 (mpp) REVERT: A 345 TYR cc_start: 0.8263 (m-80) cc_final: 0.7958 (m-80) REVERT: A 349 ILE cc_start: 0.9683 (mm) cc_final: 0.9261 (tt) REVERT: A 352 ASP cc_start: 0.9091 (t70) cc_final: 0.8798 (t70) REVERT: A 378 ASP cc_start: 0.9288 (m-30) cc_final: 0.9018 (m-30) REVERT: A 460 MET cc_start: 0.9496 (tpt) cc_final: 0.8987 (tpp) REVERT: A 464 THR cc_start: 0.9535 (m) cc_final: 0.9155 (m) REVERT: B 119 MET cc_start: 0.9220 (mtp) cc_final: 0.8951 (mtp) REVERT: B 129 SER cc_start: 0.8457 (t) cc_final: 0.8221 (p) REVERT: B 208 MET cc_start: 0.9676 (tpt) cc_final: 0.9425 (tpp) REVERT: B 469 PHE cc_start: 0.9708 (t80) cc_final: 0.9442 (t80) REVERT: D 434 PHE cc_start: 0.8747 (t80) cc_final: 0.8028 (t80) REVERT: D 437 LEU cc_start: 0.9446 (mt) cc_final: 0.9216 (mt) REVERT: E 94 ILE cc_start: 0.6755 (mt) cc_final: 0.6544 (mt) REVERT: E 131 PHE cc_start: 0.8818 (t80) cc_final: 0.8608 (t80) REVERT: E 251 TYR cc_start: 0.9224 (t80) cc_final: 0.8738 (t80) REVERT: E 342 TYR cc_start: 0.9233 (m-10) cc_final: 0.8988 (m-10) outliers start: 5 outliers final: 1 residues processed: 268 average time/residue: 0.3818 time to fit residues: 151.5155 Evaluate side-chains 184 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 31 optimal weight: 6.9990 chunk 184 optimal weight: 6.9990 chunk 196 optimal weight: 20.0000 chunk 83 optimal weight: 8.9990 chunk 160 optimal weight: 5.9990 chunk 180 optimal weight: 30.0000 chunk 99 optimal weight: 20.0000 chunk 60 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 chunk 85 optimal weight: 0.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 HIS D 407 HIS D 427 GLN ** 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 453 ASN ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.086558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.062979 restraints weight = 123218.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.064311 restraints weight = 86307.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.065190 restraints weight = 65224.309| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.5606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 16676 Z= 0.282 Angle : 0.790 10.665 22616 Z= 0.416 Chirality : 0.046 0.399 2525 Planarity : 0.005 0.056 2839 Dihedral : 5.163 33.944 2170 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.11 % Allowed : 2.77 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.71 (0.18), residues: 1963 helix: 0.22 (0.14), residues: 1218 sheet: -0.43 (0.63), residues: 73 loop : -1.68 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 412 HIS 0.009 0.002 HIS A 228 PHE 0.023 0.002 PHE D 28 TYR 0.027 0.003 TYR B 421 ARG 0.017 0.001 ARG C 161 Details of bonding type rmsd hydrogen bonds : bond 0.04712 ( 860) hydrogen bonds : angle 5.14679 ( 2493) SS BOND : bond 0.02335 ( 2) SS BOND : angle 5.29575 ( 4) covalent geometry : bond 0.00564 (16674) covalent geometry : angle 0.78647 (22612) *********************** 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 234 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 232 time to evaluate : 1.837 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: A 65 TRP cc_start: 0.9428 (t-100) cc_final: 0.9001 (t-100) REVERT: A 167 PHE cc_start: 0.9664 (m-80) cc_final: 0.9450 (m-80) REVERT: A 204 MET cc_start: 0.9423 (mmp) cc_final: 0.8940 (mmm) REVERT: A 300 ASP cc_start: 0.9304 (t0) cc_final: 0.9100 (t0) REVERT: A 345 TYR cc_start: 0.8341 (m-80) cc_final: 0.8074 (m-80) REVERT: A 349 ILE cc_start: 0.9715 (mm) cc_final: 0.9342 (tp) REVERT: A 352 ASP cc_start: 0.9091 (t70) cc_final: 0.8887 (t70) REVERT: A 419 LEU cc_start: 0.9267 (mt) cc_final: 0.9017 (mt) REVERT: A 430 LYS cc_start: 0.9668 (mptt) cc_final: 0.9220 (mmtt) REVERT: A 460 MET cc_start: 0.9687 (tpt) cc_final: 0.9144 (tpp) REVERT: A 464 THR cc_start: 0.9677 (m) cc_final: 0.9309 (m) REVERT: B 102 TRP cc_start: 0.7565 (t-100) cc_final: 0.6963 (t-100) REVERT: B 208 MET cc_start: 0.9704 (tpt) cc_final: 0.9446 (tpp) REVERT: B 348 ILE cc_start: 0.8438 (mt) cc_final: 0.8199 (mt) REVERT: B 469 PHE cc_start: 0.9772 (t80) cc_final: 0.9537 (t80) REVERT: C 30 LYS cc_start: 0.9479 (ptpp) cc_final: 0.9066 (ptpp) REVERT: C 77 MET cc_start: 0.9223 (tmm) cc_final: 0.9021 (ttm) REVERT: C 140 TYR cc_start: 0.9018 (t80) cc_final: 0.8766 (t80) REVERT: D 434 PHE cc_start: 0.9026 (t80) cc_final: 0.8340 (t80) REVERT: E 251 TYR cc_start: 0.8823 (t80) cc_final: 0.8509 (t80) REVERT: E 407 MET cc_start: 0.7169 (mtt) cc_final: 0.6588 (mtp) outliers start: 2 outliers final: 0 residues processed: 233 average time/residue: 0.3085 time to fit residues: 106.6825 Evaluate side-chains 148 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 14 optimal weight: 0.0070 chunk 27 optimal weight: 10.0000 chunk 172 optimal weight: 40.0000 chunk 164 optimal weight: 7.9990 chunk 24 optimal weight: 0.0050 chunk 181 optimal weight: 50.0000 chunk 174 optimal weight: 10.0000 chunk 78 optimal weight: 30.0000 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 158 optimal weight: 20.0000 overall best weight: 2.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 235 GLN A 303 GLN A 543 ASN B 406 GLN B 433 HIS B 461 GLN ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 252 HIS ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.088231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.065709 restraints weight = 120932.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.066818 restraints weight = 80217.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.067789 restraints weight = 58876.806| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.5871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 16676 Z= 0.146 Angle : 0.650 10.113 22616 Z= 0.338 Chirality : 0.043 0.241 2525 Planarity : 0.004 0.053 2839 Dihedral : 4.927 34.090 2170 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.11 % Allowed : 2.20 % Favored : 97.68 % 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: -0.31 (0.19), residues: 1963 helix: 0.57 (0.15), residues: 1215 sheet: -0.48 (0.65), residues: 70 loop : -1.54 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 412 HIS 0.007 0.001 HIS A 189 PHE 0.016 0.002 PHE A 167 TYR 0.029 0.002 TYR E 48 ARG 0.018 0.001 ARG E 244 Details of bonding type rmsd hydrogen bonds : bond 0.04299 ( 860) hydrogen bonds : angle 4.75029 ( 2493) SS BOND : bond 0.00263 ( 2) SS BOND : angle 4.87755 ( 4) covalent geometry : bond 0.00317 (16674) covalent geometry : angle 0.64666 (22612) *********************** 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 228 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 226 time to evaluate : 2.045 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 65 TRP cc_start: 0.9375 (t-100) cc_final: 0.9170 (t-100) REVERT: A 167 PHE cc_start: 0.9678 (m-80) cc_final: 0.9433 (m-80) REVERT: A 204 MET cc_start: 0.9374 (mmp) cc_final: 0.8910 (mmm) REVERT: A 300 ASP cc_start: 0.9312 (t0) cc_final: 0.9099 (t0) REVERT: A 345 TYR cc_start: 0.8350 (m-80) cc_final: 0.8049 (m-80) REVERT: A 349 ILE cc_start: 0.9673 (mm) cc_final: 0.9232 (tp) REVERT: A 352 ASP cc_start: 0.8986 (t70) cc_final: 0.8654 (t70) REVERT: A 397 ARG cc_start: 0.8026 (ttt90) cc_final: 0.7605 (tpt170) REVERT: A 405 PHE cc_start: 0.8894 (t80) cc_final: 0.8686 (t80) REVERT: A 419 LEU cc_start: 0.9165 (mt) cc_final: 0.8803 (mt) REVERT: A 430 LYS cc_start: 0.9652 (mptt) cc_final: 0.9447 (mmmt) REVERT: A 460 MET cc_start: 0.9674 (tpt) cc_final: 0.9116 (tpp) REVERT: A 464 THR cc_start: 0.9644 (m) cc_final: 0.9253 (m) REVERT: B 102 TRP cc_start: 0.7729 (t-100) cc_final: 0.6956 (t-100) REVERT: B 208 MET cc_start: 0.9730 (tpt) cc_final: 0.9405 (tpp) REVERT: B 348 ILE cc_start: 0.8340 (mt) cc_final: 0.8117 (mt) REVERT: B 420 ILE cc_start: 0.8705 (pt) cc_final: 0.8495 (pt) REVERT: B 469 PHE cc_start: 0.9782 (t80) cc_final: 0.9568 (t80) REVERT: C 30 LYS cc_start: 0.9323 (ptpp) cc_final: 0.8709 (ptpt) REVERT: D 434 PHE cc_start: 0.9006 (t80) cc_final: 0.8291 (t80) REVERT: D 437 LEU cc_start: 0.9738 (mt) cc_final: 0.9449 (mt) REVERT: E 251 TYR cc_start: 0.8932 (t80) cc_final: 0.8576 (t80) REVERT: E 407 MET cc_start: 0.7288 (mtt) cc_final: 0.6220 (mtp) outliers start: 2 outliers final: 0 residues processed: 227 average time/residue: 0.2794 time to fit residues: 94.2493 Evaluate side-chains 155 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 83 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 172 optimal weight: 50.0000 chunk 136 optimal weight: 0.2980 chunk 139 optimal weight: 10.0000 chunk 185 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 198 optimal weight: 40.0000 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN C 97 HIS D 427 GLN ** E 86 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.088731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.066191 restraints weight = 118082.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.067281 restraints weight = 78928.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.068267 restraints weight = 57994.864| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.6095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 16676 Z= 0.135 Angle : 0.628 9.291 22616 Z= 0.326 Chirality : 0.042 0.236 2525 Planarity : 0.004 0.046 2839 Dihedral : 4.794 32.578 2170 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.06 % Allowed : 1.30 % Favored : 98.64 % 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: -0.11 (0.19), residues: 1963 helix: 0.74 (0.15), residues: 1212 sheet: -0.38 (0.62), residues: 73 loop : -1.46 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 412 HIS 0.006 0.001 HIS B 189 PHE 0.035 0.001 PHE B 476 TYR 0.025 0.002 TYR B 421 ARG 0.005 0.000 ARG E 244 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 860) hydrogen bonds : angle 4.63183 ( 2493) SS BOND : bond 0.00333 ( 2) SS BOND : angle 4.56344 ( 4) covalent geometry : bond 0.00300 (16674) covalent geometry : angle 0.62545 (22612) *********************** 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 229 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 1.972 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 65 TRP cc_start: 0.9386 (t-100) cc_final: 0.9172 (t-100) REVERT: A 167 PHE cc_start: 0.9652 (m-80) cc_final: 0.9406 (m-80) REVERT: A 174 MET cc_start: 0.6637 (tpp) cc_final: 0.6390 (tpp) REVERT: A 204 MET cc_start: 0.9375 (mmp) cc_final: 0.8856 (mmm) REVERT: A 226 MET cc_start: 0.8354 (mpp) cc_final: 0.7855 (mmm) REVERT: A 300 ASP cc_start: 0.9288 (t0) cc_final: 0.9073 (t0) REVERT: A 345 TYR cc_start: 0.8284 (m-80) cc_final: 0.8020 (m-80) REVERT: A 349 ILE cc_start: 0.9639 (mm) cc_final: 0.9199 (tp) REVERT: A 397 ARG cc_start: 0.8007 (ttt90) cc_final: 0.7594 (tpt170) REVERT: A 405 PHE cc_start: 0.8895 (t80) cc_final: 0.8689 (t80) REVERT: A 419 LEU cc_start: 0.9171 (mt) cc_final: 0.8714 (mt) REVERT: A 426 ASP cc_start: 0.8698 (m-30) cc_final: 0.8031 (t0) REVERT: A 430 LYS cc_start: 0.9666 (mptt) cc_final: 0.8773 (mmmt) REVERT: A 460 MET cc_start: 0.9645 (tpt) cc_final: 0.9075 (tpp) REVERT: A 464 THR cc_start: 0.9632 (m) cc_final: 0.9193 (m) REVERT: B 102 TRP cc_start: 0.7694 (t-100) cc_final: 0.6896 (t-100) REVERT: B 208 MET cc_start: 0.9707 (tpt) cc_final: 0.9380 (tpp) REVERT: B 312 LEU cc_start: 0.7997 (tp) cc_final: 0.7783 (tp) REVERT: B 348 ILE cc_start: 0.8289 (mt) cc_final: 0.8075 (mt) REVERT: B 469 PHE cc_start: 0.9770 (t80) cc_final: 0.9536 (t80) REVERT: B 541 LEU cc_start: 0.9475 (mm) cc_final: 0.9226 (mm) REVERT: C 30 LYS cc_start: 0.9119 (ptpp) cc_final: 0.8600 (ptpp) REVERT: D 434 PHE cc_start: 0.9051 (t80) cc_final: 0.8124 (t80) REVERT: D 437 LEU cc_start: 0.9721 (mt) cc_final: 0.9303 (mp) REVERT: E 125 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8042 (mp) REVERT: E 251 TYR cc_start: 0.8961 (t80) cc_final: 0.8602 (t80) REVERT: E 407 MET cc_start: 0.6969 (mtt) cc_final: 0.6301 (mtp) outliers start: 1 outliers final: 0 residues processed: 228 average time/residue: 0.2851 time to fit residues: 97.8185 Evaluate side-chains 162 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 7 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 38 optimal weight: 0.3980 chunk 162 optimal weight: 20.0000 chunk 128 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 30.0000 chunk 166 optimal weight: 30.0000 chunk 99 optimal weight: 7.9990 chunk 165 optimal weight: 9.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN B 543 ASN ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN E 389 GLN ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.105109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.083614 restraints weight = 130899.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.085127 restraints weight = 90781.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.086252 restraints weight = 68787.990| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.6449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 16676 Z= 0.164 Angle : 0.642 10.048 22616 Z= 0.337 Chirality : 0.043 0.401 2525 Planarity : 0.004 0.049 2839 Dihedral : 4.759 33.934 2170 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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: -0.10 (0.19), residues: 1963 helix: 0.74 (0.15), residues: 1212 sheet: -0.48 (0.62), residues: 73 loop : -1.44 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP E 193 HIS 0.006 0.001 HIS B 189 PHE 0.022 0.002 PHE A 112 TYR 0.023 0.002 TYR E 48 ARG 0.004 0.000 ARG E 244 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 860) hydrogen bonds : angle 4.76776 ( 2493) SS BOND : bond 0.00255 ( 2) SS BOND : angle 4.99467 ( 4) covalent geometry : bond 0.00355 (16674) covalent geometry : angle 0.63876 (22612) *********************** 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 224 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 1.953 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 65 TRP cc_start: 0.9430 (t-100) cc_final: 0.9197 (t-100) REVERT: A 167 PHE cc_start: 0.9659 (m-80) cc_final: 0.9452 (m-80) REVERT: A 174 MET cc_start: 0.6787 (tpp) cc_final: 0.6548 (tpp) REVERT: A 204 MET cc_start: 0.9307 (mmp) cc_final: 0.8842 (mmm) REVERT: A 226 MET cc_start: 0.8376 (mpp) cc_final: 0.7888 (mmm) REVERT: A 300 ASP cc_start: 0.9343 (t0) cc_final: 0.9142 (t0) REVERT: A 345 TYR cc_start: 0.8229 (m-80) cc_final: 0.7919 (m-80) REVERT: A 349 ILE cc_start: 0.9672 (mm) cc_final: 0.9246 (tp) REVERT: A 352 ASP cc_start: 0.9035 (t70) cc_final: 0.8694 (t70) REVERT: A 354 ASP cc_start: 0.9465 (p0) cc_final: 0.9234 (m-30) REVERT: A 397 ARG cc_start: 0.8089 (ttt90) cc_final: 0.7650 (tpt170) REVERT: A 405 PHE cc_start: 0.8936 (t80) cc_final: 0.8736 (t80) REVERT: A 419 LEU cc_start: 0.9186 (mt) cc_final: 0.8726 (mt) REVERT: A 430 LYS cc_start: 0.9679 (mptt) cc_final: 0.9474 (mmmt) REVERT: A 460 MET cc_start: 0.9639 (tpt) cc_final: 0.9088 (tpp) REVERT: A 464 THR cc_start: 0.9643 (m) cc_final: 0.9255 (m) REVERT: B 102 TRP cc_start: 0.7680 (t-100) cc_final: 0.7091 (t-100) REVERT: B 208 MET cc_start: 0.9624 (tpp) cc_final: 0.9367 (tpp) REVERT: B 312 LEU cc_start: 0.7710 (tp) cc_final: 0.7457 (tp) REVERT: B 348 ILE cc_start: 0.8288 (mt) cc_final: 0.8071 (mt) REVERT: B 420 ILE cc_start: 0.8847 (pt) cc_final: 0.8420 (pt) REVERT: B 469 PHE cc_start: 0.9781 (t80) cc_final: 0.9554 (t80) REVERT: D 439 HIS cc_start: 0.8843 (p-80) cc_final: 0.8600 (p-80) REVERT: D 476 LEU cc_start: 0.9292 (mm) cc_final: 0.9082 (tt) REVERT: E 94 ILE cc_start: 0.7413 (mt) cc_final: 0.7204 (mt) REVERT: E 131 PHE cc_start: 0.8689 (t80) cc_final: 0.8471 (t80) REVERT: E 251 TYR cc_start: 0.9275 (t80) cc_final: 0.8927 (t80) REVERT: E 342 TYR cc_start: 0.9472 (m-80) cc_final: 0.8911 (m-80) REVERT: E 407 MET cc_start: 0.7588 (mtt) cc_final: 0.7052 (mtp) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.2929 time to fit residues: 97.4967 Evaluate side-chains 154 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 153 optimal weight: 6.9990 chunk 168 optimal weight: 50.0000 chunk 32 optimal weight: 7.9990 chunk 120 optimal weight: 20.0000 chunk 186 optimal weight: 30.0000 chunk 132 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 106 optimal weight: 0.2980 chunk 23 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- 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 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 ASN B 116 ASN B 205 GLN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.084943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.062793 restraints weight = 124139.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.063721 restraints weight = 83225.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.064627 restraints weight = 60897.704| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.6996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 16676 Z= 0.199 Angle : 0.695 11.006 22616 Z= 0.366 Chirality : 0.044 0.279 2525 Planarity : 0.005 0.047 2839 Dihedral : 4.908 32.455 2170 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % 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: -0.33 (0.19), residues: 1963 helix: 0.52 (0.14), residues: 1217 sheet: -0.56 (0.60), residues: 73 loop : -1.46 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 412 HIS 0.006 0.001 HIS A 189 PHE 0.018 0.002 PHE A 212 TYR 0.022 0.002 TYR A 301 ARG 0.006 0.001 ARG D 316 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 860) hydrogen bonds : angle 4.96674 ( 2493) SS BOND : bond 0.00279 ( 2) SS BOND : angle 4.28175 ( 4) covalent geometry : bond 0.00416 (16674) covalent geometry : angle 0.69269 (22612) *********************** 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 to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.978 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 65 TRP cc_start: 0.9507 (t-100) cc_final: 0.9228 (t-100) REVERT: A 115 MET cc_start: 0.9443 (ptm) cc_final: 0.8802 (ppp) REVERT: A 119 MET cc_start: 0.9658 (ptm) cc_final: 0.9371 (ptp) REVERT: A 167 PHE cc_start: 0.9658 (m-80) cc_final: 0.9393 (m-80) REVERT: A 174 MET cc_start: 0.6960 (tpp) cc_final: 0.6680 (tpp) REVERT: A 204 MET cc_start: 0.9260 (mmp) cc_final: 0.8837 (mmm) REVERT: A 226 MET cc_start: 0.8495 (mpp) cc_final: 0.8008 (mmm) REVERT: A 247 TYR cc_start: 0.9364 (m-80) cc_final: 0.9057 (m-80) REVERT: A 300 ASP cc_start: 0.9377 (t0) cc_final: 0.9168 (t0) REVERT: A 345 TYR cc_start: 0.8266 (m-80) cc_final: 0.7986 (m-80) REVERT: A 349 ILE cc_start: 0.9672 (mm) cc_final: 0.9105 (tp) REVERT: A 406 GLN cc_start: 0.9574 (mm110) cc_final: 0.9262 (mm110) REVERT: A 419 LEU cc_start: 0.9219 (mt) cc_final: 0.8919 (mt) REVERT: A 430 LYS cc_start: 0.9667 (mptt) cc_final: 0.9466 (mmmt) REVERT: A 460 MET cc_start: 0.9632 (tpt) cc_final: 0.8994 (tpp) REVERT: A 464 THR cc_start: 0.9638 (m) cc_final: 0.9208 (m) REVERT: B 226 MET cc_start: 0.8897 (mmm) cc_final: 0.8592 (mmm) REVERT: B 469 PHE cc_start: 0.9779 (t80) cc_final: 0.9547 (t80) REVERT: D 476 LEU cc_start: 0.9292 (mm) cc_final: 0.9028 (tt) REVERT: E 251 TYR cc_start: 0.8902 (t80) cc_final: 0.8538 (t80) REVERT: E 407 MET cc_start: 0.7038 (mtt) cc_final: 0.6364 (mtp) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.2874 time to fit residues: 93.7529 Evaluate side-chains 152 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 2.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 99 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 108 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 188 optimal weight: 8.9990 chunk 127 optimal weight: 6.9990 chunk 173 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 GLN E 86 HIS ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.086030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.063870 restraints weight = 123748.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.064746 restraints weight = 82600.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.065719 restraints weight = 59854.329| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.7109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 16676 Z= 0.144 Angle : 0.656 13.048 22616 Z= 0.339 Chirality : 0.043 0.253 2525 Planarity : 0.004 0.045 2839 Dihedral : 4.825 31.912 2170 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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: -0.11 (0.19), residues: 1963 helix: 0.70 (0.15), residues: 1213 sheet: -0.55 (0.60), residues: 73 loop : -1.37 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 412 HIS 0.005 0.001 HIS B 189 PHE 0.025 0.002 PHE B 398 TYR 0.028 0.002 TYR E 48 ARG 0.017 0.000 ARG E 246 Details of bonding type rmsd hydrogen bonds : bond 0.04068 ( 860) hydrogen bonds : angle 4.77105 ( 2493) SS BOND : bond 0.00365 ( 2) SS BOND : angle 4.31535 ( 4) covalent geometry : bond 0.00318 (16674) covalent geometry : angle 0.65320 (22612) *********************** 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 216 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 2.085 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: A 115 MET cc_start: 0.9403 (ptm) cc_final: 0.8702 (ppp) REVERT: A 119 MET cc_start: 0.9640 (ptm) cc_final: 0.9300 (ptp) REVERT: A 167 PHE cc_start: 0.9642 (m-80) cc_final: 0.9396 (m-80) REVERT: A 174 MET cc_start: 0.6961 (tpp) cc_final: 0.6666 (tpp) REVERT: A 204 MET cc_start: 0.9248 (mmp) cc_final: 0.8852 (mmm) REVERT: A 226 MET cc_start: 0.8441 (mpp) cc_final: 0.7906 (mmm) REVERT: A 300 ASP cc_start: 0.9357 (t0) cc_final: 0.9089 (t0) REVERT: A 345 TYR cc_start: 0.8157 (m-80) cc_final: 0.7841 (m-80) REVERT: A 349 ILE cc_start: 0.9650 (mm) cc_final: 0.9093 (tp) REVERT: A 352 ASP cc_start: 0.9280 (t70) cc_final: 0.9071 (t70) REVERT: A 406 GLN cc_start: 0.9554 (mm110) cc_final: 0.9200 (mm-40) REVERT: A 419 LEU cc_start: 0.9171 (mt) cc_final: 0.8881 (mt) REVERT: A 460 MET cc_start: 0.9631 (tpt) cc_final: 0.9100 (tpp) REVERT: A 464 THR cc_start: 0.9606 (m) cc_final: 0.9084 (m) REVERT: B 226 MET cc_start: 0.8920 (mmm) cc_final: 0.7612 (tpp) REVERT: B 417 MET cc_start: 0.8691 (mtm) cc_final: 0.8317 (mtm) REVERT: B 469 PHE cc_start: 0.9790 (t80) cc_final: 0.9571 (t80) REVERT: C 95 GLU cc_start: 0.9346 (tp30) cc_final: 0.8855 (mm-30) REVERT: D 267 MET cc_start: 0.9502 (ptp) cc_final: 0.9282 (mmm) REVERT: D 476 LEU cc_start: 0.9232 (mm) cc_final: 0.9028 (tp) REVERT: E 125 ILE cc_start: 0.8145 (mp) cc_final: 0.7943 (mp) REVERT: E 251 TYR cc_start: 0.8949 (t80) cc_final: 0.8643 (t80) REVERT: E 407 MET cc_start: 0.7078 (mtt) cc_final: 0.6353 (mtp) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.2787 time to fit residues: 90.3810 Evaluate side-chains 147 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 179 optimal weight: 40.0000 chunk 80 optimal weight: 0.0970 chunk 46 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 144 optimal weight: 0.2980 chunk 182 optimal weight: 20.0000 chunk 198 optimal weight: 40.0000 chunk 188 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 overall best weight: 2.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.086114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.064001 restraints weight = 123978.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.064918 restraints weight = 82215.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.065858 restraints weight = 59523.660| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.7273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 16676 Z= 0.138 Angle : 0.653 9.674 22616 Z= 0.335 Chirality : 0.043 0.238 2525 Planarity : 0.004 0.045 2839 Dihedral : 4.756 31.171 2170 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % 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: -0.07 (0.19), residues: 1963 helix: 0.74 (0.15), residues: 1217 sheet: -0.57 (0.59), residues: 73 loop : -1.38 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 412 HIS 0.005 0.001 HIS B 189 PHE 0.035 0.002 PHE B 212 TYR 0.032 0.002 TYR B 137 ARG 0.010 0.000 ARG E 246 Details of bonding type rmsd hydrogen bonds : bond 0.04042 ( 860) hydrogen bonds : angle 4.72260 ( 2493) SS BOND : bond 0.00210 ( 2) SS BOND : angle 4.00008 ( 4) covalent geometry : bond 0.00308 (16674) covalent geometry : angle 0.65055 (22612) ********************** 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 214 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 1.867 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: A 91 ASN cc_start: 0.8094 (t0) cc_final: 0.7674 (t0) REVERT: A 115 MET cc_start: 0.9393 (ptm) cc_final: 0.8747 (ppp) REVERT: A 119 MET cc_start: 0.9647 (ptm) cc_final: 0.9294 (ptp) REVERT: A 167 PHE cc_start: 0.9623 (m-80) cc_final: 0.9378 (m-80) REVERT: A 174 MET cc_start: 0.6806 (tpp) cc_final: 0.6512 (tpp) REVERT: A 204 MET cc_start: 0.9254 (mmp) cc_final: 0.8841 (mmm) REVERT: A 226 MET cc_start: 0.8387 (mpp) cc_final: 0.7879 (mmm) REVERT: A 300 ASP cc_start: 0.9375 (t0) cc_final: 0.9112 (t0) REVERT: A 345 TYR cc_start: 0.8175 (m-80) cc_final: 0.7861 (m-80) REVERT: A 349 ILE cc_start: 0.9626 (mm) cc_final: 0.9052 (tt) REVERT: A 352 ASP cc_start: 0.9285 (t70) cc_final: 0.9060 (t70) REVERT: A 406 GLN cc_start: 0.9551 (mm110) cc_final: 0.9198 (mm-40) REVERT: A 419 LEU cc_start: 0.9156 (mt) cc_final: 0.8876 (mt) REVERT: A 460 MET cc_start: 0.9590 (tpt) cc_final: 0.9099 (tpp) REVERT: A 464 THR cc_start: 0.9609 (m) cc_final: 0.9088 (m) REVERT: B 226 MET cc_start: 0.8985 (mmm) cc_final: 0.7934 (mmm) REVERT: B 398 PHE cc_start: 0.9717 (t80) cc_final: 0.9381 (t80) REVERT: B 420 ILE cc_start: 0.8755 (pt) cc_final: 0.8489 (pt) REVERT: B 430 LYS cc_start: 0.9757 (mmtm) cc_final: 0.9546 (mmmt) REVERT: B 469 PHE cc_start: 0.9784 (t80) cc_final: 0.9566 (t80) REVERT: C 95 GLU cc_start: 0.9334 (tp30) cc_final: 0.8835 (mm-30) REVERT: D 267 MET cc_start: 0.9537 (ptp) cc_final: 0.9292 (mmm) REVERT: E 251 TYR cc_start: 0.8930 (t80) cc_final: 0.8593 (t80) REVERT: E 407 MET cc_start: 0.7305 (mtt) cc_final: 0.6712 (mtp) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.2718 time to fit residues: 88.1670 Evaluate side-chains 145 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 17 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 chunk 191 optimal weight: 20.0000 chunk 3 optimal weight: 7.9990 chunk 147 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.085857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.063752 restraints weight = 125326.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.064580 restraints weight = 83913.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.065555 restraints weight = 61067.791| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.7451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 16676 Z= 0.141 Angle : 0.651 10.613 22616 Z= 0.336 Chirality : 0.043 0.255 2525 Planarity : 0.004 0.069 2839 Dihedral : 4.717 30.325 2170 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % 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: -0.01 (0.19), residues: 1963 helix: 0.78 (0.15), residues: 1218 sheet: -0.32 (0.65), residues: 63 loop : -1.36 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 412 HIS 0.010 0.001 HIS D 439 PHE 0.028 0.002 PHE B 212 TYR 0.044 0.002 TYR E 48 ARG 0.007 0.000 ARG E 246 Details of bonding type rmsd hydrogen bonds : bond 0.03983 ( 860) hydrogen bonds : angle 4.70390 ( 2493) SS BOND : bond 0.00392 ( 2) SS BOND : angle 4.26234 ( 4) covalent geometry : bond 0.00311 (16674) covalent geometry : angle 0.64859 (22612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6944.07 seconds wall clock time: 124 minutes 38.06 seconds (7478.06 seconds total)