Starting phenix.real_space_refine on Thu Sep 18 10:42:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gsa_0051/09_2025/6gsa_0051.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gsa_0051/09_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_0051/09_2025/6gsa_0051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gsa_0051/09_2025/6gsa_0051.map" model { file = "/net/cci-nas-00/data/ceres_data/6gsa_0051/09_2025/6gsa_0051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gsa_0051/09_2025/6gsa_0051.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'ARG: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: {'ASN:plan1': 3, 'ASP:plan': 3, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG: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: {'ASN:plan1': 12, 'GLU:plan': 16, 'ASP:plan': 10, 'GLN:plan1': 2, 'ARG:plan': 6, 'TYR:plan': 1} 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: 4.11, per 1000 atoms: 0.25 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: 1.28 Conformation dependent library (CDL) restraints added in 593.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3886 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 8 sheets defined 64.5% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 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: 2.76 Time building geometry restraints manager: 1.76 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: 1.700 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: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.640 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.240 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.042 0.002 ARG E 221 TYR 0.049 0.005 TYR E 291 PHE 0.064 0.005 PHE E 214 TRP 0.040 0.006 TRP E 386 HIS 0.027 0.003 HIS E 158 Details of bonding type rmsd covalent geometry : bond 0.01063 (16674) covalent geometry : angle 1.23676 (22612) SS BOND : bond 0.00483 ( 2) SS BOND : angle 2.10597 ( 4) hydrogen bonds : bond 0.15253 ( 860) hydrogen bonds : angle 6.43366 ( 2493) *********************** 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 : 0.634 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ILE cc_start: 0.6493 (mm) cc_final: 0.6202 (mm) REVERT: A 317 SER cc_start: 0.6500 (t) cc_final: 0.5987 (m) REVERT: C 29 LEU cc_start: 0.7804 (mm) cc_final: 0.7527 (mm) REVERT: D 24 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6728 (tm) outliers start: 31 outliers final: 4 residues processed: 482 average time/residue: 0.1462 time to fit residues: 100.0510 Evaluate side-chains 219 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 214 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 overall best weight: 3.6986 ------------------------------------------------------------------------------- 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 A 598 GLN B 66 GLN B 82 GLN B 104 ASN B 121 ASN B 205 GLN B 262 HIS B 406 GLN B 474 GLN B 543 ASN B 552 ASN C 128 GLN E 44 GLN E 60 GLN ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 453 ASN ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.093821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.072911 restraints weight = 118841.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.074677 restraints weight = 80632.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.075976 restraints weight = 59721.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.077016 restraints weight = 46881.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.077580 restraints weight = 38458.349| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 16676 Z= 0.200 Angle : 0.728 9.515 22616 Z= 0.384 Chirality : 0.046 0.270 2525 Planarity : 0.006 0.070 2839 Dihedral : 5.396 32.364 2170 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.17 % Allowed : 2.43 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.18), residues: 1963 helix: -0.02 (0.14), residues: 1218 sheet: -0.82 (0.59), residues: 76 loop : -1.93 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 265 TYR 0.030 0.002 TYR E 150 PHE 0.023 0.002 PHE E 279 TRP 0.028 0.003 TRP A 102 HIS 0.010 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00420 (16674) covalent geometry : angle 0.72443 (22612) SS BOND : bond 0.00720 ( 2) SS BOND : angle 5.31661 ( 4) hydrogen bonds : bond 0.05198 ( 860) hydrogen bonds : angle 5.01318 ( 2493) *********************** 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 287 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 284 time to evaluate : 0.639 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: A 65 TRP cc_start: 0.9123 (t-100) cc_final: 0.8857 (t-100) REVERT: A 204 MET cc_start: 0.9431 (mmp) cc_final: 0.9032 (mmm) REVERT: A 312 LEU cc_start: 0.9029 (tt) cc_final: 0.8668 (mt) REVERT: A 352 ASP cc_start: 0.9271 (t70) cc_final: 0.8926 (t70) REVERT: A 355 LEU cc_start: 0.9338 (tp) cc_final: 0.9009 (tt) REVERT: A 356 ASP cc_start: 0.7607 (m-30) cc_final: 0.7112 (m-30) REVERT: A 460 MET cc_start: 0.9479 (tpt) cc_final: 0.9148 (tpp) REVERT: A 464 THR cc_start: 0.9486 (m) cc_final: 0.9143 (m) REVERT: B 129 SER cc_start: 0.8818 (t) cc_final: 0.8539 (p) REVERT: D 361 MET cc_start: 0.9449 (mmm) cc_final: 0.9232 (mmm) REVERT: D 434 PHE cc_start: 0.8628 (t80) cc_final: 0.7950 (t80) REVERT: D 437 LEU cc_start: 0.9401 (mt) cc_final: 0.9187 (mt) REVERT: E 94 ILE cc_start: 0.6486 (mt) cc_final: 0.6146 (mt) REVERT: E 251 TYR cc_start: 0.8513 (t80) cc_final: 0.7979 (t80) REVERT: E 270 LEU cc_start: 0.7257 (mp) cc_final: 0.6934 (mp) REVERT: E 323 ILE cc_start: 0.9064 (tp) cc_final: 0.8856 (mm) REVERT: E 342 TYR cc_start: 0.9152 (m-10) cc_final: 0.8932 (m-10) outliers start: 3 outliers final: 0 residues processed: 287 average time/residue: 0.1237 time to fit residues: 52.2169 Evaluate side-chains 185 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 83 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 184 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 GLN B 121 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 HIS B 461 GLN E 44 GLN E 86 HIS ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.095257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.073793 restraints weight = 113809.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.075515 restraints weight = 78691.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.076822 restraints weight = 59208.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.077720 restraints weight = 46904.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.078520 restraints weight = 39369.121| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16676 Z= 0.132 Angle : 0.646 11.750 22616 Z= 0.335 Chirality : 0.043 0.306 2525 Planarity : 0.004 0.047 2839 Dihedral : 5.009 30.963 2170 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.17 % Allowed : 3.11 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.18), residues: 1963 helix: 0.45 (0.15), residues: 1212 sheet: -0.68 (0.55), residues: 95 loop : -1.89 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 161 TYR 0.023 0.002 TYR B 237 PHE 0.018 0.002 PHE B 64 TRP 0.030 0.002 TRP B 164 HIS 0.008 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00278 (16674) covalent geometry : angle 0.64018 (22612) SS BOND : bond 0.01263 ( 2) SS BOND : angle 6.53119 ( 4) hydrogen bonds : bond 0.04591 ( 860) hydrogen bonds : angle 4.69500 ( 2493) *********************** 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 268 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 265 time to evaluate : 0.656 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: A 65 TRP cc_start: 0.9116 (t-100) cc_final: 0.8896 (t-100) REVERT: A 204 MET cc_start: 0.9373 (mmp) cc_final: 0.8949 (mmm) REVERT: A 226 MET cc_start: 0.8510 (mpp) cc_final: 0.8268 (mpp) REVERT: A 349 ILE cc_start: 0.9679 (mm) cc_final: 0.9265 (tp) REVERT: A 352 ASP cc_start: 0.9153 (t70) cc_final: 0.8754 (t70) REVERT: A 356 ASP cc_start: 0.7586 (m-30) cc_final: 0.7327 (m-30) REVERT: A 378 ASP cc_start: 0.9246 (m-30) cc_final: 0.8987 (m-30) REVERT: A 397 ARG cc_start: 0.7834 (ttt90) cc_final: 0.7367 (tpt170) REVERT: A 417 MET cc_start: 0.9816 (mmp) cc_final: 0.9541 (mmp) REVERT: A 460 MET cc_start: 0.9498 (tpt) cc_final: 0.9017 (tpp) REVERT: A 464 THR cc_start: 0.9537 (m) cc_final: 0.9150 (m) REVERT: B 119 MET cc_start: 0.9323 (mtt) cc_final: 0.9097 (mtt) REVERT: B 129 SER cc_start: 0.8427 (t) cc_final: 0.8155 (p) REVERT: B 208 MET cc_start: 0.9659 (tpt) cc_final: 0.9418 (tpp) REVERT: B 361 LYS cc_start: 0.8322 (mtmt) cc_final: 0.8121 (mtmt) REVERT: D 434 PHE cc_start: 0.8733 (t80) cc_final: 0.8163 (t80) REVERT: D 437 LEU cc_start: 0.9467 (mt) cc_final: 0.9232 (mt) REVERT: D 439 HIS cc_start: 0.8479 (p-80) cc_final: 0.8221 (p-80) REVERT: E 131 PHE cc_start: 0.8777 (t80) cc_final: 0.8564 (t80) REVERT: E 251 TYR cc_start: 0.8946 (t80) cc_final: 0.8373 (t80) outliers start: 3 outliers final: 1 residues processed: 267 average time/residue: 0.1182 time to fit residues: 47.1307 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 : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 7 optimal weight: 1.9990 chunk 97 optimal weight: 0.1980 chunk 118 optimal weight: 0.8980 chunk 49 optimal weight: 0.3980 chunk 91 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 186 optimal weight: 10.0000 chunk 38 optimal weight: 0.4980 chunk 67 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 303 GLN ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN B 121 ASN B 433 HIS B 461 GLN ** D 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 GLN ** E 165 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.093399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.073550 restraints weight = 121888.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.075228 restraints weight = 83611.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.076512 restraints weight = 62424.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.077321 restraints weight = 49391.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.078201 restraints weight = 41379.802| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 16676 Z= 0.124 Angle : 0.615 10.053 22616 Z= 0.318 Chirality : 0.043 0.283 2525 Planarity : 0.004 0.045 2839 Dihedral : 4.812 34.543 2170 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.11 % Allowed : 1.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.19), residues: 1963 helix: 0.66 (0.15), residues: 1205 sheet: 0.33 (0.59), residues: 84 loop : -1.73 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 161 TYR 0.019 0.001 TYR B 126 PHE 0.019 0.001 PHE A 167 TRP 0.026 0.002 TRP E 193 HIS 0.007 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00276 (16674) covalent geometry : angle 0.61078 (22612) SS BOND : bond 0.01012 ( 2) SS BOND : angle 5.21751 ( 4) hydrogen bonds : bond 0.04261 ( 860) hydrogen bonds : angle 4.56275 ( 2493) *********************** 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 259 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 257 time to evaluate : 0.483 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: A 100 MET cc_start: 0.9065 (tmm) cc_final: 0.8779 (tmm) REVERT: A 103 MET cc_start: 0.8789 (ptt) cc_final: 0.8462 (ptt) REVERT: A 204 MET cc_start: 0.9396 (mmp) cc_final: 0.8966 (mmm) REVERT: A 352 ASP cc_start: 0.9120 (t70) cc_final: 0.8632 (t70) REVERT: A 356 ASP cc_start: 0.7517 (m-30) cc_final: 0.7306 (m-30) REVERT: A 378 ASP cc_start: 0.9255 (m-30) cc_final: 0.9011 (m-30) REVERT: A 397 ARG cc_start: 0.7715 (ttt90) cc_final: 0.7287 (tpt170) REVERT: A 417 MET cc_start: 0.9833 (mmp) cc_final: 0.9585 (mmp) REVERT: A 460 MET cc_start: 0.9548 (tpt) cc_final: 0.9109 (tpp) REVERT: A 464 THR cc_start: 0.9567 (m) cc_final: 0.9170 (m) REVERT: B 102 TRP cc_start: 0.7434 (t-100) cc_final: 0.6794 (t-100) REVERT: B 129 SER cc_start: 0.8452 (t) cc_final: 0.8144 (p) REVERT: B 208 MET cc_start: 0.9692 (tpt) cc_final: 0.9374 (tpp) REVERT: B 469 PHE cc_start: 0.9740 (t80) cc_final: 0.9502 (t80) REVERT: C 30 LYS cc_start: 0.9059 (ptpp) cc_final: 0.8449 (ptpt) REVERT: D 434 PHE cc_start: 0.8904 (t80) cc_final: 0.8096 (t80) REVERT: D 437 LEU cc_start: 0.9545 (mt) cc_final: 0.9279 (mt) REVERT: D 439 HIS cc_start: 0.8617 (p-80) cc_final: 0.8219 (p-80) REVERT: E 94 ILE cc_start: 0.6654 (mt) cc_final: 0.6383 (mt) REVERT: E 131 PHE cc_start: 0.8817 (t80) cc_final: 0.8606 (t80) REVERT: E 251 TYR cc_start: 0.9063 (t80) cc_final: 0.8505 (t80) REVERT: E 342 TYR cc_start: 0.9485 (m-80) cc_final: 0.8886 (m-80) REVERT: E 380 GLU cc_start: 0.9432 (mt-10) cc_final: 0.9224 (mp0) outliers start: 2 outliers final: 0 residues processed: 258 average time/residue: 0.1044 time to fit residues: 40.4787 Evaluate side-chains 181 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 20.0000 chunk 86 optimal weight: 0.9990 chunk 27 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 160 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN ** D 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN E 86 HIS ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.098345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.075841 restraints weight = 122965.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.077445 restraints weight = 87273.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.078660 restraints weight = 66979.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.079569 restraints weight = 54229.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.080305 restraints weight = 45762.230| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 16676 Z= 0.139 Angle : 0.612 9.857 22616 Z= 0.319 Chirality : 0.042 0.231 2525 Planarity : 0.004 0.047 2839 Dihedral : 4.651 32.687 2170 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.06 % Allowed : 2.03 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.19), residues: 1963 helix: 0.72 (0.15), residues: 1221 sheet: -0.31 (0.64), residues: 73 loop : -1.59 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 161 TYR 0.025 0.002 TYR B 237 PHE 0.018 0.002 PHE A 167 TRP 0.022 0.002 TRP A 65 HIS 0.006 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00297 (16674) covalent geometry : angle 0.60883 (22612) SS BOND : bond 0.00461 ( 2) SS BOND : angle 4.82257 ( 4) hydrogen bonds : bond 0.04041 ( 860) hydrogen bonds : angle 4.59327 ( 2493) *********************** 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 244 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 243 time to evaluate : 0.533 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 115 MET cc_start: 0.9353 (ptm) cc_final: 0.8916 (ttp) REVERT: A 204 MET cc_start: 0.9331 (mmp) cc_final: 0.8879 (mmm) REVERT: A 345 TYR cc_start: 0.8892 (m-10) cc_final: 0.8655 (m-80) REVERT: A 349 ILE cc_start: 0.9670 (mm) cc_final: 0.9243 (tp) REVERT: A 397 ARG cc_start: 0.7787 (ttt90) cc_final: 0.7338 (tpt170) REVERT: A 417 MET cc_start: 0.9822 (mmp) cc_final: 0.9582 (mmm) REVERT: A 460 MET cc_start: 0.9557 (tpt) cc_final: 0.9116 (tpp) REVERT: A 464 THR cc_start: 0.9573 (m) cc_final: 0.9200 (m) REVERT: B 102 TRP cc_start: 0.7598 (t-100) cc_final: 0.6818 (t-100) REVERT: B 119 MET cc_start: 0.9173 (mtt) cc_final: 0.8956 (mtt) REVERT: B 208 MET cc_start: 0.9681 (tpt) cc_final: 0.9353 (tpp) REVERT: B 312 LEU cc_start: 0.7997 (tp) cc_final: 0.7458 (tp) REVERT: B 417 MET cc_start: 0.8710 (mtm) cc_final: 0.8397 (mtm) REVERT: B 469 PHE cc_start: 0.9761 (t80) cc_final: 0.9506 (t80) REVERT: C 30 LYS cc_start: 0.9049 (ptpp) cc_final: 0.8363 (ptpt) REVERT: D 434 PHE cc_start: 0.8912 (t80) cc_final: 0.8175 (t80) REVERT: D 439 HIS cc_start: 0.8681 (p-80) cc_final: 0.8450 (p-80) REVERT: D 476 LEU cc_start: 0.9266 (mm) cc_final: 0.9004 (tp) REVERT: E 251 TYR cc_start: 0.8940 (t80) cc_final: 0.8465 (t80) REVERT: E 342 TYR cc_start: 0.9502 (m-80) cc_final: 0.9001 (m-80) outliers start: 1 outliers final: 0 residues processed: 243 average time/residue: 0.1123 time to fit residues: 40.6968 Evaluate side-chains 173 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 163 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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** B 116 ASN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN B 461 GLN B 474 GLN ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 HIS ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 HIS ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.087994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.065773 restraints weight = 123815.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.066729 restraints weight = 83794.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.067738 restraints weight = 60870.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.068491 restraints weight = 47344.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.068918 restraints weight = 39348.970| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.5923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 16676 Z= 0.198 Angle : 0.686 11.091 22616 Z= 0.358 Chirality : 0.043 0.240 2525 Planarity : 0.005 0.049 2839 Dihedral : 4.753 31.443 2170 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.06 % Allowed : 1.81 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.19), residues: 1963 helix: 0.68 (0.15), residues: 1220 sheet: -0.25 (0.65), residues: 73 loop : -1.61 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 244 TYR 0.020 0.002 TYR A 301 PHE 0.016 0.002 PHE D 170 TRP 0.047 0.002 TRP E 87 HIS 0.007 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00414 (16674) covalent geometry : angle 0.68300 (22612) SS BOND : bond 0.00332 ( 2) SS BOND : angle 4.58817 ( 4) hydrogen bonds : bond 0.04227 ( 860) hydrogen bonds : angle 4.82858 ( 2493) *********************** 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 233 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 232 time to evaluate : 0.528 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 115 MET cc_start: 0.9277 (ptm) cc_final: 0.8909 (ppp) REVERT: A 204 MET cc_start: 0.9345 (mmp) cc_final: 0.8882 (mmm) REVERT: A 247 TYR cc_start: 0.9424 (m-80) cc_final: 0.9169 (m-80) REVERT: A 345 TYR cc_start: 0.9034 (m-10) cc_final: 0.8772 (m-80) REVERT: A 349 ILE cc_start: 0.9679 (mm) cc_final: 0.9245 (tp) REVERT: A 352 ASP cc_start: 0.9329 (t70) cc_final: 0.9111 (t70) REVERT: A 367 LEU cc_start: 0.8689 (mp) cc_final: 0.8465 (mp) REVERT: A 397 ARG cc_start: 0.7964 (ttt90) cc_final: 0.7495 (tpt170) REVERT: A 417 MET cc_start: 0.9857 (mmp) cc_final: 0.9596 (mmm) REVERT: A 430 LYS cc_start: 0.9652 (mptt) cc_final: 0.9185 (mmtt) REVERT: A 460 MET cc_start: 0.9581 (tpt) cc_final: 0.9036 (tpp) REVERT: A 464 THR cc_start: 0.9629 (m) cc_final: 0.9222 (m) REVERT: B 102 TRP cc_start: 0.7700 (t-100) cc_final: 0.7064 (t-100) REVERT: B 208 MET cc_start: 0.9668 (tpp) cc_final: 0.9416 (tpp) REVERT: B 312 LEU cc_start: 0.8139 (tp) cc_final: 0.7660 (tp) REVERT: B 353 ARG cc_start: 0.9311 (ptt90) cc_final: 0.9103 (ptt90) REVERT: B 417 MET cc_start: 0.8902 (mtm) cc_final: 0.8538 (mtm) REVERT: C 15 ARG cc_start: 0.8779 (mmm-85) cc_final: 0.8414 (mmm-85) REVERT: C 140 TYR cc_start: 0.9030 (t80) cc_final: 0.8654 (t80) REVERT: D 434 PHE cc_start: 0.8951 (t80) cc_final: 0.8140 (t80) REVERT: D 437 LEU cc_start: 0.9696 (mt) cc_final: 0.9461 (mt) REVERT: D 439 HIS cc_start: 0.8725 (p-80) cc_final: 0.8501 (p-80) REVERT: D 476 LEU cc_start: 0.9223 (mm) cc_final: 0.8942 (tp) outliers start: 1 outliers final: 0 residues processed: 233 average time/residue: 0.1119 time to fit residues: 38.9403 Evaluate side-chains 159 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 31 optimal weight: 3.9990 chunk 52 optimal weight: 20.0000 chunk 125 optimal weight: 6.9990 chunk 97 optimal weight: 20.0000 chunk 159 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 173 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN A 313 HIS B 116 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 HIS ** D 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.086783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.063569 restraints weight = 126166.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.064493 restraints weight = 87234.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.065420 restraints weight = 65325.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.066058 restraints weight = 51440.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.066800 restraints weight = 43930.866| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.6351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 16676 Z= 0.190 Angle : 0.672 10.659 22616 Z= 0.351 Chirality : 0.044 0.290 2525 Planarity : 0.005 0.053 2839 Dihedral : 4.791 33.166 2170 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.19), residues: 1963 helix: 0.68 (0.15), residues: 1216 sheet: -0.13 (0.65), residues: 73 loop : -1.59 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 244 TYR 0.036 0.002 TYR E 48 PHE 0.037 0.002 PHE B 476 TRP 0.022 0.002 TRP D 150 HIS 0.006 0.001 HIS E 86 Details of bonding type rmsd covalent geometry : bond 0.00400 (16674) covalent geometry : angle 0.66922 (22612) SS BOND : bond 0.02019 ( 2) SS BOND : angle 4.44156 ( 4) hydrogen bonds : bond 0.04151 ( 860) hydrogen bonds : angle 4.86299 ( 2493) *********************** 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 : 0.640 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 115 MET cc_start: 0.9346 (ptm) cc_final: 0.8632 (ppp) REVERT: A 119 MET cc_start: 0.9280 (ptp) cc_final: 0.8143 (ptp) REVERT: A 204 MET cc_start: 0.9292 (mmp) cc_final: 0.8825 (mmm) REVERT: A 247 TYR cc_start: 0.9408 (m-80) cc_final: 0.9139 (m-80) REVERT: A 300 ASP cc_start: 0.9342 (t0) cc_final: 0.9128 (t0) REVERT: A 345 TYR cc_start: 0.9036 (m-10) cc_final: 0.8781 (m-80) REVERT: A 349 ILE cc_start: 0.9677 (mm) cc_final: 0.9245 (tp) REVERT: A 352 ASP cc_start: 0.9329 (t70) cc_final: 0.9108 (t70) REVERT: A 397 ARG cc_start: 0.8031 (ttt90) cc_final: 0.7550 (tpt170) REVERT: A 417 MET cc_start: 0.9857 (mmp) cc_final: 0.9603 (mmm) REVERT: A 430 LYS cc_start: 0.9636 (mptt) cc_final: 0.9143 (mmtt) REVERT: A 460 MET cc_start: 0.9576 (tpt) cc_final: 0.8981 (tpp) REVERT: A 464 THR cc_start: 0.9620 (m) cc_final: 0.9184 (m) REVERT: B 102 TRP cc_start: 0.7559 (t-100) cc_final: 0.6933 (t-100) REVERT: B 183 PHE cc_start: 0.8623 (m-80) cc_final: 0.8174 (m-80) REVERT: B 208 MET cc_start: 0.9655 (tpp) cc_final: 0.9437 (tpp) REVERT: B 312 LEU cc_start: 0.8126 (tp) cc_final: 0.7587 (tp) REVERT: B 417 MET cc_start: 0.8971 (mtm) cc_final: 0.8601 (mtm) REVERT: C 77 MET cc_start: 0.9251 (tmm) cc_final: 0.8970 (ttm) REVERT: C 140 TYR cc_start: 0.8981 (t80) cc_final: 0.8542 (t80) REVERT: C 157 MET cc_start: 0.9365 (ppp) cc_final: 0.9157 (ppp) REVERT: D 320 ILE cc_start: 0.8267 (mp) cc_final: 0.7545 (mp) REVERT: D 361 MET cc_start: 0.9380 (mmp) cc_final: 0.9146 (mmm) REVERT: D 434 PHE cc_start: 0.9034 (t80) cc_final: 0.8147 (t80) REVERT: D 437 LEU cc_start: 0.9721 (mt) cc_final: 0.9356 (mp) REVERT: D 439 HIS cc_start: 0.8725 (p-80) cc_final: 0.8258 (p-80) REVERT: D 476 LEU cc_start: 0.9224 (mm) cc_final: 0.8953 (tp) REVERT: E 125 ILE cc_start: 0.7537 (mp) cc_final: 0.7230 (mp) REVERT: E 251 TYR cc_start: 0.8766 (t80) cc_final: 0.8541 (t80) REVERT: E 407 MET cc_start: 0.7452 (mtt) cc_final: 0.7014 (mtp) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1134 time to fit residues: 38.2956 Evaluate side-chains 157 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 181 optimal weight: 40.0000 chunk 30 optimal weight: 40.0000 chunk 40 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 161 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 ASN B 121 ASN B 303 GLN B 543 ASN ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN E 389 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.088122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.065617 restraints weight = 122306.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.066506 restraints weight = 83607.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.067490 restraints weight = 61634.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.068199 restraints weight = 47929.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.068930 restraints weight = 40447.319| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.6504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 16676 Z= 0.136 Angle : 0.637 10.682 22616 Z= 0.327 Chirality : 0.043 0.246 2525 Planarity : 0.004 0.046 2839 Dihedral : 4.737 32.306 2170 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.19), residues: 1963 helix: 0.82 (0.15), residues: 1217 sheet: -0.11 (0.65), residues: 73 loop : -1.49 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 397 TYR 0.030 0.002 TYR E 48 PHE 0.023 0.002 PHE A 212 TRP 0.024 0.002 TRP E 87 HIS 0.014 0.001 HIS E 86 Details of bonding type rmsd covalent geometry : bond 0.00301 (16674) covalent geometry : angle 0.63408 (22612) SS BOND : bond 0.00160 ( 2) SS BOND : angle 4.28439 ( 4) hydrogen bonds : bond 0.04064 ( 860) hydrogen bonds : angle 4.70207 ( 2493) *********************** 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 228 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.647 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: A 115 MET cc_start: 0.9301 (ptm) cc_final: 0.8856 (ppp) REVERT: A 119 MET cc_start: 0.9288 (ptp) cc_final: 0.8426 (ptp) REVERT: A 174 MET cc_start: 0.6872 (tpp) cc_final: 0.6596 (tpp) REVERT: A 204 MET cc_start: 0.9190 (mmp) cc_final: 0.8799 (mmm) REVERT: A 247 TYR cc_start: 0.9325 (m-80) cc_final: 0.9002 (m-80) REVERT: A 345 TYR cc_start: 0.8923 (m-10) cc_final: 0.8704 (m-80) REVERT: A 349 ILE cc_start: 0.9671 (mm) cc_final: 0.9237 (tp) REVERT: A 367 LEU cc_start: 0.8781 (mp) cc_final: 0.8399 (mp) REVERT: A 397 ARG cc_start: 0.7976 (ttt90) cc_final: 0.7479 (tpt170) REVERT: A 417 MET cc_start: 0.9834 (mmp) cc_final: 0.9615 (mmm) REVERT: A 430 LYS cc_start: 0.9620 (mptt) cc_final: 0.9417 (mmmt) REVERT: A 460 MET cc_start: 0.9496 (tpt) cc_final: 0.8914 (tpp) REVERT: A 464 THR cc_start: 0.9594 (m) cc_final: 0.9145 (m) REVERT: B 312 LEU cc_start: 0.8368 (tp) cc_final: 0.7902 (tp) REVERT: B 422 TYR cc_start: 0.7981 (m-10) cc_final: 0.7772 (m-10) REVERT: C 157 MET cc_start: 0.9350 (ppp) cc_final: 0.9121 (ppp) REVERT: D 358 SER cc_start: 0.8844 (t) cc_final: 0.8519 (t) REVERT: D 434 PHE cc_start: 0.9054 (t80) cc_final: 0.8119 (t80) REVERT: D 437 LEU cc_start: 0.9694 (mt) cc_final: 0.9296 (mp) REVERT: D 439 HIS cc_start: 0.8677 (p-80) cc_final: 0.8348 (p-80) REVERT: E 125 ILE cc_start: 0.8129 (mp) cc_final: 0.7713 (mp) REVERT: E 407 MET cc_start: 0.7408 (mtt) cc_final: 0.6896 (mtp) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1061 time to fit residues: 37.0592 Evaluate side-chains 161 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 109 optimal weight: 8.9990 chunk 78 optimal weight: 30.0000 chunk 136 optimal weight: 9.9990 chunk 153 optimal weight: 9.9990 chunk 181 optimal weight: 30.0000 chunk 168 optimal weight: 9.9990 chunk 144 optimal weight: 0.9980 chunk 186 optimal weight: 0.8980 chunk 174 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- 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** B 116 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.086481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.064268 restraints weight = 124420.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.065176 restraints weight = 86114.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.066149 restraints weight = 62986.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.066827 restraints weight = 48737.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.067529 restraints weight = 41228.358| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.6858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 16676 Z= 0.181 Angle : 0.668 11.430 22616 Z= 0.350 Chirality : 0.043 0.248 2525 Planarity : 0.004 0.048 2839 Dihedral : 4.767 30.858 2170 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.19), residues: 1963 helix: 0.75 (0.15), residues: 1217 sheet: -0.27 (0.63), residues: 73 loop : -1.46 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 214 TYR 0.036 0.002 TYR B 137 PHE 0.031 0.002 PHE B 212 TRP 0.024 0.002 TRP D 150 HIS 0.013 0.001 HIS E 86 Details of bonding type rmsd covalent geometry : bond 0.00389 (16674) covalent geometry : angle 0.66529 (22612) SS BOND : bond 0.00392 ( 2) SS BOND : angle 4.37246 ( 4) hydrogen bonds : bond 0.04168 ( 860) hydrogen bonds : angle 4.88996 ( 2493) *********************** 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 : 0.501 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 115 MET cc_start: 0.9349 (ptm) cc_final: 0.9146 (ptt) REVERT: A 119 MET cc_start: 0.9278 (ptp) cc_final: 0.9021 (ptp) REVERT: A 174 MET cc_start: 0.7169 (tpp) cc_final: 0.6861 (tpp) REVERT: A 204 MET cc_start: 0.9199 (mmp) cc_final: 0.8857 (mmm) REVERT: A 247 TYR cc_start: 0.9362 (m-80) cc_final: 0.9062 (m-80) REVERT: A 300 ASP cc_start: 0.9296 (t0) cc_final: 0.9055 (t0) REVERT: A 345 TYR cc_start: 0.8962 (m-10) cc_final: 0.8736 (m-80) REVERT: A 349 ILE cc_start: 0.9671 (mm) cc_final: 0.9245 (tp) REVERT: A 397 ARG cc_start: 0.8037 (ttt90) cc_final: 0.7546 (tpt170) REVERT: A 417 MET cc_start: 0.9840 (mmp) cc_final: 0.9583 (mmm) REVERT: A 460 MET cc_start: 0.9492 (tpt) cc_final: 0.8927 (tpp) REVERT: A 464 THR cc_start: 0.9580 (m) cc_final: 0.9164 (m) REVERT: A 606 ILE cc_start: 0.9494 (pt) cc_final: 0.9179 (mp) REVERT: B 312 LEU cc_start: 0.8306 (tp) cc_final: 0.7793 (tp) REVERT: B 417 MET cc_start: 0.9079 (mtm) cc_final: 0.8722 (mtm) REVERT: C 77 MET cc_start: 0.9236 (tmm) cc_final: 0.8959 (tmm) REVERT: C 157 MET cc_start: 0.9388 (ppp) cc_final: 0.9142 (ppp) REVERT: D 358 SER cc_start: 0.9001 (t) cc_final: 0.8672 (t) REVERT: D 434 PHE cc_start: 0.9095 (t80) cc_final: 0.8166 (t80) REVERT: D 437 LEU cc_start: 0.9703 (mt) cc_final: 0.9351 (mp) REVERT: D 439 HIS cc_start: 0.8680 (p-80) cc_final: 0.8344 (p-80) REVERT: D 476 LEU cc_start: 0.9099 (mm) cc_final: 0.8861 (tp) REVERT: E 125 ILE cc_start: 0.8156 (mp) cc_final: 0.7748 (mp) REVERT: E 251 TYR cc_start: 0.8806 (t80) cc_final: 0.8329 (t80) REVERT: E 407 MET cc_start: 0.7525 (mtt) cc_final: 0.6921 (mtp) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1096 time to fit residues: 36.0021 Evaluate side-chains 149 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 67 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 165 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- 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 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.087922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.065543 restraints weight = 121732.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.066507 restraints weight = 82315.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.067520 restraints weight = 59972.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.068278 restraints weight = 46077.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.068714 restraints weight = 38358.720| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.6949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 16676 Z= 0.129 Angle : 0.642 11.311 22616 Z= 0.330 Chirality : 0.043 0.234 2525 Planarity : 0.004 0.044 2839 Dihedral : 4.741 30.325 2170 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.19), residues: 1963 helix: 0.84 (0.15), residues: 1217 sheet: -0.10 (0.64), residues: 73 loop : -1.39 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 397 TYR 0.025 0.002 TYR B 137 PHE 0.028 0.002 PHE B 212 TRP 0.034 0.002 TRP E 87 HIS 0.013 0.001 HIS E 86 Details of bonding type rmsd covalent geometry : bond 0.00290 (16674) covalent geometry : angle 0.63949 (22612) SS BOND : bond 0.00219 ( 2) SS BOND : angle 4.15001 ( 4) hydrogen bonds : bond 0.04036 ( 860) hydrogen bonds : angle 4.74104 ( 2493) ********************** 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 219 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.613 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 103 MET cc_start: 0.8951 (ptt) cc_final: 0.8632 (ptt) REVERT: A 115 MET cc_start: 0.9331 (ptm) cc_final: 0.8628 (ppp) REVERT: A 119 MET cc_start: 0.9242 (ptp) cc_final: 0.7993 (ptp) REVERT: A 204 MET cc_start: 0.9179 (mmp) cc_final: 0.8818 (mmm) REVERT: A 247 TYR cc_start: 0.9347 (m-80) cc_final: 0.9059 (m-80) REVERT: A 300 ASP cc_start: 0.9312 (t0) cc_final: 0.9060 (t0) REVERT: A 345 TYR cc_start: 0.8962 (m-10) cc_final: 0.8735 (m-80) REVERT: A 349 ILE cc_start: 0.9655 (mm) cc_final: 0.9211 (tp) REVERT: A 397 ARG cc_start: 0.7979 (ttt90) cc_final: 0.7505 (tpt170) REVERT: A 417 MET cc_start: 0.9836 (mmp) cc_final: 0.9580 (mmm) REVERT: A 430 LYS cc_start: 0.9564 (mptt) cc_final: 0.9052 (mmtp) REVERT: A 500 PHE cc_start: 0.8070 (m-80) cc_final: 0.6823 (m-80) REVERT: A 606 ILE cc_start: 0.9487 (pt) cc_final: 0.9172 (mp) REVERT: B 312 LEU cc_start: 0.8311 (tp) cc_final: 0.7796 (tp) REVERT: B 417 MET cc_start: 0.9077 (mtm) cc_final: 0.8732 (mtm) REVERT: C 77 MET cc_start: 0.9214 (tmm) cc_final: 0.8950 (tmm) REVERT: C 140 TYR cc_start: 0.8691 (t80) cc_final: 0.8428 (t80) REVERT: C 157 MET cc_start: 0.9370 (ppp) cc_final: 0.9128 (ppp) REVERT: D 358 SER cc_start: 0.8863 (t) cc_final: 0.8603 (t) REVERT: D 434 PHE cc_start: 0.9073 (t80) cc_final: 0.8102 (t80) REVERT: D 437 LEU cc_start: 0.9723 (mt) cc_final: 0.9366 (mp) REVERT: D 439 HIS cc_start: 0.8649 (p-80) cc_final: 0.8306 (p-80) REVERT: E 87 TRP cc_start: 0.9381 (t60) cc_final: 0.9107 (t-100) REVERT: E 251 TYR cc_start: 0.8762 (t80) cc_final: 0.8468 (t80) REVERT: E 407 MET cc_start: 0.7408 (mtt) cc_final: 0.6827 (mtp) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.1161 time to fit residues: 38.6891 Evaluate side-chains 153 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 156 optimal weight: 10.0000 chunk 181 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 25 optimal weight: 0.0040 chunk 184 optimal weight: 4.9990 overall best weight: 3.0000 ------------------------------------------------------------------------------- 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** B 121 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.086383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.064015 restraints weight = 124310.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.064892 restraints weight = 85928.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.065902 restraints weight = 62926.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.066573 restraints weight = 48398.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.067274 restraints weight = 40799.633| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.7220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 16676 Z= 0.156 Angle : 0.652 12.520 22616 Z= 0.339 Chirality : 0.043 0.216 2525 Planarity : 0.004 0.045 2839 Dihedral : 4.691 29.414 2170 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.19), residues: 1963 helix: 0.85 (0.15), residues: 1209 sheet: 0.42 (0.71), residues: 63 loop : -1.30 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 17 TYR 0.021 0.002 TYR A 301 PHE 0.026 0.002 PHE A 212 TRP 0.025 0.002 TRP B 102 HIS 0.012 0.001 HIS E 86 Details of bonding type rmsd covalent geometry : bond 0.00340 (16674) covalent geometry : angle 0.64879 (22612) SS BOND : bond 0.00819 ( 2) SS BOND : angle 4.76316 ( 4) hydrogen bonds : bond 0.04069 ( 860) hydrogen bonds : angle 4.81049 ( 2493) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3094.74 seconds wall clock time: 54 minutes 1.89 seconds (3241.89 seconds total)