Starting phenix.real_space_refine on Wed Feb 4 19:33:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yy5_39667/02_2026/8yy5_39667.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yy5_39667/02_2026/8yy5_39667.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yy5_39667/02_2026/8yy5_39667.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yy5_39667/02_2026/8yy5_39667.map" model { file = "/net/cci-nas-00/data/ceres_data/8yy5_39667/02_2026/8yy5_39667.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yy5_39667/02_2026/8yy5_39667.cif" } resolution = 3.99 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= 0.001 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 9 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 7699 2.51 5 N 2134 2.21 5 O 2384 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12315 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3352 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3356 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 2836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2836 Classifications: {'peptide': 355} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 342} Chain breaks: 1 Chain: "D" Number of atoms: 2650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2650 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.96, per 1000 atoms: 0.24 Number of scatterers: 12315 At special positions: 0 Unit cell: (89.488, 132.352, 119.568, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 82 16.00 P 9 15.00 Al 1 13.00 Mg 2 11.99 F 4 9.00 O 2384 8.00 N 2134 7.00 C 7699 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.08 Conformation dependent library (CDL) restraints added in 460.7 milliseconds 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2900 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 15 sheets defined 49.1% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 removed outlier: 3.541A pdb=" N VAL A 14 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN A 15 " --> pdb=" O GLN A 11 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.371A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 85 removed outlier: 4.208A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 82 through 85' Processing helix chain 'A' and resid 102 through 109 Processing helix chain 'A' and resid 110 through 129 removed outlier: 4.714A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.617A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 193 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 239 Processing helix chain 'A' and resid 239 through 244 Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 382 through 401 removed outlier: 4.100A pdb=" N GLU A 386 " --> pdb=" O THR A 382 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.662A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 46 through 49 Processing helix chain 'B' and resid 70 through 79 Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 107 through 127 removed outlier: 3.526A pdb=" N GLU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP B 118 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.663A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'B' and resid 221 through 242 removed outlier: 3.637A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N CYS B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 257 removed outlier: 3.571A pdb=" N LEU B 253 " --> pdb=" O ASP B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 292 Processing helix chain 'B' and resid 295 through 299 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 374 through 391 removed outlier: 4.447A pdb=" N ARG B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 401 removed outlier: 3.772A pdb=" N GLU B 401 " --> pdb=" O TRP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 428 removed outlier: 4.182A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 347 removed outlier: 3.535A pdb=" N ASP C 344 " --> pdb=" O ASN C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 385 through 391 removed outlier: 3.511A pdb=" N SER C 389 " --> pdb=" O ALA C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 413 Processing helix chain 'C' and resid 415 through 426 Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 452 through 470 Processing helix chain 'C' and resid 524 through 542 Processing helix chain 'C' and resid 549 through 553 removed outlier: 3.717A pdb=" N SER C 553 " --> pdb=" O SER C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 616 Processing helix chain 'C' and resid 625 through 631 Processing helix chain 'C' and resid 631 through 637 Processing helix chain 'C' and resid 653 through 669 Processing helix chain 'D' and resid 326 through 347 Processing helix chain 'D' and resid 384 through 389 removed outlier: 3.729A pdb=" N SER D 389 " --> pdb=" O ALA D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 413 removed outlier: 3.504A pdb=" N ILE D 411 " --> pdb=" O SER D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 423 Processing helix chain 'D' and resid 439 through 445 Processing helix chain 'D' and resid 452 through 469 removed outlier: 3.651A pdb=" N ARG D 456 " --> pdb=" O GLY D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 540 removed outlier: 3.734A pdb=" N ALA D 540 " --> pdb=" O LYS D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 553 removed outlier: 3.538A pdb=" N ARG D 552 " --> pdb=" O ARG D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 615 removed outlier: 3.532A pdb=" N GLU D 605 " --> pdb=" O ARG D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 624 removed outlier: 3.724A pdb=" N ASN D 624 " --> pdb=" O PRO D 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 621 through 624' Processing helix chain 'D' and resid 625 through 631 Processing helix chain 'D' and resid 632 through 636 removed outlier: 4.212A pdb=" N GLY D 636 " --> pdb=" O PRO D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 669 removed outlier: 3.868A pdb=" N LYS D 659 " --> pdb=" O GLN D 655 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL D 667 " --> pdb=" O PHE D 663 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN D 668 " --> pdb=" O ALA D 664 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 67 removed outlier: 7.773A pdb=" N ILE A 5 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N PHE A 138 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE A 7 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N SER A 140 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 170 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 204 " --> pdb=" O SER A 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 272 removed outlier: 6.630A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 63 through 66 removed outlier: 8.743A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLY B 132 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 5 " --> pdb=" O GLY B 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 55 removed outlier: 6.729A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 199 through 200 removed outlier: 5.795A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 310 through 313 removed outlier: 4.194A pdb=" N THR B 312 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 400 through 402 removed outlier: 4.088A pdb=" N GLN C 400 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ARG C 350 " --> pdb=" O MET C 643 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ILE C 645 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N PHE C 352 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL C 647 " --> pdb=" O PHE C 352 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG C 354 " --> pdb=" O VAL C 647 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE C 428 " --> pdb=" O ASN C 577 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL C 579 " --> pdb=" O ILE C 428 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ILE C 430 " --> pdb=" O VAL C 579 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU C 581 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA C 432 " --> pdb=" O LEU C 581 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLY C 583 " --> pdb=" O ALA C 432 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLY C 434 " --> pdb=" O GLY C 583 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU C 520 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 488 through 491 removed outlier: 3.537A pdb=" N VAL C 573 " --> pdb=" O ASN C 678 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASN C 678 " --> pdb=" O VAL C 573 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 371 through 374 removed outlier: 6.477A pdb=" N THR C 377 " --> pdb=" O HIS C 373 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 501 through 504 removed outlier: 4.231A pdb=" N GLU C 501 " --> pdb=" O SER C 515 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 400 through 402 removed outlier: 7.032A pdb=" N VAL D 351 " --> pdb=" O GLN D 400 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N PHE D 402 " --> pdb=" O VAL D 351 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N CYS D 353 " --> pdb=" O PHE D 402 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ARG D 350 " --> pdb=" O MET D 643 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ILE D 645 " --> pdb=" O ARG D 350 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE D 352 " --> pdb=" O ILE D 645 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL D 647 " --> pdb=" O PHE D 352 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ARG D 354 " --> pdb=" O VAL D 647 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE D 428 " --> pdb=" O ASN D 577 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL D 579 " --> pdb=" O ILE D 428 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE D 430 " --> pdb=" O VAL D 579 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N GLU D 570 " --> pdb=" O HIS D 565 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N HIS D 565 " --> pdb=" O GLU D 570 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 400 through 402 removed outlier: 7.032A pdb=" N VAL D 351 " --> pdb=" O GLN D 400 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N PHE D 402 " --> pdb=" O VAL D 351 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N CYS D 353 " --> pdb=" O PHE D 402 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ARG D 350 " --> pdb=" O MET D 643 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ILE D 645 " --> pdb=" O ARG D 350 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE D 352 " --> pdb=" O ILE D 645 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL D 647 " --> pdb=" O PHE D 352 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ARG D 354 " --> pdb=" O VAL D 647 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE D 428 " --> pdb=" O ASN D 577 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL D 579 " --> pdb=" O ILE D 428 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE D 430 " --> pdb=" O VAL D 579 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N GLU D 570 " --> pdb=" O HIS D 565 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N HIS D 565 " --> pdb=" O GLU D 570 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE D 477 " --> pdb=" O VAL D 522 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 369 through 371 removed outlier: 3.592A pdb=" N THR D 371 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU D 379 " --> pdb=" O THR D 371 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 502 through 504 645 hydrogen bonds defined for protein. 1851 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: 2.03 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3104 1.33 - 1.45: 2420 1.45 - 1.57: 6888 1.57 - 1.70: 14 1.70 - 1.82: 137 Bond restraints: 12563 Sorted by residual: bond pdb=" C5 GDP B 501 " pdb=" C4 GDP B 501 " ideal model delta sigma weight residual 1.490 1.376 0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" F2 ALF C 903 " pdb="AL ALF C 903 " ideal model delta sigma weight residual 1.685 1.786 -0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" F1 ALF C 903 " pdb="AL ALF C 903 " ideal model delta sigma weight residual 1.684 1.785 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" F3 ALF C 903 " pdb="AL ALF C 903 " ideal model delta sigma weight residual 1.685 1.785 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" F4 ALF C 903 " pdb="AL ALF C 903 " ideal model delta sigma weight residual 1.686 1.784 -0.098 2.00e-02 2.50e+03 2.41e+01 ... (remaining 12558 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.23: 17017 14.23 - 28.46: 4 28.46 - 42.69: 0 42.69 - 56.92: 0 56.92 - 71.15: 2 Bond angle restraints: 17023 Sorted by residual: angle pdb=" F1 ALF C 903 " pdb="AL ALF C 903 " pdb=" F2 ALF C 903 " ideal model delta sigma weight residual 108.68 179.83 -71.15 3.00e+00 1.11e-01 5.62e+02 angle pdb=" F3 ALF C 903 " pdb="AL ALF C 903 " pdb=" F4 ALF C 903 " ideal model delta sigma weight residual 109.63 179.81 -70.18 3.00e+00 1.11e-01 5.47e+02 angle pdb=" F2 ALF C 903 " pdb="AL ALF C 903 " pdb=" F4 ALF C 903 " ideal model delta sigma weight residual 110.21 89.83 20.38 3.00e+00 1.11e-01 4.62e+01 angle pdb=" F1 ALF C 903 " pdb="AL ALF C 903 " pdb=" F3 ALF C 903 " ideal model delta sigma weight residual 109.69 89.77 19.92 3.00e+00 1.11e-01 4.41e+01 angle pdb=" F2 ALF C 903 " pdb="AL ALF C 903 " pdb=" F3 ALF C 903 " ideal model delta sigma weight residual 109.59 90.26 19.33 3.00e+00 1.11e-01 4.15e+01 ... (remaining 17018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.13: 7309 29.13 - 58.26: 219 58.26 - 87.39: 37 87.39 - 116.53: 1 116.53 - 145.66: 5 Dihedral angle restraints: 7571 sinusoidal: 3080 harmonic: 4491 Sorted by residual: dihedral pdb=" O2G GTP A 501 " pdb=" O3B GTP A 501 " pdb=" PG GTP A 501 " pdb=" PB GTP A 501 " ideal model delta sinusoidal sigma weight residual 177.30 -37.04 -145.66 1 2.00e+01 2.50e-03 4.38e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -38.97 143.56 1 2.00e+01 2.50e-03 4.33e+01 dihedral pdb=" O3B GTP A 501 " pdb=" O3A GTP A 501 " pdb=" PB GTP A 501 " pdb=" PA GTP A 501 " ideal model delta sinusoidal sigma weight residual 291.08 163.74 127.34 1 2.00e+01 2.50e-03 3.86e+01 ... (remaining 7568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1088 0.047 - 0.094: 445 0.094 - 0.141: 243 0.141 - 0.188: 95 0.188 - 0.235: 16 Chirality restraints: 1887 Sorted by residual: chirality pdb=" C3' GTP A 501 " pdb=" C2' GTP A 501 " pdb=" C4' GTP A 501 " pdb=" O3' GTP A 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.71 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA ASP D 374 " pdb=" N ASP D 374 " pdb=" C ASP D 374 " pdb=" CB ASP D 374 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ILE A 16 " pdb=" N ILE A 16 " pdb=" C ILE A 16 " pdb=" CB ILE A 16 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1884 not shown) Planarity restraints: 2202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 121 " 0.859 9.50e-02 1.11e+02 3.85e-01 9.00e+01 pdb=" NE ARG A 121 " -0.053 2.00e-02 2.50e+03 pdb=" CZ ARG A 121 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 121 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 121 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 84 " 0.749 9.50e-02 1.11e+02 3.36e-01 6.86e+01 pdb=" NE ARG A 84 " -0.046 2.00e-02 2.50e+03 pdb=" CZ ARG A 84 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 84 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 84 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 105 " -0.587 9.50e-02 1.11e+02 2.63e-01 4.24e+01 pdb=" NE ARG A 105 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG A 105 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 105 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 105 " -0.018 2.00e-02 2.50e+03 ... (remaining 2199 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 7 2.02 - 2.74: 1064 2.74 - 3.46: 20466 3.46 - 4.18: 33104 4.18 - 4.90: 55968 Nonbonded interactions: 110609 Sorted by model distance: nonbonded pdb=" O VAL A 409 " pdb=" ND2 ASN C 600 " model vdw 1.296 3.120 nonbonded pdb=" OE2 GLU B 410 " pdb=" NH1 ARG C 503 " model vdw 1.646 3.120 nonbonded pdb=" OE2 GLU B 194 " pdb=" NZ LYS C 626 " model vdw 1.704 3.120 nonbonded pdb=" O GLY A 410 " pdb=" CD LYS C 597 " model vdw 1.732 3.440 nonbonded pdb=" OE1 GLU A 414 " pdb=" OG SER C 586 " model vdw 1.834 3.040 ... (remaining 110604 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 'C' and (resid 325 through 587 or resid 599 through 617 or (resid 618 and \ (name N or name CA or name C or name O or name CB )) or resid 619 through 669 o \ r resid 902)) selection = (chain 'D' and (resid 325 through 542 or resid 548 through 801)) } 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=1.00 max=1.00 mean=1.00 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: 18.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.190 Find NCS groups from input model: 0.150 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3673 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 : 0.008 0.114 12563 Z= 0.600 Angle : 1.377 71.148 17023 Z= 0.811 Chirality : 0.070 0.235 1887 Planarity : 0.019 0.385 2202 Dihedral : 14.488 145.657 4671 Min Nonbonded Distance : 1.296 Molprobity Statistics. All-atom Clashscore : 31.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.62 % Favored : 94.19 % Rotamer: Outliers : 3.70 % Allowed : 5.11 % Favored : 91.19 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.07 % 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 are not related in a simple way. whole: -0.57 (0.21), residues: 1531 helix: 0.51 (0.20), residues: 650 sheet: 0.34 (0.39), residues: 208 loop : -1.50 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 77 TYR 0.022 0.002 TYR D 442 PHE 0.042 0.002 PHE B 133 TRP 0.030 0.002 TRP B 21 HIS 0.007 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00833 (12563) covalent geometry : angle 1.37670 (17023) hydrogen bonds : bond 0.17310 ( 592) hydrogen bonds : angle 7.82784 ( 1851) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 335 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7535 (mt) REVERT: A 76 ASP cc_start: 0.9036 (t0) cc_final: 0.8666 (m-30) REVERT: A 103 TYR cc_start: 0.5924 (OUTLIER) cc_final: 0.4350 (t80) REVERT: A 167 LEU cc_start: 0.8095 (tp) cc_final: 0.7767 (mp) REVERT: A 238 ILE cc_start: 0.7034 (mt) cc_final: 0.6694 (mt) REVERT: A 306 ASP cc_start: 0.5267 (p0) cc_final: 0.4901 (p0) REVERT: B 37 HIS cc_start: 0.8000 (m-70) cc_final: 0.7664 (m-70) REVERT: B 108 GLU cc_start: 0.7466 (mp0) cc_final: 0.6499 (tt0) REVERT: B 164 MET cc_start: 0.7319 (OUTLIER) cc_final: 0.7116 (mpp) REVERT: B 282 ARG cc_start: 0.7609 (pmt-80) cc_final: 0.7128 (ptt180) REVERT: B 300 MET cc_start: 0.5120 (mmt) cc_final: 0.4904 (mmt) REVERT: B 303 CYS cc_start: 0.8822 (m) cc_final: 0.8436 (m) REVERT: B 376 GLU cc_start: 0.8612 (pp20) cc_final: 0.8399 (pt0) REVERT: C 348 ASN cc_start: 0.3276 (OUTLIER) cc_final: 0.2892 (p0) REVERT: C 400 GLN cc_start: 0.4625 (tp40) cc_final: 0.4419 (tm-30) REVERT: C 412 PHE cc_start: 0.6983 (t80) cc_final: 0.6639 (t80) REVERT: C 486 ASN cc_start: 0.6161 (p0) cc_final: 0.5532 (t0) REVERT: C 501 GLU cc_start: 0.4955 (tm-30) cc_final: 0.4319 (mt-10) REVERT: C 504 MET cc_start: 0.6954 (pmm) cc_final: 0.6326 (ptt) REVERT: C 516 ASN cc_start: 0.7387 (t0) cc_final: 0.6684 (t0) REVERT: C 538 ASN cc_start: 0.6409 (m110) cc_final: 0.6036 (t0) REVERT: C 581 LEU cc_start: 0.6872 (mt) cc_final: 0.6656 (mt) REVERT: C 593 MET cc_start: 0.3130 (mmt) cc_final: 0.2089 (tmm) REVERT: C 634 SER cc_start: 0.8056 (m) cc_final: 0.7766 (t) REVERT: C 638 ASN cc_start: 0.7818 (p0) cc_final: 0.7211 (m-40) REVERT: C 651 GLN cc_start: 0.6602 (tp40) cc_final: 0.6108 (tp40) outliers start: 50 outliers final: 18 residues processed: 366 average time/residue: 0.1215 time to fit residues: 63.1601 Evaluate side-chains 232 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 103 TYR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 162 ARG Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain D residue 348 ASN Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 374 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 50.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 88 HIS A 91 GLN ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN A 266 HIS ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS B 190 HIS ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 GLN ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 577 ASN C 598 ASN ** C 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 GLN D 516 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4947 r_free = 0.4947 target = 0.226628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.143662 restraints weight = 22170.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.141507 restraints weight = 13476.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.141551 restraints weight = 10038.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.141661 restraints weight = 8604.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.141659 restraints weight = 7697.119| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12563 Z= 0.232 Angle : 0.774 12.159 17023 Z= 0.393 Chirality : 0.050 0.274 1887 Planarity : 0.006 0.098 2202 Dihedral : 10.533 137.117 1758 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.03 % Allowed : 13.55 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.07 % 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 are not related in a simple way. whole: -0.52 (0.21), residues: 1531 helix: 0.55 (0.19), residues: 668 sheet: -0.09 (0.37), residues: 233 loop : -1.38 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 350 TYR 0.013 0.002 TYR C 442 PHE 0.041 0.002 PHE C 396 TRP 0.033 0.002 TRP B 21 HIS 0.010 0.002 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00479 (12563) covalent geometry : angle 0.77428 (17023) hydrogen bonds : bond 0.05160 ( 592) hydrogen bonds : angle 5.57097 ( 1851) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 232 time to evaluate : 0.436 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: A 36 MET cc_start: 0.7611 (ppp) cc_final: 0.7324 (tmm) REVERT: A 70 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7889 (mt) REVERT: A 120 ASP cc_start: 0.7791 (m-30) cc_final: 0.7509 (m-30) REVERT: A 300 ASN cc_start: 0.8514 (t0) cc_final: 0.8003 (m-40) REVERT: A 304 LYS cc_start: 0.7900 (mmmm) cc_final: 0.7345 (mmtp) REVERT: A 408 TYR cc_start: 0.7048 (m-80) cc_final: 0.6807 (m-10) REVERT: B 208 TYR cc_start: 0.8070 (m-10) cc_final: 0.7564 (m-80) REVERT: B 282 ARG cc_start: 0.7236 (pmt-80) cc_final: 0.7035 (ptt180) REVERT: B 403 MET cc_start: 0.7240 (mmm) cc_final: 0.5489 (mtp) REVERT: C 412 PHE cc_start: 0.5716 (t80) cc_final: 0.5218 (t80) REVERT: C 486 ASN cc_start: 0.6361 (p0) cc_final: 0.5840 (t0) REVERT: C 500 MET cc_start: 0.4801 (mmp) cc_final: 0.4449 (mmp) REVERT: C 516 ASN cc_start: 0.6460 (t0) cc_final: 0.6225 (t0) REVERT: C 537 MET cc_start: 0.5698 (mmp) cc_final: 0.5368 (ttp) REVERT: C 593 MET cc_start: 0.3985 (mmt) cc_final: 0.3382 (tmm) REVERT: C 651 GLN cc_start: 0.5715 (tp40) cc_final: 0.5499 (tp40) REVERT: C 654 PHE cc_start: 0.4635 (t80) cc_final: 0.4185 (t80) outliers start: 41 outliers final: 25 residues processed: 261 average time/residue: 0.1019 time to fit residues: 38.8205 Evaluate side-chains 214 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain C residue 666 SER Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 374 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 25 optimal weight: 0.9980 chunk 94 optimal weight: 40.0000 chunk 63 optimal weight: 8.9990 chunk 143 optimal weight: 0.1980 chunk 61 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 98 optimal weight: 50.0000 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 GLN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 HIS C 435 GLN ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 598 ASN ** C 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 600 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.226557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.146579 restraints weight = 22667.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.140688 restraints weight = 13743.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.141373 restraints weight = 9457.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.140696 restraints weight = 7796.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.140704 restraints weight = 7208.118| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12563 Z= 0.163 Angle : 0.686 11.507 17023 Z= 0.342 Chirality : 0.047 0.275 1887 Planarity : 0.005 0.083 2202 Dihedral : 10.103 145.048 1739 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.18 % Allowed : 16.14 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.07 % 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 are not related in a simple way. whole: -0.34 (0.21), residues: 1531 helix: 0.69 (0.20), residues: 665 sheet: 0.06 (0.36), residues: 238 loop : -1.30 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 503 TYR 0.011 0.001 TYR C 372 PHE 0.021 0.002 PHE C 462 TRP 0.012 0.001 TRP B 21 HIS 0.008 0.001 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00361 (12563) covalent geometry : angle 0.68567 (17023) hydrogen bonds : bond 0.04590 ( 592) hydrogen bonds : angle 5.05092 ( 1851) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 194 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.7756 (ppp) cc_final: 0.7523 (ppp) REVERT: A 70 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7742 (mt) REVERT: A 285 GLN cc_start: 0.4258 (mm-40) cc_final: 0.4036 (mm110) REVERT: B 114 ASP cc_start: 0.8058 (t0) cc_final: 0.7810 (t0) REVERT: B 403 MET cc_start: 0.7152 (mmm) cc_final: 0.5411 (mtp) REVERT: C 396 PHE cc_start: 0.3293 (m-80) cc_final: 0.3047 (m-10) REVERT: C 399 ASP cc_start: 0.5159 (m-30) cc_final: 0.4909 (m-30) REVERT: C 412 PHE cc_start: 0.5891 (t80) cc_final: 0.5475 (t80) REVERT: C 500 MET cc_start: 0.5384 (mmp) cc_final: 0.5043 (mmp) REVERT: C 516 ASN cc_start: 0.7109 (t0) cc_final: 0.6792 (t0) REVERT: C 537 MET cc_start: 0.5681 (mmp) cc_final: 0.5309 (ttp) REVERT: C 593 MET cc_start: 0.3942 (mmt) cc_final: 0.3501 (tmm) REVERT: C 594 THR cc_start: 0.5301 (t) cc_final: 0.4935 (p) REVERT: C 651 GLN cc_start: 0.5962 (tp40) cc_final: 0.5711 (tp40) outliers start: 43 outliers final: 25 residues processed: 228 average time/residue: 0.0907 time to fit residues: 31.2459 Evaluate side-chains 195 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 666 SER Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain D residue 504 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 82 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 121 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 96 optimal weight: 50.0000 chunk 102 optimal weight: 50.0000 chunk 20 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 129 optimal weight: 20.0000 chunk 141 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 overall best weight: 5.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 HIS C 598 ASN ** C 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.222867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.146080 restraints weight = 23394.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.144136 restraints weight = 13858.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.144532 restraints weight = 10328.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.143803 restraints weight = 8494.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.143796 restraints weight = 7626.418| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12563 Z= 0.198 Angle : 0.709 9.976 17023 Z= 0.354 Chirality : 0.047 0.272 1887 Planarity : 0.005 0.087 2202 Dihedral : 10.221 155.868 1735 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.55 % Allowed : 16.36 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.07 % 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 are not related in a simple way. whole: -0.32 (0.21), residues: 1531 helix: 0.80 (0.20), residues: 651 sheet: -0.05 (0.35), residues: 238 loop : -1.30 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 662 TYR 0.018 0.002 TYR A 83 PHE 0.015 0.002 PHE B 20 TRP 0.014 0.002 TRP A 21 HIS 0.007 0.002 HIS C 619 Details of bonding type rmsd covalent geometry : bond 0.00451 (12563) covalent geometry : angle 0.70867 (17023) hydrogen bonds : bond 0.04690 ( 592) hydrogen bonds : angle 4.93452 ( 1851) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 181 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.7785 (ppp) cc_final: 0.7561 (ppp) REVERT: A 112 LYS cc_start: 0.8121 (pptt) cc_final: 0.7843 (tmmt) REVERT: A 203 MET cc_start: 0.8424 (mmm) cc_final: 0.8122 (mmm) REVERT: A 285 GLN cc_start: 0.4367 (mm-40) cc_final: 0.3782 (mm110) REVERT: A 300 ASN cc_start: 0.9012 (OUTLIER) cc_final: 0.8027 (m-40) REVERT: A 302 MET cc_start: 0.8696 (mmp) cc_final: 0.8290 (mmt) REVERT: A 313 MET cc_start: 0.8916 (mpp) cc_final: 0.8660 (mmm) REVERT: A 413 MET cc_start: 0.5437 (mmm) cc_final: 0.5061 (mmm) REVERT: B 8 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.6070 (mt0) REVERT: B 282 ARG cc_start: 0.7508 (ptt180) cc_final: 0.7191 (ttp-170) REVERT: B 347 ASN cc_start: 0.7856 (p0) cc_final: 0.7056 (p0) REVERT: B 403 MET cc_start: 0.7371 (mmm) cc_final: 0.6116 (mtp) REVERT: C 396 PHE cc_start: 0.4049 (m-80) cc_final: 0.3688 (m-80) REVERT: C 399 ASP cc_start: 0.5225 (m-30) cc_final: 0.4962 (m-30) REVERT: C 412 PHE cc_start: 0.5954 (t80) cc_final: 0.5584 (t80) REVERT: C 500 MET cc_start: 0.5388 (mmp) cc_final: 0.4993 (mmp) REVERT: C 516 ASN cc_start: 0.7353 (t0) cc_final: 0.7084 (t0) REVERT: C 537 MET cc_start: 0.5792 (mmp) cc_final: 0.5433 (ttp) REVERT: C 651 GLN cc_start: 0.6232 (tp40) cc_final: 0.5873 (tp40) REVERT: C 654 PHE cc_start: 0.5555 (t80) cc_final: 0.5141 (t80) outliers start: 48 outliers final: 28 residues processed: 221 average time/residue: 0.0993 time to fit residues: 31.9327 Evaluate side-chains 189 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 344 TRP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 462 PHE Chi-restraints excluded: chain C residue 524 ASP Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain D residue 411 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 2 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 146 optimal weight: 40.0000 chunk 79 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 135 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 69 optimal weight: 0.0060 chunk 66 optimal weight: 0.0870 overall best weight: 0.7576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN B 14 ASN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** C 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.226774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.149399 restraints weight = 23448.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.148923 restraints weight = 13783.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.148909 restraints weight = 8740.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.149072 restraints weight = 8103.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.148780 restraints weight = 7587.035| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12563 Z= 0.127 Angle : 0.649 8.963 17023 Z= 0.319 Chirality : 0.046 0.301 1887 Planarity : 0.005 0.074 2202 Dihedral : 9.871 153.953 1730 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.96 % Allowed : 18.43 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.07 % 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 are not related in a simple way. whole: -0.05 (0.21), residues: 1531 helix: 0.98 (0.20), residues: 655 sheet: 0.31 (0.36), residues: 222 loop : -1.20 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 339 TYR 0.015 0.001 TYR B 208 PHE 0.017 0.001 PHE C 663 TRP 0.015 0.001 TRP A 21 HIS 0.007 0.001 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00278 (12563) covalent geometry : angle 0.64858 (17023) hydrogen bonds : bond 0.04086 ( 592) hydrogen bonds : angle 4.78672 ( 1851) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 0.432 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: A 36 MET cc_start: 0.7749 (ppp) cc_final: 0.7510 (ppp) REVERT: A 112 LYS cc_start: 0.8180 (pptt) cc_final: 0.7838 (tmmt) REVERT: A 121 ARG cc_start: 0.8556 (mmm160) cc_final: 0.8187 (mmm-85) REVERT: A 203 MET cc_start: 0.8352 (mmm) cc_final: 0.8102 (mmm) REVERT: A 285 GLN cc_start: 0.4473 (mm-40) cc_final: 0.4023 (mm110) REVERT: A 413 MET cc_start: 0.5078 (mmm) cc_final: 0.4786 (mmm) REVERT: B 282 ARG cc_start: 0.7356 (ptt180) cc_final: 0.7079 (ttt180) REVERT: B 347 ASN cc_start: 0.7478 (p0) cc_final: 0.6728 (p0) REVERT: B 403 MET cc_start: 0.7101 (mmm) cc_final: 0.5847 (mtp) REVERT: C 412 PHE cc_start: 0.6045 (t80) cc_final: 0.5666 (t80) REVERT: C 500 MET cc_start: 0.5071 (mmp) cc_final: 0.4741 (mmp) REVERT: C 516 ASN cc_start: 0.7188 (t0) cc_final: 0.6921 (t0) REVERT: C 537 MET cc_start: 0.5802 (mmp) cc_final: 0.5438 (ttp) REVERT: C 597 LYS cc_start: 0.6239 (mmtt) cc_final: 0.4517 (tmtt) REVERT: C 672 MET cc_start: 0.0924 (tpt) cc_final: 0.0517 (mmm) outliers start: 40 outliers final: 27 residues processed: 217 average time/residue: 0.1016 time to fit residues: 32.3844 Evaluate side-chains 195 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 344 TRP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 462 PHE Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain D residue 504 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 105 optimal weight: 50.0000 chunk 106 optimal weight: 50.0000 chunk 81 optimal weight: 0.0970 chunk 67 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 85 optimal weight: 50.0000 chunk 99 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 overall best weight: 3.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 600 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.224725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.152796 restraints weight = 23568.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.145661 restraints weight = 15238.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.147966 restraints weight = 11498.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.146351 restraints weight = 8641.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.146659 restraints weight = 8557.532| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.5754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12563 Z= 0.148 Angle : 0.665 13.018 17023 Z= 0.330 Chirality : 0.046 0.315 1887 Planarity : 0.005 0.067 2202 Dihedral : 9.830 154.260 1730 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.48 % Allowed : 18.65 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.07 % 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 are not related in a simple way. whole: -0.06 (0.21), residues: 1531 helix: 1.00 (0.20), residues: 654 sheet: 0.48 (0.37), residues: 214 loop : -1.28 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 390 TYR 0.013 0.001 TYR A 83 PHE 0.040 0.002 PHE B 20 TRP 0.014 0.001 TRP B 344 HIS 0.006 0.001 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00332 (12563) covalent geometry : angle 0.66453 (17023) hydrogen bonds : bond 0.04225 ( 592) hydrogen bonds : angle 4.76433 ( 1851) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 174 time to evaluate : 0.489 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: A 36 MET cc_start: 0.7762 (ppp) cc_final: 0.7509 (ppp) REVERT: A 71 GLU cc_start: 0.6682 (tp30) cc_final: 0.6319 (tt0) REVERT: A 85 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8221 (mp10) REVERT: A 112 LYS cc_start: 0.8393 (pptt) cc_final: 0.8089 (tmmt) REVERT: A 285 GLN cc_start: 0.4279 (mm-40) cc_final: 0.3805 (mm110) REVERT: A 300 ASN cc_start: 0.8549 (OUTLIER) cc_final: 0.8250 (m-40) REVERT: A 313 MET cc_start: 0.8978 (mpp) cc_final: 0.8618 (mmm) REVERT: A 413 MET cc_start: 0.5433 (mmm) cc_final: 0.5168 (mmm) REVERT: B 8 GLN cc_start: 0.7344 (OUTLIER) cc_final: 0.5628 (mt0) REVERT: B 14 ASN cc_start: 0.8498 (m-40) cc_final: 0.8125 (m110) REVERT: B 347 ASN cc_start: 0.7691 (p0) cc_final: 0.6961 (p0) REVERT: B 403 MET cc_start: 0.6966 (mmm) cc_final: 0.5592 (mtp) REVERT: C 350 ARG cc_start: 0.6227 (mpp80) cc_final: 0.5574 (mpp80) REVERT: C 412 PHE cc_start: 0.6185 (t80) cc_final: 0.5813 (t80) REVERT: C 500 MET cc_start: 0.5368 (mmp) cc_final: 0.4976 (mmp) REVERT: C 516 ASN cc_start: 0.7291 (t0) cc_final: 0.7022 (t0) REVERT: C 537 MET cc_start: 0.5817 (mmp) cc_final: 0.5420 (ttp) REVERT: D 343 MET cc_start: 0.2547 (mmt) cc_final: 0.2337 (mmt) outliers start: 47 outliers final: 35 residues processed: 207 average time/residue: 0.1052 time to fit residues: 32.5109 Evaluate side-chains 203 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 344 TRP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain C residue 462 PHE Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 524 ASP Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 504 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 86 optimal weight: 6.9990 chunk 45 optimal weight: 0.0170 chunk 78 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 118 optimal weight: 50.0000 chunk 50 optimal weight: 7.9990 chunk 151 optimal weight: 50.0000 chunk 97 optimal weight: 9.9990 chunk 126 optimal weight: 40.0000 chunk 1 optimal weight: 10.0000 overall best weight: 6.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS C 598 ASN ** C 624 ASN ** 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 = 0.4804 r_free = 0.4804 target = 0.221558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.143582 restraints weight = 23518.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.143394 restraints weight = 13737.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.142853 restraints weight = 9244.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.142519 restraints weight = 8102.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.142569 restraints weight = 7346.715| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.6320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12563 Z= 0.202 Angle : 0.723 17.974 17023 Z= 0.357 Chirality : 0.048 0.408 1887 Planarity : 0.005 0.087 2202 Dihedral : 10.127 162.813 1730 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.00 % Allowed : 19.02 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.07 % 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 are not related in a simple way. whole: -0.17 (0.21), residues: 1531 helix: 0.92 (0.20), residues: 644 sheet: 0.53 (0.37), residues: 209 loop : -1.35 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 339 TYR 0.021 0.002 TYR A 83 PHE 0.033 0.002 PHE B 20 TRP 0.011 0.002 TRP A 21 HIS 0.006 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00463 (12563) covalent geometry : angle 0.72336 (17023) hydrogen bonds : bond 0.04551 ( 592) hydrogen bonds : angle 4.84311 ( 1851) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 168 time to evaluate : 0.472 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: A 36 MET cc_start: 0.7756 (ppp) cc_final: 0.7536 (ppp) REVERT: A 112 LYS cc_start: 0.8673 (pptt) cc_final: 0.8389 (tmmt) REVERT: A 203 MET cc_start: 0.8463 (mmm) cc_final: 0.8099 (mmm) REVERT: A 285 GLN cc_start: 0.4330 (mm-40) cc_final: 0.4003 (mm110) REVERT: A 300 ASN cc_start: 0.8858 (OUTLIER) cc_final: 0.8311 (m-40) REVERT: A 413 MET cc_start: 0.6042 (mmm) cc_final: 0.5423 (mmm) REVERT: B 8 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.5872 (mt0) REVERT: B 14 ASN cc_start: 0.8356 (m-40) cc_final: 0.8135 (m110) REVERT: B 37 HIS cc_start: 0.7762 (m-70) cc_final: 0.7459 (m-70) REVERT: B 207 LEU cc_start: 0.8976 (mp) cc_final: 0.8566 (mm) REVERT: B 347 ASN cc_start: 0.7753 (p0) cc_final: 0.7232 (p0) REVERT: B 363 MET cc_start: 0.8428 (ttm) cc_final: 0.8066 (ttm) REVERT: B 403 MET cc_start: 0.7199 (mmm) cc_final: 0.6963 (mmm) REVERT: C 350 ARG cc_start: 0.6328 (mpp80) cc_final: 0.5690 (mpp80) REVERT: C 412 PHE cc_start: 0.6038 (t80) cc_final: 0.5670 (t80) REVERT: C 500 MET cc_start: 0.5680 (mmp) cc_final: 0.5312 (mmp) REVERT: C 516 ASN cc_start: 0.7370 (t0) cc_final: 0.7098 (t0) REVERT: C 537 MET cc_start: 0.5840 (mmp) cc_final: 0.5474 (ttp) outliers start: 54 outliers final: 41 residues processed: 208 average time/residue: 0.1034 time to fit residues: 31.5014 Evaluate side-chains 203 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 160 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 344 TRP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain C residue 462 PHE Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 504 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 16 optimal weight: 0.7980 chunk 134 optimal weight: 20.0000 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 149 optimal weight: 50.0000 chunk 18 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN B 105 HIS ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 598 ASN ** C 624 ASN ** 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 = 0.4834 r_free = 0.4834 target = 0.223365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.145666 restraints weight = 23677.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.144384 restraints weight = 14166.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.144633 restraints weight = 10091.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.144675 restraints weight = 8358.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.144675 restraints weight = 8241.801| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.6473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12563 Z= 0.140 Angle : 0.677 12.146 17023 Z= 0.333 Chirality : 0.047 0.418 1887 Planarity : 0.005 0.087 2202 Dihedral : 9.955 161.506 1730 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.70 % Allowed : 19.84 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.07 % 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 are not related in a simple way. whole: -0.13 (0.21), residues: 1531 helix: 0.92 (0.20), residues: 650 sheet: 0.47 (0.37), residues: 214 loop : -1.29 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 529 TYR 0.018 0.001 TYR A 83 PHE 0.028 0.002 PHE C 396 TRP 0.015 0.001 TRP B 344 HIS 0.008 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00313 (12563) covalent geometry : angle 0.67744 (17023) hydrogen bonds : bond 0.04212 ( 592) hydrogen bonds : angle 4.74015 ( 1851) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 170 time to evaluate : 0.397 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: A 36 MET cc_start: 0.7731 (ppp) cc_final: 0.7487 (ppp) REVERT: A 112 LYS cc_start: 0.8743 (pptt) cc_final: 0.8426 (tmmt) REVERT: A 203 MET cc_start: 0.8359 (mmm) cc_final: 0.8067 (mmm) REVERT: A 285 GLN cc_start: 0.4230 (mm-40) cc_final: 0.3986 (mm110) REVERT: A 300 ASN cc_start: 0.8768 (OUTLIER) cc_final: 0.8293 (m-40) REVERT: A 313 MET cc_start: 0.9029 (mpp) cc_final: 0.8781 (mmm) REVERT: A 413 MET cc_start: 0.5647 (mmm) cc_final: 0.5140 (mmm) REVERT: B 37 HIS cc_start: 0.7813 (m-70) cc_final: 0.7515 (m-70) REVERT: C 412 PHE cc_start: 0.5763 (t80) cc_final: 0.5326 (t80) REVERT: C 500 MET cc_start: 0.4805 (mmp) cc_final: 0.4520 (mmp) REVERT: C 516 ASN cc_start: 0.7224 (t0) cc_final: 0.7009 (t0) REVERT: C 537 MET cc_start: 0.5838 (mmp) cc_final: 0.5495 (ttp) REVERT: D 343 MET cc_start: 0.2706 (mmt) cc_final: 0.2470 (mmt) outliers start: 50 outliers final: 43 residues processed: 204 average time/residue: 0.0974 time to fit residues: 29.7464 Evaluate side-chains 204 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 160 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 344 TRP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain C residue 462 PHE Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 524 ASP Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 504 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 50 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 145 optimal weight: 20.0000 chunk 40 optimal weight: 0.0770 chunk 80 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 122 optimal weight: 40.0000 overall best weight: 2.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN B 14 ASN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 598 ASN ** C 624 ASN ** 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 = 0.4835 r_free = 0.4835 target = 0.223431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.144685 restraints weight = 23720.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.144018 restraints weight = 13902.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.144443 restraints weight = 10242.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.143244 restraints weight = 8845.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 70)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.140373 restraints weight = 7525.208| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.6617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12563 Z= 0.140 Angle : 0.686 11.723 17023 Z= 0.338 Chirality : 0.047 0.358 1887 Planarity : 0.005 0.078 2202 Dihedral : 9.852 160.316 1730 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.48 % Allowed : 20.58 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.07 % 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 are not related in a simple way. whole: -0.15 (0.21), residues: 1531 helix: 0.86 (0.20), residues: 660 sheet: 0.59 (0.37), residues: 212 loop : -1.32 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 601 TYR 0.014 0.001 TYR B 208 PHE 0.059 0.002 PHE B 20 TRP 0.014 0.001 TRP B 344 HIS 0.010 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00312 (12563) covalent geometry : angle 0.68644 (17023) hydrogen bonds : bond 0.04177 ( 592) hydrogen bonds : angle 4.70707 ( 1851) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 164 time to evaluate : 0.389 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: A 36 MET cc_start: 0.7680 (ppp) cc_final: 0.7461 (ppp) REVERT: A 112 LYS cc_start: 0.8693 (pptt) cc_final: 0.8420 (tmmt) REVERT: A 203 MET cc_start: 0.8340 (mmm) cc_final: 0.8137 (mmm) REVERT: A 285 GLN cc_start: 0.4307 (mm-40) cc_final: 0.4004 (mm110) REVERT: A 300 ASN cc_start: 0.8788 (OUTLIER) cc_final: 0.8239 (m-40) REVERT: A 313 MET cc_start: 0.9024 (mpp) cc_final: 0.7110 (mpp) REVERT: A 413 MET cc_start: 0.5420 (mmm) cc_final: 0.4768 (mmm) REVERT: B 37 HIS cc_start: 0.7784 (m-70) cc_final: 0.7511 (m-70) REVERT: B 347 ASN cc_start: 0.7474 (p0) cc_final: 0.7032 (p0) REVERT: B 363 MET cc_start: 0.8464 (ttm) cc_final: 0.7928 (ttm) REVERT: C 412 PHE cc_start: 0.6378 (t80) cc_final: 0.5928 (t80) REVERT: C 500 MET cc_start: 0.6751 (mmp) cc_final: 0.6494 (mmp) REVERT: C 516 ASN cc_start: 0.7752 (t0) cc_final: 0.7407 (t0) REVERT: C 537 MET cc_start: 0.5819 (mmp) cc_final: 0.5456 (ttp) REVERT: C 597 LYS cc_start: 0.6557 (mmtt) cc_final: 0.4994 (mttt) outliers start: 47 outliers final: 41 residues processed: 196 average time/residue: 0.0993 time to fit residues: 29.4680 Evaluate side-chains 199 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 344 TRP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain C residue 462 PHE Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 524 ASP Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain D residue 504 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 50.0000 chunk 64 optimal weight: 2.9990 chunk 119 optimal weight: 30.0000 chunk 112 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 4 optimal weight: 0.4980 chunk 85 optimal weight: 40.0000 chunk 95 optimal weight: 30.0000 chunk 75 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 HIS C 598 ASN ** C 624 ASN ** 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 = 0.4813 r_free = 0.4813 target = 0.221921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.143815 restraints weight = 23790.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.142678 restraints weight = 15414.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.140574 restraints weight = 10179.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.140545 restraints weight = 8480.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.140608 restraints weight = 7674.127| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.6834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12563 Z= 0.172 Angle : 0.701 11.615 17023 Z= 0.350 Chirality : 0.049 0.412 1887 Planarity : 0.005 0.077 2202 Dihedral : 9.942 163.306 1730 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.33 % Allowed : 20.50 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.07 % 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 are not related in a simple way. whole: -0.17 (0.21), residues: 1531 helix: 0.85 (0.20), residues: 653 sheet: 0.77 (0.37), residues: 200 loop : -1.36 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 601 TYR 0.016 0.001 TYR A 83 PHE 0.054 0.002 PHE B 20 TRP 0.012 0.001 TRP B 344 HIS 0.012 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00390 (12563) covalent geometry : angle 0.70135 (17023) hydrogen bonds : bond 0.04332 ( 592) hydrogen bonds : angle 4.74048 ( 1851) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 158 time to evaluate : 0.490 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: A 35 GLN cc_start: 0.8658 (pm20) cc_final: 0.8429 (pm20) REVERT: A 36 MET cc_start: 0.7689 (ppp) cc_final: 0.7450 (ppp) REVERT: A 112 LYS cc_start: 0.8820 (pptt) cc_final: 0.8521 (tmmt) REVERT: A 285 GLN cc_start: 0.4286 (mm-40) cc_final: 0.3945 (mm110) REVERT: A 300 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8259 (m-40) REVERT: A 313 MET cc_start: 0.8985 (mpp) cc_final: 0.7064 (mpp) REVERT: A 377 MET cc_start: 0.8566 (tmm) cc_final: 0.8323 (ttp) REVERT: A 413 MET cc_start: 0.5832 (mmm) cc_final: 0.5234 (mmm) REVERT: B 37 HIS cc_start: 0.7854 (m-70) cc_final: 0.7560 (m-70) REVERT: B 363 MET cc_start: 0.8482 (ttm) cc_final: 0.7938 (ttm) REVERT: B 403 MET cc_start: 0.7124 (mmm) cc_final: 0.6148 (mtp) REVERT: C 412 PHE cc_start: 0.5969 (t80) cc_final: 0.5504 (t80) REVERT: C 500 MET cc_start: 0.6025 (mmp) cc_final: 0.5579 (mmp) REVERT: C 516 ASN cc_start: 0.7576 (t0) cc_final: 0.7246 (t0) REVERT: C 537 MET cc_start: 0.5811 (mmp) cc_final: 0.5429 (ttp) REVERT: C 593 MET cc_start: 0.7524 (ptt) cc_final: 0.7064 (tpt) REVERT: C 651 GLN cc_start: 0.6391 (tp40) cc_final: 0.6052 (tp40) outliers start: 45 outliers final: 44 residues processed: 190 average time/residue: 0.1045 time to fit residues: 30.0563 Evaluate side-chains 202 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 157 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 344 TRP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain C residue 462 PHE Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 524 ASP Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 598 ASN Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain D residue 504 MET Chi-restraints excluded: chain D residue 532 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 78 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 97 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 129 optimal weight: 50.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 598 ASN ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.219649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.144406 restraints weight = 23827.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.141980 restraints weight = 14501.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.142218 restraints weight = 9553.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.142454 restraints weight = 7993.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.142454 restraints weight = 7339.548| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.7082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12563 Z= 0.231 Angle : 0.743 13.084 17023 Z= 0.374 Chirality : 0.050 0.411 1887 Planarity : 0.005 0.071 2202 Dihedral : 10.216 168.664 1730 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.48 % Allowed : 20.58 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.07 % 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 are not related in a simple way. whole: -0.33 (0.21), residues: 1531 helix: 0.62 (0.20), residues: 660 sheet: 0.77 (0.37), residues: 203 loop : -1.39 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 601 TYR 0.018 0.002 TYR A 83 PHE 0.052 0.003 PHE B 20 TRP 0.011 0.002 TRP A 21 HIS 0.013 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00525 (12563) covalent geometry : angle 0.74288 (17023) hydrogen bonds : bond 0.04691 ( 592) hydrogen bonds : angle 4.80335 ( 1851) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3276.57 seconds wall clock time: 57 minutes 10.76 seconds (3430.76 seconds total)