Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 11 03:40:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5c_31722/08_2023/7v5c_31722_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5c_31722/08_2023/7v5c_31722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5c_31722/08_2023/7v5c_31722.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5c_31722/08_2023/7v5c_31722.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5c_31722/08_2023/7v5c_31722_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5c_31722/08_2023/7v5c_31722_trim_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 104 atoms to isotropic. 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 P 4 5.49 5 Mg 2 5.21 5 S 40 5.16 5 Be 2 3.05 5 C 5680 2.51 5 N 1522 2.21 5 O 1660 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 198": "OE1" <-> "OE2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "A GLU 380": "OE1" <-> "OE2" Residue "A GLU 401": "OE1" <-> "OE2" Residue "A GLU 473": "OE1" <-> "OE2" Residue "A GLU 606": "OE1" <-> "OE2" Residue "A GLU 672": "OE1" <-> "OE2" Residue "A GLU 701": "OE1" <-> "OE2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "B GLU 401": "OE1" <-> "OE2" Residue "B PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 672": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 8916 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4425 Classifications: {'peptide': 572} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 556} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 4427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4427 Classifications: {'peptide': 572} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 556} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.86, per 1000 atoms: 0.55 Number of scatterers: 8916 At special positions: 0 Unit cell: (85.49, 74.7, 135.29, 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 40 16.00 P 4 15.00 Mg 2 11.99 F 6 9.00 O 1660 8.00 N 1522 7.00 C 5680 6.00 Be 2 4.00 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.51 Conformation dependent library (CDL) restraints added in 1.4 seconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2116 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 6 sheets defined 53.6% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 170 through 177 removed outlier: 3.616A pdb=" N TYR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 214 Proline residue: A 202 - end of helix Processing helix chain 'A' and resid 217 through 220 No H-bonds generated for 'chain 'A' and resid 217 through 220' Processing helix chain 'A' and resid 222 through 265 removed outlier: 5.388A pdb=" N VAL A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER A 264 " --> pdb=" O CYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.560A pdb=" N ASP A 274 " --> pdb=" O THR A 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 270 through 274' Processing helix chain 'A' and resid 278 through 318 removed outlier: 3.795A pdb=" N ILE A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 339 removed outlier: 4.481A pdb=" N PHE A 329 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Proline residue: A 333 - end of helix removed outlier: 3.544A pdb=" N MET A 336 " --> pdb=" O PRO A 333 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL A 338 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 357 removed outlier: 3.981A pdb=" N GLU A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN A 354 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 400 removed outlier: 3.723A pdb=" N ARG A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLN A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL A 394 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A 396 " --> pdb=" O GLN A 392 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU A 397 " --> pdb=" O GLN A 393 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 431 removed outlier: 3.684A pdb=" N SER A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TRP A 410 " --> pdb=" O MET A 406 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY A 411 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR A 415 " --> pdb=" O GLY A 411 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 424 " --> pdb=" O GLN A 420 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 427 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 454 removed outlier: 3.907A pdb=" N PHE A 444 " --> pdb=" O ASN A 440 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 449 " --> pdb=" O ILE A 445 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 451 " --> pdb=" O TYR A 447 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASP A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 473 removed outlier: 3.788A pdb=" N LEU A 465 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET A 466 " --> pdb=" O TYR A 462 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY A 470 " --> pdb=" O MET A 466 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 478 No H-bonds generated for 'chain 'A' and resid 475 through 478' Processing helix chain 'A' and resid 542 through 544 No H-bonds generated for 'chain 'A' and resid 542 through 544' Processing helix chain 'A' and resid 566 through 568 No H-bonds generated for 'chain 'A' and resid 566 through 568' Processing helix chain 'A' and resid 571 through 577 removed outlier: 3.987A pdb=" N HIS A 575 " --> pdb=" O HIS A 571 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ARG A 576 " --> pdb=" O LYS A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 610 removed outlier: 3.697A pdb=" N VAL A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 removed outlier: 3.659A pdb=" N MET A 622 " --> pdb=" O HIS A 618 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLU A 623 " --> pdb=" O GLY A 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 618 through 623' Processing helix chain 'A' and resid 627 through 629 No H-bonds generated for 'chain 'A' and resid 627 through 629' Processing helix chain 'A' and resid 633 through 636 No H-bonds generated for 'chain 'A' and resid 633 through 636' Processing helix chain 'A' and resid 643 through 653 removed outlier: 3.681A pdb=" N ALA A 650 " --> pdb=" O ARG A 646 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG A 651 " --> pdb=" O VAL A 647 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA A 652 " --> pdb=" O ALA A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 669 No H-bonds generated for 'chain 'A' and resid 666 through 669' Processing helix chain 'A' and resid 674 through 681 removed outlier: 3.526A pdb=" N GLN A 678 " --> pdb=" O GLU A 674 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN A 679 " --> pdb=" O TYR A 675 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 681 " --> pdb=" O ILE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 701 Processing helix chain 'A' and resid 720 through 724 Processing helix chain 'A' and resid 734 through 737 Processing helix chain 'B' and resid 170 through 173 No H-bonds generated for 'chain 'B' and resid 170 through 173' Processing helix chain 'B' and resid 181 through 214 removed outlier: 4.089A pdb=" N ALA B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA B 194 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY B 197 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU B 201 " --> pdb=" O GLY B 197 " (cutoff:3.500A) Proline residue: B 202 - end of helix removed outlier: 3.548A pdb=" N ARG B 207 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 243 removed outlier: 5.003A pdb=" N VAL B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 231 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA B 238 " --> pdb=" O GLY B 234 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 265 removed outlier: 3.668A pdb=" N LEU B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER B 264 " --> pdb=" O CYS B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 273 No H-bonds generated for 'chain 'B' and resid 270 through 273' Processing helix chain 'B' and resid 280 through 286 removed outlier: 3.608A pdb=" N LEU B 285 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 302 removed outlier: 3.672A pdb=" N SER B 293 " --> pdb=" O THR B 289 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER B 297 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 319 removed outlier: 3.694A pdb=" N VAL B 310 " --> pdb=" O ASN B 306 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR B 311 " --> pdb=" O THR B 307 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET B 317 " --> pdb=" O VAL B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 341 removed outlier: 4.230A pdb=" N PHE B 329 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE B 332 " --> pdb=" O PHE B 329 " (cutoff:3.500A) Proline residue: B 333 - end of helix removed outlier: 4.131A pdb=" N MET B 336 " --> pdb=" O PRO B 333 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL B 338 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN B 340 " --> pdb=" O MET B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 358 removed outlier: 3.517A pdb=" N LYS B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ARG B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU B 352 " --> pdb=" O ARG B 348 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN B 354 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 395 removed outlier: 3.713A pdb=" N ARG B 389 " --> pdb=" O GLU B 385 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLN B 393 " --> pdb=" O ARG B 389 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL B 394 " --> pdb=" O LYS B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 433 removed outlier: 3.899A pdb=" N ALA B 403 " --> pdb=" O ARG B 399 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B 404 " --> pdb=" O LYS B 400 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR B 405 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TYR B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR B 415 " --> pdb=" O GLY B 411 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU B 424 " --> pdb=" O GLN B 420 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU B 430 " --> pdb=" O TYR B 426 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 431 " --> pdb=" O GLY B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 454 removed outlier: 4.548A pdb=" N PHE B 444 " --> pdb=" O ASN B 440 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE B 449 " --> pdb=" O ILE B 445 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL B 450 " --> pdb=" O ILE B 446 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 451 " --> pdb=" O TYR B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 473 removed outlier: 3.805A pdb=" N LEU B 465 " --> pdb=" O VAL B 461 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET B 466 " --> pdb=" O TYR B 462 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY B 470 " --> pdb=" O MET B 466 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 478 No H-bonds generated for 'chain 'B' and resid 475 through 478' Processing helix chain 'B' and resid 542 through 544 No H-bonds generated for 'chain 'B' and resid 542 through 544' Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 571 through 576 removed outlier: 4.022A pdb=" N HIS B 575 " --> pdb=" O HIS B 571 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG B 576 " --> pdb=" O LYS B 572 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 571 through 576' Processing helix chain 'B' and resid 605 through 610 removed outlier: 3.676A pdb=" N VAL B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 removed outlier: 3.677A pdb=" N MET B 622 " --> pdb=" O HIS B 618 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU B 623 " --> pdb=" O GLY B 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 618 through 623' Processing helix chain 'B' and resid 627 through 629 No H-bonds generated for 'chain 'B' and resid 627 through 629' Processing helix chain 'B' and resid 633 through 636 No H-bonds generated for 'chain 'B' and resid 633 through 636' Processing helix chain 'B' and resid 643 through 653 removed outlier: 3.669A pdb=" N ALA B 650 " --> pdb=" O ARG B 646 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 651 " --> pdb=" O VAL B 647 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA B 652 " --> pdb=" O ALA B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 666 No H-bonds generated for 'chain 'B' and resid 664 through 666' Processing helix chain 'B' and resid 674 through 682 removed outlier: 4.589A pdb=" N ILE B 681 " --> pdb=" O ILE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 724 Processing helix chain 'B' and resid 730 through 737 removed outlier: 3.627A pdb=" N GLN B 735 " --> pdb=" O ALA B 731 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ARG B 736 " --> pdb=" O LYS B 732 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLN B 737 " --> pdb=" O LEU B 733 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 523 through 525 removed outlier: 3.672A pdb=" N VAL A 500 " --> pdb=" O LEU A 525 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 531 through 533 Processing sheet with id= C, first strand: chain 'A' and resid 707 through 710 removed outlier: 6.362A pdb=" N ASP A 710 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL A 714 " --> pdb=" O ASP A 710 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 523 through 525 removed outlier: 3.710A pdb=" N VAL B 500 " --> pdb=" O LEU B 525 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 531 through 533 Processing sheet with id= F, first strand: chain 'B' and resid 707 through 709 299 hydrogen bonds defined for protein. 840 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: 2.49 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2667 1.33 - 1.45: 1243 1.45 - 1.57: 5079 1.57 - 1.69: 6 1.69 - 1.81: 78 Bond restraints: 9073 Sorted by residual: bond pdb=" BE BEF B 802 " pdb=" F3 BEF B 802 " ideal model delta sigma weight residual 1.476 1.764 -0.288 2.00e-02 2.50e+03 2.07e+02 bond pdb=" BE BEF A 802 " pdb=" F1 BEF A 802 " ideal model delta sigma weight residual 1.476 1.763 -0.287 2.00e-02 2.50e+03 2.06e+02 bond pdb=" BE BEF B 802 " pdb=" F1 BEF B 802 " ideal model delta sigma weight residual 1.476 1.763 -0.287 2.00e-02 2.50e+03 2.06e+02 bond pdb=" BE BEF A 802 " pdb=" F3 BEF A 802 " ideal model delta sigma weight residual 1.476 1.762 -0.286 2.00e-02 2.50e+03 2.05e+02 bond pdb=" BE BEF B 802 " pdb=" F2 BEF B 802 " ideal model delta sigma weight residual 1.476 1.761 -0.285 2.00e-02 2.50e+03 2.03e+02 ... (remaining 9068 not shown) Histogram of bond angle deviations from ideal: 100.19 - 107.45: 261 107.45 - 114.70: 5495 114.70 - 121.96: 4888 121.96 - 129.22: 1620 129.22 - 136.47: 36 Bond angle restraints: 12300 Sorted by residual: angle pdb=" N VAL B 647 " pdb=" CA VAL B 647 " pdb=" C VAL B 647 " ideal model delta sigma weight residual 113.39 108.18 5.21 1.47e+00 4.63e-01 1.26e+01 angle pdb=" CA GLN B 435 " pdb=" C GLN B 435 " pdb=" O GLN B 435 " ideal model delta sigma weight residual 121.81 117.82 3.99 1.18e+00 7.18e-01 1.14e+01 angle pdb=" C HIS B 429 " pdb=" N LEU B 430 " pdb=" CA LEU B 430 " ideal model delta sigma weight residual 120.58 115.23 5.35 1.71e+00 3.42e-01 9.79e+00 angle pdb=" N LEU A 729 " pdb=" CA LEU A 729 " pdb=" CB LEU A 729 " ideal model delta sigma weight residual 114.17 110.66 3.51 1.14e+00 7.69e-01 9.46e+00 angle pdb=" C GLN B 435 " pdb=" N MET B 436 " pdb=" CA MET B 436 " ideal model delta sigma weight residual 120.97 126.25 -5.28 1.82e+00 3.02e-01 8.41e+00 ... (remaining 12295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.79: 5273 28.79 - 57.57: 118 57.57 - 86.36: 11 86.36 - 115.14: 1 115.14 - 143.93: 4 Dihedral angle restraints: 5407 sinusoidal: 2107 harmonic: 3300 Sorted by residual: dihedral pdb=" O2A ADP B 801 " pdb=" O3A ADP B 801 " pdb=" PA ADP B 801 " pdb=" PB ADP B 801 " ideal model delta sinusoidal sigma weight residual -60.00 83.93 -143.93 1 2.00e+01 2.50e-03 4.34e+01 dihedral pdb=" O2A ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PA ADP A 801 " pdb=" PB ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 81.55 -141.55 1 2.00e+01 2.50e-03 4.28e+01 dihedral pdb=" O1B ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PB ADP A 801 " pdb=" PA ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 76.66 -136.66 1 2.00e+01 2.50e-03 4.15e+01 ... (remaining 5404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1303 0.061 - 0.121: 138 0.121 - 0.181: 4 0.181 - 0.242: 0 0.242 - 0.302: 1 Chirality restraints: 1446 Sorted by residual: chirality pdb=" CA GLN B 435 " pdb=" N GLN B 435 " pdb=" C GLN B 435 " pdb=" CB GLN B 435 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA ILE B 693 " pdb=" N ILE B 693 " pdb=" C ILE B 693 " pdb=" CB ILE B 693 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA ILE B 578 " pdb=" N ILE B 578 " pdb=" C ILE B 578 " pdb=" CB ILE B 578 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 1443 not shown) Planarity restraints: 1552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 435 " 0.017 2.00e-02 2.50e+03 3.47e-02 1.21e+01 pdb=" C GLN B 435 " -0.060 2.00e-02 2.50e+03 pdb=" O GLN B 435 " 0.023 2.00e-02 2.50e+03 pdb=" N MET B 436 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 434 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.26e+00 pdb=" C GLY B 434 " -0.047 2.00e-02 2.50e+03 pdb=" O GLY B 434 " 0.017 2.00e-02 2.50e+03 pdb=" N GLN B 435 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 430 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.94e+00 pdb=" C LEU B 430 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU B 430 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL B 431 " 0.014 2.00e-02 2.50e+03 ... (remaining 1549 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 28 2.39 - 3.02: 6272 3.02 - 3.65: 11950 3.65 - 4.27: 19563 4.27 - 4.90: 32339 Nonbonded interactions: 70152 Sorted by model distance: nonbonded pdb=" OG SER A 542 " pdb="MG MG A 803 " model vdw 1.766 2.170 nonbonded pdb=" F3 BEF B 802 " pdb="MG MG B 803 " model vdw 1.779 2.120 nonbonded pdb=" F3 BEF A 802 " pdb="MG MG A 803 " model vdw 1.795 2.120 nonbonded pdb=" OG SER B 542 " pdb="MG MG B 803 " model vdw 1.833 2.170 nonbonded pdb=" N GLU B 269 " pdb=" OE1 GLU B 269 " model vdw 2.137 2.520 ... (remaining 70147 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 168 through 197 or (resid 198 and (name N or name CA or na \ me C or name O or name CB )) or resid 199 through 739 or resid 801 through 803)) \ selection = (chain 'B' and (resid 168 through 220 or (resid 221 and (name N or name CA or na \ me C or name O or name CB )) or resid 222 through 739 or resid 801 through 803)) \ } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 4.460 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.000 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 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 : 0.009 0.288 9073 Z= 0.633 Angle : 0.633 7.987 12300 Z= 0.372 Chirality : 0.039 0.302 1446 Planarity : 0.003 0.040 1552 Dihedral : 13.829 143.925 3291 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 28.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.06 (0.18), residues: 1140 helix: -4.03 (0.14), residues: 648 sheet: -4.14 (0.51), residues: 72 loop : -3.65 (0.23), residues: 420 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.053 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2066 time to fit residues: 48.0191 Evaluate side-chains 130 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.013 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN A 354 GLN A 514 HIS A 595 ASN A 618 HIS B 276 ASN B 514 HIS B 595 ASN B 618 HIS B 678 GLN B 679 GLN B 737 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9073 Z= 0.198 Angle : 0.634 8.180 12300 Z= 0.317 Chirality : 0.041 0.140 1446 Planarity : 0.004 0.038 1552 Dihedral : 8.947 133.789 1264 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 1.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.50 (0.21), residues: 1140 helix: -2.81 (0.17), residues: 660 sheet: -3.76 (0.51), residues: 72 loop : -2.80 (0.27), residues: 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 160 time to evaluate : 1.072 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 13 residues processed: 170 average time/residue: 0.1845 time to fit residues: 45.2900 Evaluate side-chains 149 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 136 time to evaluate : 0.919 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0881 time to fit residues: 3.3478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN A 306 ASN A 595 ASN A 679 GLN B 299 ASN B 595 ASN B 678 GLN B 726 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.024 9073 Z= 0.240 Angle : 0.599 8.531 12300 Z= 0.296 Chirality : 0.041 0.148 1446 Planarity : 0.003 0.037 1552 Dihedral : 8.402 125.447 1264 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.23), residues: 1140 helix: -1.91 (0.19), residues: 676 sheet: -3.31 (0.53), residues: 72 loop : -2.56 (0.28), residues: 392 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 145 time to evaluate : 1.088 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 152 average time/residue: 0.1894 time to fit residues: 41.7434 Evaluate side-chains 140 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 133 time to evaluate : 0.997 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0873 time to fit residues: 2.4073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 0.1980 chunk 110 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 9073 Z= 0.196 Angle : 0.573 8.729 12300 Z= 0.282 Chirality : 0.040 0.135 1446 Planarity : 0.003 0.036 1552 Dihedral : 8.226 125.637 1264 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.24), residues: 1140 helix: -1.34 (0.20), residues: 664 sheet: -2.93 (0.57), residues: 72 loop : -2.29 (0.28), residues: 404 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 0.961 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 156 average time/residue: 0.2045 time to fit residues: 45.4716 Evaluate side-chains 150 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 138 time to evaluate : 0.993 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0936 time to fit residues: 3.7245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.7980 chunk 62 optimal weight: 0.4980 chunk 1 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN A 595 ASN A 616 ASN B 298 GLN B 595 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.028 9073 Z= 0.331 Angle : 0.625 8.508 12300 Z= 0.306 Chirality : 0.043 0.228 1446 Planarity : 0.004 0.041 1552 Dihedral : 8.325 126.389 1264 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.24), residues: 1140 helix: -1.18 (0.20), residues: 678 sheet: -2.82 (0.57), residues: 72 loop : -2.29 (0.30), residues: 390 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 138 time to evaluate : 1.082 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 151 average time/residue: 0.1853 time to fit residues: 40.9962 Evaluate side-chains 147 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0967 time to fit residues: 3.6766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 0.0770 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 91 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 ASN B 595 ASN B 645 GLN B 678 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 9073 Z= 0.152 Angle : 0.547 8.128 12300 Z= 0.268 Chirality : 0.039 0.136 1446 Planarity : 0.003 0.035 1552 Dihedral : 7.978 124.237 1264 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.25), residues: 1140 helix: -0.57 (0.21), residues: 642 sheet: -2.48 (0.59), residues: 72 loop : -1.76 (0.28), residues: 426 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 148 time to evaluate : 1.053 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 157 average time/residue: 0.1816 time to fit residues: 41.5840 Evaluate side-chains 139 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 134 time to evaluate : 1.044 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0854 time to fit residues: 2.0914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 62 optimal weight: 0.3980 chunk 80 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 679 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 9073 Z= 0.185 Angle : 0.574 9.061 12300 Z= 0.277 Chirality : 0.041 0.406 1446 Planarity : 0.003 0.034 1552 Dihedral : 7.935 126.310 1264 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.25), residues: 1140 helix: -0.46 (0.21), residues: 668 sheet: -2.23 (0.61), residues: 72 loop : -1.76 (0.29), residues: 400 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 150 time to evaluate : 0.920 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 155 average time/residue: 0.1829 time to fit residues: 41.3462 Evaluate side-chains 145 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 136 time to evaluate : 1.131 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0891 time to fit residues: 2.8586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.0570 chunk 65 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 0.1980 overall best weight: 1.2504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 595 ASN B 678 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9073 Z= 0.213 Angle : 0.578 8.995 12300 Z= 0.282 Chirality : 0.041 0.267 1446 Planarity : 0.003 0.030 1552 Dihedral : 7.942 127.021 1264 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.25), residues: 1140 helix: -0.32 (0.21), residues: 660 sheet: -2.07 (0.61), residues: 72 loop : -1.63 (0.29), residues: 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 141 time to evaluate : 0.935 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 146 average time/residue: 0.1845 time to fit residues: 38.6094 Evaluate side-chains 143 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 138 time to evaluate : 0.915 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0885 time to fit residues: 2.0583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.0870 chunk 102 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 61 optimal weight: 0.0170 chunk 44 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 595 ASN B 678 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 9073 Z= 0.140 Angle : 0.560 9.092 12300 Z= 0.270 Chirality : 0.039 0.198 1446 Planarity : 0.003 0.028 1552 Dihedral : 7.685 124.577 1264 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.25), residues: 1140 helix: 0.06 (0.22), residues: 646 sheet: -1.74 (0.63), residues: 72 loop : -1.37 (0.28), residues: 422 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 152 time to evaluate : 0.927 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 156 average time/residue: 0.1926 time to fit residues: 43.3135 Evaluate side-chains 143 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 139 time to evaluate : 0.960 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0839 time to fit residues: 2.0342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 113 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 96 optimal weight: 0.0170 chunk 27 optimal weight: 10.0000 overall best weight: 1.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN A 595 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 678 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 9073 Z= 0.233 Angle : 0.598 8.717 12300 Z= 0.289 Chirality : 0.042 0.188 1446 Planarity : 0.003 0.031 1552 Dihedral : 7.858 128.858 1264 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.25), residues: 1140 helix: 0.15 (0.22), residues: 648 sheet: -1.60 (0.64), residues: 72 loop : -1.36 (0.28), residues: 420 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 142 time to evaluate : 1.110 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 144 average time/residue: 0.1972 time to fit residues: 40.5808 Evaluate side-chains 138 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 135 time to evaluate : 0.950 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1019 time to fit residues: 1.8599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 11 optimal weight: 0.2980 chunk 16 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 5 optimal weight: 0.0470 chunk 65 optimal weight: 1.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 678 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.131742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.098192 restraints weight = 11957.685| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.52 r_work: 0.3083 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 9073 Z= 0.156 Angle : 0.566 8.871 12300 Z= 0.272 Chirality : 0.040 0.162 1446 Planarity : 0.003 0.030 1552 Dihedral : 7.656 126.023 1264 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.25), residues: 1140 helix: 0.38 (0.22), residues: 648 sheet: -1.43 (0.65), residues: 72 loop : -1.24 (0.29), residues: 420 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1979.28 seconds wall clock time: 36 minutes 37.21 seconds (2197.21 seconds total)