Starting phenix.real_space_refine on Tue Mar 3 23:08:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v5c_31722/03_2026/7v5c_31722_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v5c_31722/03_2026/7v5c_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 { model { file = "/net/cci-nas-00/data/ceres_data/7v5c_31722/03_2026/7v5c_31722_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v5c_31722/03_2026/7v5c_31722_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v5c_31722/03_2026/7v5c_31722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v5c_31722/03_2026/7v5c_31722.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.57, per 1000 atoms: 0.29 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 - 3.00 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: 0.89 Conformation dependent library (CDL) restraints added in 447.4 milliseconds 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... Secondary structure from input PDB file: 56 helices and 8 sheets defined 59.9% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 169 through 176 removed outlier: 3.633A pdb=" N LEU A 173 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 215 Proline residue: A 202 - end of helix removed outlier: 4.164A pdb=" N GLN A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.832A pdb=" N GLN A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 266 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 269 through 274 removed outlier: 4.021A pdb=" N PHE A 273 " --> pdb=" O GLU A 269 " (cutoff:3.500A) 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 269 through 274' Processing helix chain 'A' and resid 277 through 319 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 329 Processing helix chain 'A' and resid 331 through 339 removed outlier: 3.517A pdb=" N SER A 339 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 358 removed outlier: 3.943A pdb=" N ARG A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) 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 384 through 401 removed outlier: 3.638A pdb=" N LEU A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) 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 401 through 432 removed outlier: 3.854A pdb=" N TYR A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) 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 436 through 455 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 460 through 472 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) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.597A pdb=" N ILE A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 545 Processing helix chain 'A' and resid 567 through 569 No H-bonds generated for 'chain 'A' and resid 567 through 569' Processing helix chain 'A' and resid 570 through 575 removed outlier: 3.987A pdb=" N HIS A 575 " --> pdb=" O HIS A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 611 removed outlier: 3.595A pdb=" N VAL A 608 " --> pdb=" O PRO A 604 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 622 removed outlier: 3.659A pdb=" N MET A 622 " --> pdb=" O HIS A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 630 Processing helix chain 'A' and resid 632 through 637 removed outlier: 3.614A pdb=" N GLY A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 654 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 665 through 670 removed outlier: 4.541A pdb=" N LEU A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP A 670 " --> pdb=" O THR A 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 670' Processing helix chain 'A' and resid 673 through 682 removed outlier: 3.829A pdb=" N ILE A 677 " --> pdb=" O SER A 673 " (cutoff:3.500A) 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 696 through 702 removed outlier: 4.299A pdb=" N VAL A 700 " --> pdb=" O ARG A 696 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ARG A 702 " --> pdb=" O SER A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 725 Processing helix chain 'A' and resid 733 through 738 removed outlier: 3.827A pdb=" N ARG A 736 " --> pdb=" O LEU A 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 174 removed outlier: 3.734A pdb=" N LEU B 173 " --> pdb=" O THR B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 215 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) removed outlier: 3.768A pdb=" N GLN B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 244 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 248 through 266 removed outlier: 3.937A pdb=" N ARG B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) 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 269 through 274 removed outlier: 4.129A pdb=" N PHE B 273 " --> pdb=" O GLU B 269 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP B 274 " --> pdb=" O THR B 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 269 through 274' Processing helix chain 'B' and resid 279 through 287 removed outlier: 3.608A pdb=" N LEU B 285 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 303 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) removed outlier: 3.668A pdb=" N PHE B 303 " --> pdb=" O ASN B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 315 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) Processing helix chain 'B' and resid 315 through 320 Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 331 through 342 removed outlier: 3.667A pdb=" N MET B 337 " --> pdb=" O PRO B 333 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 341 " --> pdb=" O MET B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 359 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 384 through 396 removed outlier: 3.661A pdb=" N LEU B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) 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) removed outlier: 3.516A pdb=" N LYS B 396 " --> pdb=" O GLN B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 434 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 438 through 455 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 460 through 472 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) Processing helix chain 'B' and resid 474 through 479 removed outlier: 3.620A pdb=" N ILE B 479 " --> pdb=" O VAL B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 545 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 570 through 575 removed outlier: 4.022A pdb=" N HIS B 575 " --> pdb=" O HIS B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 611 removed outlier: 3.583A pdb=" N VAL B 608 " --> pdb=" O PRO B 604 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 622 removed outlier: 3.677A pdb=" N MET B 622 " --> pdb=" O HIS B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 630 Processing helix chain 'B' and resid 632 through 637 removed outlier: 3.617A pdb=" N GLY B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 654 removed outlier: 3.730A pdb=" N ARG B 646 " --> pdb=" O GLY B 642 " (cutoff:3.500A) 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 673 through 683 removed outlier: 3.910A pdb=" N ILE B 677 " --> pdb=" O SER B 673 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE B 681 " --> pdb=" O ILE B 677 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY B 683 " --> pdb=" O GLN B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 725 Processing helix chain 'B' and resid 729 through 734 removed outlier: 3.710A pdb=" N LEU B 733 " --> pdb=" O LEU B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 738 Processing sheet with id=AA1, first strand: chain 'A' and resid 518 through 525 removed outlier: 6.745A pdb=" N GLN A 519 " --> pdb=" O THR A 506 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR A 506 " --> pdb=" O GLN A 519 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N VAL A 521 " --> pdb=" O ASN A 504 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 500 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS A 564 " --> pdb=" O LEU A 561 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 531 through 533 Processing sheet with id=AA3, first strand: chain 'A' and resid 578 through 581 Processing sheet with id=AA4, first strand: chain 'A' and resid 707 through 710 removed outlier: 6.614A pdb=" N VAL A 708 " --> pdb=" O VAL A 715 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 519 through 524 removed outlier: 6.703A pdb=" N GLN B 519 " --> pdb=" O THR B 506 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR B 506 " --> pdb=" O GLN B 519 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N VAL B 521 " --> pdb=" O ASN B 504 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS B 564 " --> pdb=" O LEU B 561 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 531 through 533 Processing sheet with id=AA7, first strand: chain 'B' and resid 578 through 581 Processing sheet with id=AA8, first strand: chain 'B' and resid 707 through 709 removed outlier: 6.626A pdb=" N VAL B 708 " --> pdb=" O VAL B 715 " (cutoff:3.500A) 359 hydrogen bonds defined for protein. 1035 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: 1.40 Time building geometry restraints manager: 1.16 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=" F3 BEF B 802 " pdb="BE 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=" F1 BEF A 802 " pdb="BE 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=" F1 BEF B 802 " pdb="BE 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=" F3 BEF A 802 " pdb="BE 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=" F2 BEF B 802 " pdb="BE 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: 0.00 - 1.60: 11976 1.60 - 3.20: 273 3.20 - 4.79: 31 4.79 - 6.39: 15 6.39 - 7.99: 5 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: 6258 3.02 - 3.65: 11882 3.65 - 4.27: 19441 4.27 - 4.90: 32303 Nonbonded interactions: 69912 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 3.120 ... (remaining 69907 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 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 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 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.860 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.270 ------------------------------------------------------------------------------- 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= 0.428 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 % Allowed : 4.24 % Favored : 95.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 242 TYR 0.017 0.001 TYR A 675 PHE 0.010 0.001 PHE A 246 TRP 0.002 0.000 TRP B 322 HIS 0.002 0.000 HIS B 571 Details of bonding type rmsd covalent geometry : bond 0.00867 ( 9073) covalent geometry : angle 0.63299 (12300) hydrogen bonds : bond 0.25817 ( 359) hydrogen bonds : angle 10.90254 ( 1035) *********************** 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 to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 189 PHE cc_start: 0.8387 (t80) cc_final: 0.8150 (t80) REVERT: A 420 GLN cc_start: 0.8886 (tt0) cc_final: 0.8682 (tt0) REVERT: A 423 ILE cc_start: 0.9110 (tt) cc_final: 0.8847 (tt) REVERT: A 425 TYR cc_start: 0.7835 (m-10) cc_final: 0.7196 (t80) REVERT: A 455 MET cc_start: 0.8082 (tmm) cc_final: 0.7848 (tmm) REVERT: A 635 LYS cc_start: 0.9134 (mttt) cc_final: 0.8922 (mttp) REVERT: A 702 ARG cc_start: 0.8621 (mtm180) cc_final: 0.8022 (ptm-80) REVERT: A 711 LYS cc_start: 0.8766 (mttt) cc_final: 0.8492 (mttp) REVERT: B 336 MET cc_start: 0.8096 (mmm) cc_final: 0.7880 (mmm) REVERT: B 346 TYR cc_start: 0.7998 (t80) cc_final: 0.7451 (t80) REVERT: B 381 GLU cc_start: 0.8542 (pp20) cc_final: 0.8157 (tm-30) REVERT: B 503 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7834 (tt0) REVERT: B 564 LYS cc_start: 0.8386 (mptt) cc_final: 0.8151 (mmtp) REVERT: B 674 GLU cc_start: 0.7955 (mm-30) cc_final: 0.6915 (mm-30) REVERT: B 678 GLN cc_start: 0.7779 (mt0) cc_final: 0.7392 (mt0) REVERT: B 702 ARG cc_start: 0.8563 (mtm180) cc_final: 0.7802 (ttp-170) REVERT: B 711 LYS cc_start: 0.8783 (mttt) cc_final: 0.8500 (mttp) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.0947 time to fit residues: 22.3195 Evaluate side-chains 134 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.0070 chunk 100 optimal weight: 3.9990 overall best weight: 2.1804 ------------------------------------------------------------------------------- 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 354 GLN A 514 HIS A 595 ASN A 618 HIS B 276 ASN B 299 ASN B 354 GLN B 514 HIS B 595 ASN B 618 HIS B 679 GLN B 737 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.121950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.088728 restraints weight = 12467.125| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.62 r_work: 0.2937 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9073 Z= 0.217 Angle : 0.686 7.769 12300 Z= 0.347 Chirality : 0.043 0.143 1446 Planarity : 0.005 0.043 1552 Dihedral : 9.088 137.492 1264 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.17 % Allowed : 10.56 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.62 (0.21), residues: 1140 helix: -2.84 (0.17), residues: 684 sheet: -3.74 (0.52), residues: 72 loop : -2.96 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 242 TYR 0.019 0.002 TYR A 675 PHE 0.019 0.002 PHE A 332 TRP 0.010 0.001 TRP B 322 HIS 0.002 0.001 HIS B 571 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 9073) covalent geometry : angle 0.68612 (12300) hydrogen bonds : bond 0.06559 ( 359) hydrogen bonds : angle 5.76595 ( 1035) *********************** 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 175 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 346 TYR cc_start: 0.7607 (t80) cc_final: 0.7361 (t80) REVERT: A 425 TYR cc_start: 0.7648 (m-10) cc_final: 0.7062 (t80) REVERT: A 455 MET cc_start: 0.8092 (tmm) cc_final: 0.7851 (tmm) REVERT: A 675 TYR cc_start: 0.7573 (t80) cc_final: 0.7318 (t80) REVERT: A 687 ARG cc_start: 0.8359 (mmp-170) cc_final: 0.8105 (mmp-170) REVERT: A 702 ARG cc_start: 0.8735 (mtm180) cc_final: 0.8023 (ptm-80) REVERT: A 711 LYS cc_start: 0.8909 (mttt) cc_final: 0.8678 (mttp) REVERT: B 323 GLN cc_start: 0.7591 (mp10) cc_final: 0.7382 (mp10) REVERT: B 346 TYR cc_start: 0.8058 (t80) cc_final: 0.7215 (t80) REVERT: B 381 GLU cc_start: 0.8803 (pp20) cc_final: 0.8355 (tm-30) REVERT: B 687 ARG cc_start: 0.7961 (mmp-170) cc_final: 0.7678 (mmp-170) REVERT: B 702 ARG cc_start: 0.8697 (mtm180) cc_final: 0.7714 (ttp-170) REVERT: B 711 LYS cc_start: 0.8943 (mttt) cc_final: 0.8707 (mttp) outliers start: 21 outliers final: 18 residues processed: 167 average time/residue: 0.0867 time to fit residues: 20.9274 Evaluate side-chains 148 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 595 ASN Chi-restraints excluded: chain B residue 666 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 62 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN A 504 ASN A 595 ASN A 679 GLN B 298 GLN B 504 ASN B 595 ASN B 678 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.120566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.087316 restraints weight = 12493.448| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.61 r_work: 0.2905 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 9073 Z= 0.259 Angle : 0.689 8.182 12300 Z= 0.345 Chirality : 0.044 0.158 1446 Planarity : 0.004 0.047 1552 Dihedral : 8.937 136.614 1264 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.52 % Allowed : 13.66 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.79 (0.23), residues: 1140 helix: -2.14 (0.19), residues: 672 sheet: -3.46 (0.53), residues: 72 loop : -2.68 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 242 TYR 0.015 0.002 TYR B 342 PHE 0.015 0.001 PHE A 387 TRP 0.015 0.002 TRP B 322 HIS 0.003 0.001 HIS A 682 Details of bonding type rmsd covalent geometry : bond 0.00609 ( 9073) covalent geometry : angle 0.68943 (12300) hydrogen bonds : bond 0.06308 ( 359) hydrogen bonds : angle 5.18957 ( 1035) *********************** 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 178 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 346 TYR cc_start: 0.7951 (t80) cc_final: 0.7335 (t80) REVERT: A 425 TYR cc_start: 0.7538 (m-10) cc_final: 0.7129 (t80) REVERT: A 455 MET cc_start: 0.8064 (tmm) cc_final: 0.7836 (tmm) REVERT: A 687 ARG cc_start: 0.8333 (mmp-170) cc_final: 0.7976 (mmp-170) REVERT: A 702 ARG cc_start: 0.8703 (mtm180) cc_final: 0.7946 (ptm-80) REVERT: A 711 LYS cc_start: 0.8931 (mttt) cc_final: 0.8698 (mttp) REVERT: B 336 MET cc_start: 0.8155 (mmm) cc_final: 0.7877 (mmm) REVERT: B 346 TYR cc_start: 0.8168 (t80) cc_final: 0.7261 (t80) REVERT: B 381 GLU cc_start: 0.8794 (pp20) cc_final: 0.8362 (tm-30) REVERT: B 674 GLU cc_start: 0.7760 (mm-30) cc_final: 0.6546 (mm-30) REVERT: B 678 GLN cc_start: 0.7739 (mt0) cc_final: 0.7358 (mt0) REVERT: B 702 ARG cc_start: 0.8755 (mtm180) cc_final: 0.7792 (ttp-170) REVERT: B 711 LYS cc_start: 0.8933 (mttt) cc_final: 0.8698 (mttp) outliers start: 34 outliers final: 27 residues processed: 168 average time/residue: 0.0790 time to fit residues: 19.5316 Evaluate side-chains 162 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 674 GLU Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 666 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 67 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 51 optimal weight: 0.0980 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 595 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.123989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.090148 restraints weight = 12363.084| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.66 r_work: 0.2953 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9073 Z= 0.153 Angle : 0.604 7.861 12300 Z= 0.302 Chirality : 0.041 0.158 1446 Planarity : 0.004 0.044 1552 Dihedral : 8.643 133.451 1264 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.42 % Allowed : 15.84 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.24), residues: 1140 helix: -1.66 (0.20), residues: 674 sheet: -3.23 (0.55), residues: 72 loop : -2.25 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 305 TYR 0.010 0.001 TYR B 408 PHE 0.011 0.001 PHE A 387 TRP 0.016 0.002 TRP B 322 HIS 0.002 0.000 HIS A 682 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9073) covalent geometry : angle 0.60397 (12300) hydrogen bonds : bond 0.05435 ( 359) hydrogen bonds : angle 4.69481 ( 1035) *********************** 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 177 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 TYR cc_start: 0.7950 (t80) cc_final: 0.7224 (t80) REVERT: A 371 MET cc_start: 0.9283 (tpt) cc_final: 0.8904 (tpt) REVERT: A 425 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.7150 (t80) REVERT: A 455 MET cc_start: 0.8044 (tmm) cc_final: 0.7570 (tmm) REVERT: A 487 HIS cc_start: 0.9016 (OUTLIER) cc_final: 0.8463 (p90) REVERT: A 675 TYR cc_start: 0.7803 (t80) cc_final: 0.7548 (t80) REVERT: A 687 ARG cc_start: 0.8346 (mmp-170) cc_final: 0.8135 (mmp-170) REVERT: A 702 ARG cc_start: 0.8658 (mtm180) cc_final: 0.7934 (ptm-80) REVERT: A 711 LYS cc_start: 0.8913 (mttt) cc_final: 0.8682 (mttp) REVERT: B 260 CYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8652 (m) REVERT: B 346 TYR cc_start: 0.8058 (t80) cc_final: 0.7160 (t80) REVERT: B 371 MET cc_start: 0.9297 (tpt) cc_final: 0.8895 (tpt) REVERT: B 455 MET cc_start: 0.7745 (tmm) cc_final: 0.7459 (tmm) REVERT: B 456 GLU cc_start: 0.8033 (tp30) cc_final: 0.7708 (tp30) REVERT: B 702 ARG cc_start: 0.8755 (mtm180) cc_final: 0.7729 (ttp-170) REVERT: B 711 LYS cc_start: 0.8919 (mttt) cc_final: 0.8677 (mttp) outliers start: 33 outliers final: 24 residues processed: 166 average time/residue: 0.0862 time to fit residues: 20.7835 Evaluate side-chains 162 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 674 GLU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 654 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 107 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 15 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 679 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.127079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.093721 restraints weight = 12132.457| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.58 r_work: 0.3008 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9073 Z= 0.123 Angle : 0.581 8.749 12300 Z= 0.286 Chirality : 0.040 0.190 1446 Planarity : 0.003 0.039 1552 Dihedral : 8.313 132.637 1264 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.31 % Allowed : 17.08 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.24), residues: 1140 helix: -1.18 (0.20), residues: 668 sheet: -2.98 (0.57), residues: 72 loop : -1.96 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 305 TYR 0.009 0.001 TYR A 426 PHE 0.027 0.001 PHE B 189 TRP 0.017 0.002 TRP B 322 HIS 0.003 0.000 HIS B 571 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9073) covalent geometry : angle 0.58137 (12300) hydrogen bonds : bond 0.04721 ( 359) hydrogen bonds : angle 4.24267 ( 1035) *********************** 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 187 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 346 TYR cc_start: 0.7988 (t80) cc_final: 0.7166 (t80) REVERT: A 371 MET cc_start: 0.9212 (tpt) cc_final: 0.8926 (tpt) REVERT: A 425 TYR cc_start: 0.7312 (OUTLIER) cc_final: 0.7019 (t80) REVERT: A 487 HIS cc_start: 0.9021 (OUTLIER) cc_final: 0.8451 (p90) REVERT: A 675 TYR cc_start: 0.7749 (t80) cc_final: 0.7462 (t80) REVERT: A 687 ARG cc_start: 0.8353 (mmp-170) cc_final: 0.8112 (mmp-170) REVERT: A 702 ARG cc_start: 0.8701 (mtm180) cc_final: 0.7946 (ptm-80) REVERT: A 711 LYS cc_start: 0.8848 (mttt) cc_final: 0.8623 (mttp) REVERT: B 203 TYR cc_start: 0.8544 (t80) cc_final: 0.8321 (t80) REVERT: B 260 CYS cc_start: 0.9057 (t) cc_final: 0.8651 (m) REVERT: B 346 TYR cc_start: 0.7984 (OUTLIER) cc_final: 0.7050 (t80) REVERT: B 371 MET cc_start: 0.9199 (tpt) cc_final: 0.8861 (tpt) REVERT: B 381 GLU cc_start: 0.8757 (pp20) cc_final: 0.8310 (tm-30) REVERT: B 447 TYR cc_start: 0.7495 (t80) cc_final: 0.7257 (t80) REVERT: B 455 MET cc_start: 0.7659 (tmm) cc_final: 0.7361 (tmm) REVERT: B 456 GLU cc_start: 0.7939 (tp30) cc_final: 0.7500 (tp30) REVERT: B 674 GLU cc_start: 0.7559 (mm-30) cc_final: 0.6646 (mm-30) REVERT: B 702 ARG cc_start: 0.8751 (mtm180) cc_final: 0.7726 (ppt170) REVERT: B 711 LYS cc_start: 0.8917 (mttt) cc_final: 0.8679 (mttp) outliers start: 32 outliers final: 18 residues processed: 175 average time/residue: 0.0807 time to fit residues: 20.7947 Evaluate side-chains 163 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 674 GLU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 346 TYR Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 595 ASN Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 719 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 94 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN A 595 ASN B 595 ASN B 678 GLN B 679 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.124686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.091032 restraints weight = 12292.415| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.59 r_work: 0.2973 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9073 Z= 0.177 Angle : 0.614 8.428 12300 Z= 0.301 Chirality : 0.042 0.235 1446 Planarity : 0.003 0.039 1552 Dihedral : 8.326 136.215 1264 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.55 % Allowed : 17.18 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.25), residues: 1140 helix: -1.00 (0.20), residues: 670 sheet: -2.88 (0.58), residues: 72 loop : -1.93 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 305 TYR 0.010 0.001 TYR B 345 PHE 0.019 0.001 PHE B 189 TRP 0.013 0.001 TRP B 322 HIS 0.002 0.000 HIS A 682 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 9073) covalent geometry : angle 0.61431 (12300) hydrogen bonds : bond 0.05089 ( 359) hydrogen bonds : angle 4.22815 ( 1035) *********************** 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 189 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 145 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 346 TYR cc_start: 0.8093 (t80) cc_final: 0.7210 (t80) REVERT: A 371 MET cc_start: 0.9203 (tpt) cc_final: 0.8808 (tpt) REVERT: A 425 TYR cc_start: 0.7360 (OUTLIER) cc_final: 0.7084 (t80) REVERT: A 455 MET cc_start: 0.7630 (tmm) cc_final: 0.7429 (tmm) REVERT: A 456 GLU cc_start: 0.8181 (tp30) cc_final: 0.7750 (tt0) REVERT: A 487 HIS cc_start: 0.9009 (OUTLIER) cc_final: 0.8434 (p90) REVERT: A 675 TYR cc_start: 0.7660 (t80) cc_final: 0.7398 (t80) REVERT: A 687 ARG cc_start: 0.8382 (mmp-170) cc_final: 0.8137 (mmp-170) REVERT: A 702 ARG cc_start: 0.8724 (mtm180) cc_final: 0.7998 (ptm-80) REVERT: A 711 LYS cc_start: 0.8923 (mttt) cc_final: 0.8711 (mttp) REVERT: B 346 TYR cc_start: 0.8059 (OUTLIER) cc_final: 0.7115 (t80) REVERT: B 381 GLU cc_start: 0.8764 (pp20) cc_final: 0.8327 (tm-30) REVERT: B 674 GLU cc_start: 0.7525 (mm-30) cc_final: 0.6551 (mm-30) REVERT: B 702 ARG cc_start: 0.8802 (mtm180) cc_final: 0.7742 (ppt170) REVERT: B 709 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7985 (pp) REVERT: B 711 LYS cc_start: 0.8930 (mttt) cc_final: 0.8700 (mttp) outliers start: 44 outliers final: 32 residues processed: 176 average time/residue: 0.0799 time to fit residues: 20.6907 Evaluate side-chains 173 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 322 TRP Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 674 GLU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 346 TYR Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 595 ASN Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 709 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 ASN B 595 ASN B 678 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.125340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.091813 restraints weight = 12251.473| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.56 r_work: 0.2984 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9073 Z= 0.163 Angle : 0.620 8.143 12300 Z= 0.302 Chirality : 0.043 0.290 1446 Planarity : 0.003 0.038 1552 Dihedral : 8.260 136.102 1264 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.55 % Allowed : 18.22 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.25), residues: 1140 helix: -0.89 (0.20), residues: 678 sheet: -2.79 (0.58), residues: 72 loop : -1.84 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 305 TYR 0.013 0.001 TYR B 203 PHE 0.017 0.001 PHE B 316 TRP 0.013 0.001 TRP B 322 HIS 0.002 0.000 HIS A 682 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 9073) covalent geometry : angle 0.62005 (12300) hydrogen bonds : bond 0.05055 ( 359) hydrogen bonds : angle 4.19833 ( 1035) *********************** 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 191 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 346 TYR cc_start: 0.8020 (t80) cc_final: 0.7133 (t80) REVERT: A 425 TYR cc_start: 0.7346 (OUTLIER) cc_final: 0.7079 (t80) REVERT: A 455 MET cc_start: 0.7656 (tmm) cc_final: 0.7446 (tmm) REVERT: A 456 GLU cc_start: 0.8186 (tp30) cc_final: 0.7790 (tt0) REVERT: A 487 HIS cc_start: 0.8993 (OUTLIER) cc_final: 0.8398 (p90) REVERT: A 675 TYR cc_start: 0.7590 (t80) cc_final: 0.7342 (t80) REVERT: A 687 ARG cc_start: 0.8397 (mmp-170) cc_final: 0.8151 (mmp-170) REVERT: A 702 ARG cc_start: 0.8741 (mtm180) cc_final: 0.8052 (ptm-80) REVERT: A 711 LYS cc_start: 0.8938 (mttt) cc_final: 0.8717 (mttp) REVERT: B 346 TYR cc_start: 0.8087 (OUTLIER) cc_final: 0.7188 (t80) REVERT: B 674 GLU cc_start: 0.7551 (mm-30) cc_final: 0.6589 (mm-30) REVERT: B 678 GLN cc_start: 0.7630 (mt0) cc_final: 0.7429 (mt0) REVERT: B 702 ARG cc_start: 0.8843 (mtm180) cc_final: 0.7661 (ppt170) REVERT: B 709 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8033 (pp) REVERT: B 711 LYS cc_start: 0.8949 (mttt) cc_final: 0.8712 (mttp) outliers start: 44 outliers final: 33 residues processed: 177 average time/residue: 0.0831 time to fit residues: 21.4825 Evaluate side-chains 181 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 674 GLU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 346 TYR Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 709 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 113 optimal weight: 0.0060 chunk 65 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.129406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.095617 restraints weight = 12067.195| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.61 r_work: 0.3045 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9073 Z= 0.112 Angle : 0.586 8.522 12300 Z= 0.283 Chirality : 0.040 0.150 1446 Planarity : 0.003 0.036 1552 Dihedral : 7.921 132.926 1264 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.62 % Allowed : 19.46 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.25), residues: 1140 helix: -0.56 (0.20), residues: 680 sheet: -2.48 (0.60), residues: 72 loop : -1.72 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 687 TYR 0.010 0.001 TYR B 345 PHE 0.020 0.001 PHE B 189 TRP 0.015 0.001 TRP B 322 HIS 0.001 0.000 HIS B 688 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 9073) covalent geometry : angle 0.58555 (12300) hydrogen bonds : bond 0.04397 ( 359) hydrogen bonds : angle 4.02270 ( 1035) *********************** 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 195 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 322 TRP cc_start: 0.8732 (p-90) cc_final: 0.8465 (p-90) REVERT: A 346 TYR cc_start: 0.7945 (t80) cc_final: 0.7132 (t80) REVERT: A 425 TYR cc_start: 0.7143 (OUTLIER) cc_final: 0.6935 (t80) REVERT: A 456 GLU cc_start: 0.8133 (tp30) cc_final: 0.7779 (tt0) REVERT: A 487 HIS cc_start: 0.8998 (OUTLIER) cc_final: 0.8422 (p90) REVERT: A 675 TYR cc_start: 0.7558 (t80) cc_final: 0.7302 (t80) REVERT: A 687 ARG cc_start: 0.8363 (mmp-170) cc_final: 0.8113 (mmp-170) REVERT: A 702 ARG cc_start: 0.8755 (mtm180) cc_final: 0.8090 (ptm-80) REVERT: B 260 CYS cc_start: 0.8976 (t) cc_final: 0.8594 (m) REVERT: B 346 TYR cc_start: 0.8044 (OUTLIER) cc_final: 0.7169 (t80) REVERT: B 365 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8462 (tm-30) REVERT: B 674 GLU cc_start: 0.7469 (mm-30) cc_final: 0.6518 (mm-30) REVERT: B 702 ARG cc_start: 0.8842 (mtm180) cc_final: 0.7862 (ptm-80) REVERT: B 709 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7972 (pp) REVERT: B 711 LYS cc_start: 0.8925 (mttt) cc_final: 0.8714 (mttp) outliers start: 35 outliers final: 22 residues processed: 182 average time/residue: 0.0806 time to fit residues: 21.6916 Evaluate side-chains 173 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 346 TYR Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 719 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 85 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 678 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.123832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.089655 restraints weight = 12360.802| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.69 r_work: 0.2954 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9073 Z= 0.212 Angle : 0.652 8.873 12300 Z= 0.320 Chirality : 0.043 0.174 1446 Planarity : 0.003 0.038 1552 Dihedral : 8.125 142.139 1264 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.62 % Allowed : 19.57 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.25), residues: 1140 helix: -0.62 (0.20), residues: 674 sheet: -2.46 (0.58), residues: 72 loop : -1.66 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 687 TYR 0.014 0.001 TYR B 203 PHE 0.020 0.002 PHE B 189 TRP 0.014 0.001 TRP B 322 HIS 0.003 0.001 HIS A 682 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 9073) covalent geometry : angle 0.65228 (12300) hydrogen bonds : bond 0.05341 ( 359) hydrogen bonds : angle 4.21714 ( 1035) *********************** 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 185 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 322 TRP cc_start: 0.8717 (p-90) cc_final: 0.8472 (p-90) REVERT: A 346 TYR cc_start: 0.8051 (t80) cc_final: 0.7090 (t80) REVERT: A 422 SER cc_start: 0.8463 (t) cc_final: 0.8241 (t) REVERT: A 456 GLU cc_start: 0.8109 (tp30) cc_final: 0.7738 (tt0) REVERT: A 487 HIS cc_start: 0.8988 (OUTLIER) cc_final: 0.8413 (p90) REVERT: A 675 TYR cc_start: 0.7525 (t80) cc_final: 0.7180 (t80) REVERT: A 687 ARG cc_start: 0.8413 (mmp-170) cc_final: 0.8131 (mmp-170) REVERT: A 702 ARG cc_start: 0.8723 (mtm180) cc_final: 0.7995 (ptm-80) REVERT: B 346 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.7102 (t80) REVERT: B 455 MET cc_start: 0.7626 (tmm) cc_final: 0.7389 (tmm) REVERT: B 674 GLU cc_start: 0.7485 (mm-30) cc_final: 0.6435 (mm-30) REVERT: B 678 GLN cc_start: 0.7652 (mt0) cc_final: 0.7436 (mt0) REVERT: B 687 ARG cc_start: 0.7983 (mmm160) cc_final: 0.7592 (mmp80) REVERT: B 702 ARG cc_start: 0.8886 (mtm180) cc_final: 0.7682 (ppt170) REVERT: B 711 LYS cc_start: 0.8896 (mttt) cc_final: 0.8677 (mttp) outliers start: 35 outliers final: 27 residues processed: 173 average time/residue: 0.0758 time to fit residues: 19.5477 Evaluate side-chains 176 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 674 GLU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 346 TYR Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 595 ASN Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 666 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 98 optimal weight: 0.4980 chunk 14 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 27 optimal weight: 0.0980 chunk 9 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 67 optimal weight: 0.2980 chunk 110 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.130450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.096048 restraints weight = 12019.904| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.70 r_work: 0.3045 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9073 Z= 0.112 Angle : 0.598 9.002 12300 Z= 0.289 Chirality : 0.039 0.156 1446 Planarity : 0.003 0.035 1552 Dihedral : 7.690 134.579 1264 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.59 % Allowed : 21.43 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.25), residues: 1140 helix: -0.17 (0.21), residues: 664 sheet: -2.14 (0.59), residues: 72 loop : -1.54 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 687 TYR 0.010 0.001 TYR A 447 PHE 0.023 0.001 PHE B 189 TRP 0.014 0.001 TRP B 322 HIS 0.001 0.000 HIS B 682 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 9073) covalent geometry : angle 0.59832 (12300) hydrogen bonds : bond 0.04354 ( 359) hydrogen bonds : angle 3.97501 ( 1035) ********************** 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 174 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 322 TRP cc_start: 0.8710 (p-90) cc_final: 0.8495 (p-90) REVERT: A 346 TYR cc_start: 0.7872 (t80) cc_final: 0.7132 (t80) REVERT: A 416 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.6838 (tt) REVERT: A 456 GLU cc_start: 0.8144 (tp30) cc_final: 0.7813 (tt0) REVERT: A 487 HIS cc_start: 0.8966 (OUTLIER) cc_final: 0.8400 (p90) REVERT: A 675 TYR cc_start: 0.7543 (t80) cc_final: 0.7326 (t80) REVERT: A 687 ARG cc_start: 0.8369 (mmp-170) cc_final: 0.8122 (mmp-170) REVERT: A 702 ARG cc_start: 0.8737 (mtm180) cc_final: 0.8049 (ptm-80) REVERT: B 260 CYS cc_start: 0.8974 (t) cc_final: 0.8576 (m) REVERT: B 346 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.7089 (t80) REVERT: B 365 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8483 (tm-30) REVERT: B 455 MET cc_start: 0.7522 (tmm) cc_final: 0.7293 (tmm) REVERT: B 674 GLU cc_start: 0.7405 (mm-30) cc_final: 0.6988 (tp30) REVERT: B 687 ARG cc_start: 0.8007 (mmm160) cc_final: 0.7644 (mmp80) REVERT: B 702 ARG cc_start: 0.8891 (mtm180) cc_final: 0.7847 (ptm-80) REVERT: B 709 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7840 (pp) REVERT: B 711 LYS cc_start: 0.8901 (mttt) cc_final: 0.8687 (mttp) outliers start: 25 outliers final: 20 residues processed: 168 average time/residue: 0.0736 time to fit residues: 18.3190 Evaluate side-chains 170 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain A residue 674 GLU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 346 TYR Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 595 ASN Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 709 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 42 optimal weight: 0.1980 chunk 25 optimal weight: 4.9990 chunk 46 optimal weight: 0.3980 chunk 96 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 67 optimal weight: 0.0270 chunk 20 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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 678 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.131814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.097194 restraints weight = 11969.795| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.72 r_work: 0.3064 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9073 Z= 0.106 Angle : 0.585 8.965 12300 Z= 0.281 Chirality : 0.039 0.159 1446 Planarity : 0.003 0.035 1552 Dihedral : 7.542 134.533 1264 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.80 % Allowed : 21.22 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.25), residues: 1140 helix: 0.07 (0.21), residues: 664 sheet: -1.88 (0.60), residues: 72 loop : -1.42 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 687 TYR 0.015 0.001 TYR B 203 PHE 0.022 0.001 PHE B 189 TRP 0.014 0.001 TRP B 322 HIS 0.001 0.000 HIS B 682 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 9073) covalent geometry : angle 0.58525 (12300) hydrogen bonds : bond 0.04136 ( 359) hydrogen bonds : angle 3.85968 ( 1035) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2047.83 seconds wall clock time: 35 minutes 46.42 seconds (2146.42 seconds total)