Starting phenix.real_space_refine on Fri Mar 6 00:26:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t0v_25582/03_2026/7t0v_25582.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t0v_25582/03_2026/7t0v_25582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t0v_25582/03_2026/7t0v_25582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t0v_25582/03_2026/7t0v_25582.map" model { file = "/net/cci-nas-00/data/ceres_data/7t0v_25582/03_2026/7t0v_25582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t0v_25582/03_2026/7t0v_25582.cif" } resolution = 3.67 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 ------------------------------------------------------------------------------- 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= 0.048 sd= 0.158 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 31 5.49 5 Mg 9 5.21 5 S 124 5.16 5 C 16462 2.51 5 N 4698 2.21 5 O 5073 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s 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: 26397 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4365 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 536} Chain breaks: 3 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 4387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4387 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 537} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 4385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4385 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 538} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 4385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4385 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 538} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 4121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4121 Classifications: {'peptide': 540} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 509} Chain breaks: 5 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 29 Chain: "F" Number of atoms: 4251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4251 Classifications: {'peptide': 557} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 526} Chain breaks: 3 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 29 Chain: "G" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 161 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.06, per 1000 atoms: 0.23 Number of scatterers: 26397 At special positions: 0 Unit cell: (114.895, 150.088, 152.158, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 124 16.00 P 31 15.00 Mg 9 11.99 O 5073 8.00 N 4698 7.00 C 16462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 1.1 seconds 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6312 Finding SS restraints... Secondary structure from input PDB file: 191 helices and 12 sheets defined 60.4% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 207 through 218 removed outlier: 3.952A pdb=" N LYS A 216 " --> pdb=" O GLN A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 224 through 232 removed outlier: 3.882A pdb=" N CYS A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 261 removed outlier: 3.575A pdb=" N GLY A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 removed outlier: 4.078A pdb=" N ILE A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 269 through 273' Processing helix chain 'A' and resid 276 through 294 removed outlier: 4.265A pdb=" N GLU A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 307 Processing helix chain 'A' and resid 316 through 336 removed outlier: 3.859A pdb=" N VAL A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP A 331 " --> pdb=" O MET A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 356 through 361 Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 407 through 423 Processing helix chain 'A' and resid 423 through 438 removed outlier: 3.682A pdb=" N LEU A 430 " --> pdb=" O ASN A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 460 removed outlier: 3.833A pdb=" N HIS A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 483 removed outlier: 3.624A pdb=" N PHE A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 489 Processing helix chain 'A' and resid 506 through 517 Processing helix chain 'A' and resid 517 through 523 Processing helix chain 'A' and resid 523 through 530 removed outlier: 4.025A pdb=" N VAL A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 577 through 591 removed outlier: 3.781A pdb=" N VAL A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 606 Processing helix chain 'A' and resid 614 through 632 removed outlier: 4.388A pdb=" N SER A 618 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA A 619 " --> pdb=" O SER A 615 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ARG A 620 " --> pdb=" O ASP A 616 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 650 removed outlier: 3.610A pdb=" N ILE A 650 " --> pdb=" O PRO A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 656 removed outlier: 3.853A pdb=" N ARG A 656 " --> pdb=" O ALA A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 686 removed outlier: 3.674A pdb=" N VAL A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A 676 " --> pdb=" O GLU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 724 removed outlier: 3.574A pdb=" N GLU A 720 " --> pdb=" O ASP A 716 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A 721 " --> pdb=" O ALA A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 729 Processing helix chain 'A' and resid 732 through 758 Processing helix chain 'A' and resid 776 through 786 removed outlier: 3.503A pdb=" N TRP A 780 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN A 785 " --> pdb=" O GLU A 781 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 786 " --> pdb=" O LYS A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 799 removed outlier: 3.561A pdb=" N TYR A 797 " --> pdb=" O PRO A 794 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N HIS A 799 " --> pdb=" O LYS A 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 207 through 218 removed outlier: 4.249A pdb=" N LYS B 216 " --> pdb=" O GLN B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 224 Processing helix chain 'B' and resid 224 through 231 removed outlier: 3.556A pdb=" N CYS B 228 " --> pdb=" O GLY B 224 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 Processing helix chain 'B' and resid 270 through 273 Processing helix chain 'B' and resid 278 through 294 removed outlier: 3.633A pdb=" N ILE B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 307 Processing helix chain 'B' and resid 316 through 337 removed outlier: 3.998A pdb=" N ARG B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 337 " --> pdb=" O ILE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 395 through 402 removed outlier: 3.642A pdb=" N LYS B 401 " --> pdb=" O LYS B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 423 Processing helix chain 'B' and resid 423 through 436 removed outlier: 3.512A pdb=" N SER B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 430 " --> pdb=" O ASN B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 458 Processing helix chain 'B' and resid 472 through 483 removed outlier: 3.504A pdb=" N PHE B 476 " --> pdb=" O THR B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 489 Processing helix chain 'B' and resid 499 through 503 Processing helix chain 'B' and resid 506 through 517 Processing helix chain 'B' and resid 517 through 523 Processing helix chain 'B' and resid 523 through 531 removed outlier: 3.824A pdb=" N VAL B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 559 Processing helix chain 'B' and resid 577 through 593 removed outlier: 3.741A pdb=" N SER B 592 " --> pdb=" O SER B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 606 Processing helix chain 'B' and resid 618 through 630 Processing helix chain 'B' and resid 646 through 650 Processing helix chain 'B' and resid 670 through 684 removed outlier: 3.870A pdb=" N VAL B 675 " --> pdb=" O ALA B 671 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS B 676 " --> pdb=" O GLU B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 725 Processing helix chain 'B' and resid 726 through 729 Processing helix chain 'B' and resid 732 through 761 Processing helix chain 'B' and resid 776 through 787 removed outlier: 3.667A pdb=" N TRP B 780 " --> pdb=" O THR B 776 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 782 " --> pdb=" O GLU B 778 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN B 785 " --> pdb=" O GLU B 781 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU B 786 " --> pdb=" O LYS B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 799 Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 208 through 218 removed outlier: 4.077A pdb=" N LYS C 216 " --> pdb=" O GLN C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 224 Processing helix chain 'C' and resid 224 through 231 removed outlier: 3.557A pdb=" N CYS C 228 " --> pdb=" O GLY C 224 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N MET C 231 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 259 Processing helix chain 'C' and resid 270 through 273 Processing helix chain 'C' and resid 278 through 294 removed outlier: 3.682A pdb=" N ILE C 284 " --> pdb=" O SER C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 307 Processing helix chain 'C' and resid 317 through 337 removed outlier: 4.177A pdb=" N ARG C 334 " --> pdb=" O MET C 330 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN C 335 " --> pdb=" O ASP C 331 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR C 337 " --> pdb=" O ILE C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 355 Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'C' and resid 373 through 385 removed outlier: 3.514A pdb=" N GLN C 379 " --> pdb=" O ARG C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 402 Processing helix chain 'C' and resid 407 through 423 Processing helix chain 'C' and resid 424 through 436 removed outlier: 3.654A pdb=" N LEU C 430 " --> pdb=" O ASN C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 459 removed outlier: 3.514A pdb=" N GLU C 457 " --> pdb=" O TRP C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 483 removed outlier: 3.951A pdb=" N SER C 481 " --> pdb=" O ARG C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 489 removed outlier: 3.564A pdb=" N ARG C 489 " --> pdb=" O ALA C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 503 Processing helix chain 'C' and resid 506 through 517 Processing helix chain 'C' and resid 517 through 523 Processing helix chain 'C' and resid 523 through 530 removed outlier: 3.786A pdb=" N PHE C 527 " --> pdb=" O ASN C 523 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL C 530 " --> pdb=" O LEU C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 559 Processing helix chain 'C' and resid 577 through 593 removed outlier: 3.519A pdb=" N VAL C 583 " --> pdb=" O SER C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 606 Processing helix chain 'C' and resid 615 through 630 removed outlier: 3.903A pdb=" N VAL C 621 " --> pdb=" O ALA C 617 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL C 622 " --> pdb=" O SER C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 650 Processing helix chain 'C' and resid 670 through 684 removed outlier: 3.597A pdb=" N VAL C 675 " --> pdb=" O ALA C 671 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS C 676 " --> pdb=" O GLU C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 724 Processing helix chain 'C' and resid 725 through 729 Processing helix chain 'C' and resid 732 through 762 Processing helix chain 'C' and resid 776 through 785 removed outlier: 3.550A pdb=" N LYS C 782 " --> pdb=" O GLU C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 799 removed outlier: 3.921A pdb=" N TYR C 797 " --> pdb=" O ASP C 793 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 Processing helix chain 'D' and resid 207 through 218 removed outlier: 3.730A pdb=" N LEU D 211 " --> pdb=" O VAL D 207 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS D 216 " --> pdb=" O GLN D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 224 through 231 removed outlier: 3.518A pdb=" N MET D 231 " --> pdb=" O ALA D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 261 Processing helix chain 'D' and resid 269 through 273 removed outlier: 4.134A pdb=" N ILE D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 269 through 273' Processing helix chain 'D' and resid 276 through 294 removed outlier: 4.339A pdb=" N SER D 280 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE D 284 " --> pdb=" O SER D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 307 Processing helix chain 'D' and resid 317 through 337 removed outlier: 4.349A pdb=" N ARG D 334 " --> pdb=" O MET D 330 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR D 337 " --> pdb=" O ILE D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'D' and resid 356 through 361 Processing helix chain 'D' and resid 373 through 385 removed outlier: 3.556A pdb=" N GLN D 379 " --> pdb=" O ARG D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 402 Processing helix chain 'D' and resid 407 through 423 Processing helix chain 'D' and resid 424 through 435 removed outlier: 3.754A pdb=" N LEU D 430 " --> pdb=" O ASN D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 460 Processing helix chain 'D' and resid 472 through 483 removed outlier: 3.553A pdb=" N SER D 481 " --> pdb=" O ARG D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 489 removed outlier: 3.631A pdb=" N ARG D 489 " --> pdb=" O ALA D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 503 Processing helix chain 'D' and resid 506 through 517 Processing helix chain 'D' and resid 517 through 523 Processing helix chain 'D' and resid 523 through 530 removed outlier: 3.851A pdb=" N VAL D 530 " --> pdb=" O LEU D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.519A pdb=" N ASN D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 593 Processing helix chain 'D' and resid 603 through 606 Processing helix chain 'D' and resid 618 through 630 removed outlier: 3.531A pdb=" N VAL D 622 " --> pdb=" O SER D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 650 Processing helix chain 'D' and resid 670 through 684 removed outlier: 3.689A pdb=" N VAL D 675 " --> pdb=" O ALA D 671 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS D 676 " --> pdb=" O GLU D 672 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN D 684 " --> pdb=" O THR D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 716 through 725 Processing helix chain 'D' and resid 726 through 729 Processing helix chain 'D' and resid 732 through 754 Processing helix chain 'D' and resid 776 through 787 removed outlier: 3.975A pdb=" N ASN D 785 " --> pdb=" O GLU D 781 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU D 786 " --> pdb=" O LYS D 782 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 204 Processing helix chain 'E' and resid 207 through 218 removed outlier: 3.972A pdb=" N LYS E 216 " --> pdb=" O GLN E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 224 Processing helix chain 'E' and resid 224 through 232 removed outlier: 4.140A pdb=" N CYS E 228 " --> pdb=" O GLY E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 261 removed outlier: 3.573A pdb=" N LEU E 252 " --> pdb=" O GLY E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 273 removed outlier: 4.030A pdb=" N ILE E 273 " --> pdb=" O ALA E 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 269 through 273' Processing helix chain 'E' and resid 276 through 294 removed outlier: 3.638A pdb=" N SER E 280 " --> pdb=" O THR E 276 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU E 281 " --> pdb=" O SER E 277 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP E 289 " --> pdb=" O ARG E 285 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU E 290 " --> pdb=" O ASP E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 307 Processing helix chain 'E' and resid 316 through 337 removed outlier: 3.988A pdb=" N VAL E 323 " --> pdb=" O GLU E 319 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA E 324 " --> pdb=" O SER E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 355 Processing helix chain 'E' and resid 356 through 361 Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 395 through 402 Processing helix chain 'E' and resid 407 through 423 Processing helix chain 'E' and resid 423 through 438 Processing helix chain 'E' and resid 447 through 460 removed outlier: 3.827A pdb=" N HIS E 459 " --> pdb=" O LEU E 455 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG E 460 " --> pdb=" O LEU E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 483 removed outlier: 3.729A pdb=" N PHE E 476 " --> pdb=" O THR E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 517 Processing helix chain 'E' and resid 518 through 523 removed outlier: 3.613A pdb=" N LYS E 522 " --> pdb=" O ILE E 518 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN E 523 " --> pdb=" O GLY E 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 518 through 523' Processing helix chain 'E' and resid 523 through 530 removed outlier: 4.082A pdb=" N VAL E 530 " --> pdb=" O LEU E 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 559 Processing helix chain 'E' and resid 577 through 593 removed outlier: 3.825A pdb=" N VAL E 583 " --> pdb=" O SER E 579 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER E 592 " --> pdb=" O SER E 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 602 through 606 Processing helix chain 'E' and resid 618 through 631 removed outlier: 3.629A pdb=" N THR E 624 " --> pdb=" O ARG E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 646 through 650 removed outlier: 3.790A pdb=" N ILE E 650 " --> pdb=" O PRO E 647 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 686 removed outlier: 3.616A pdb=" N VAL E 675 " --> pdb=" O ALA E 671 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR E 685 " --> pdb=" O LEU E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 716 through 725 removed outlier: 3.551A pdb=" N LYS E 721 " --> pdb=" O ALA E 717 " (cutoff:3.500A) Processing helix chain 'E' and resid 726 through 729 Processing helix chain 'E' and resid 732 through 755 Processing helix chain 'E' and resid 776 through 786 removed outlier: 3.551A pdb=" N TRP E 780 " --> pdb=" O THR E 776 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN E 785 " --> pdb=" O GLU E 781 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU E 786 " --> pdb=" O LYS E 782 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 204 Processing helix chain 'F' and resid 207 through 218 removed outlier: 3.880A pdb=" N LYS F 216 " --> pdb=" O GLN F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 224 Processing helix chain 'F' and resid 224 through 232 removed outlier: 3.975A pdb=" N CYS F 228 " --> pdb=" O GLY F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 261 removed outlier: 3.528A pdb=" N GLY F 261 " --> pdb=" O ALA F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 273 Processing helix chain 'F' and resid 276 through 294 removed outlier: 4.352A pdb=" N GLU F 281 " --> pdb=" O SER F 277 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP F 289 " --> pdb=" O ARG F 285 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU F 290 " --> pdb=" O ASP F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 307 Processing helix chain 'F' and resid 316 through 336 removed outlier: 3.998A pdb=" N VAL F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA F 324 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP F 331 " --> pdb=" O MET F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 355 Processing helix chain 'F' and resid 356 through 361 Processing helix chain 'F' and resid 373 through 385 removed outlier: 3.678A pdb=" N GLN F 379 " --> pdb=" O ARG F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 402 Processing helix chain 'F' and resid 407 through 423 Processing helix chain 'F' and resid 423 through 438 removed outlier: 3.617A pdb=" N LEU F 430 " --> pdb=" O ASN F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 460 removed outlier: 3.824A pdb=" N HIS F 459 " --> pdb=" O LEU F 455 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG F 460 " --> pdb=" O LEU F 456 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 483 removed outlier: 3.570A pdb=" N PHE F 476 " --> pdb=" O THR F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 485 through 490 removed outlier: 3.582A pdb=" N GLU F 490 " --> pdb=" O SER F 487 " (cutoff:3.500A) Processing helix chain 'F' and resid 506 through 517 Processing helix chain 'F' and resid 517 through 523 Processing helix chain 'F' and resid 523 through 529 removed outlier: 3.774A pdb=" N THR F 528 " --> pdb=" O PRO F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 559 Processing helix chain 'F' and resid 577 through 593 removed outlier: 3.681A pdb=" N VAL F 583 " --> pdb=" O SER F 579 " (cutoff:3.500A) Processing helix chain 'F' and resid 602 through 606 Processing helix chain 'F' and resid 614 through 631 removed outlier: 3.963A pdb=" N SER F 618 " --> pdb=" O LEU F 614 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ARG F 620 " --> pdb=" O ASP F 616 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL F 621 " --> pdb=" O ALA F 617 " (cutoff:3.500A) Processing helix chain 'F' and resid 670 through 685 removed outlier: 3.626A pdb=" N LYS F 676 " --> pdb=" O GLU F 672 " (cutoff:3.500A) Processing helix chain 'F' and resid 716 through 725 removed outlier: 3.734A pdb=" N LYS F 721 " --> pdb=" O ALA F 717 " (cutoff:3.500A) Processing helix chain 'F' and resid 726 through 729 removed outlier: 3.555A pdb=" N THR F 729 " --> pdb=" O LEU F 726 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 726 through 729' Processing helix chain 'F' and resid 732 through 758 Processing helix chain 'F' and resid 776 through 786 removed outlier: 3.565A pdb=" N LYS F 782 " --> pdb=" O GLU F 778 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN F 785 " --> pdb=" O GLU F 781 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU F 786 " --> pdb=" O LYS F 782 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 263 through 268 removed outlier: 6.294A pdb=" N CYS A 297 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LEU A 346 " --> pdb=" O CYS A 297 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ILE A 299 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ALA A 348 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU A 301 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A 240 " --> pdb=" O ILE A 367 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 562 through 567 removed outlier: 6.456A pdb=" N CYS A 596 " --> pdb=" O TYR A 639 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ILE A 641 " --> pdb=" O CYS A 596 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU A 598 " --> pdb=" O ILE A 641 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ALA A 643 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE A 600 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 536 " --> pdb=" O ILE A 638 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 263 through 268 removed outlier: 3.501A pdb=" N PHE B 300 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N CYS B 297 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LEU B 346 " --> pdb=" O CYS B 297 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ILE B 299 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ALA B 348 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU B 301 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 562 through 567 removed outlier: 6.294A pdb=" N CYS B 596 " --> pdb=" O TYR B 639 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE B 641 " --> pdb=" O CYS B 596 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU B 598 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ALA B 643 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE B 600 " --> pdb=" O ALA B 643 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 263 through 268 removed outlier: 6.302A pdb=" N CYS C 297 " --> pdb=" O VAL C 344 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LEU C 346 " --> pdb=" O CYS C 297 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE C 299 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ALA C 348 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU C 301 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 562 through 567 removed outlier: 6.188A pdb=" N CYS C 596 " --> pdb=" O TYR C 639 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ILE C 641 " --> pdb=" O CYS C 596 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU C 598 " --> pdb=" O ILE C 641 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ALA C 643 " --> pdb=" O LEU C 598 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE C 600 " --> pdb=" O ALA C 643 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 263 through 268 removed outlier: 6.422A pdb=" N CYS D 297 " --> pdb=" O VAL D 344 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU D 346 " --> pdb=" O CYS D 297 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ILE D 299 " --> pdb=" O LEU D 346 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ALA D 348 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU D 301 " --> pdb=" O ALA D 348 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 562 through 567 removed outlier: 6.186A pdb=" N CYS D 596 " --> pdb=" O TYR D 639 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ILE D 641 " --> pdb=" O CYS D 596 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU D 598 " --> pdb=" O ILE D 641 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ALA D 643 " --> pdb=" O LEU D 598 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE D 600 " --> pdb=" O ALA D 643 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 263 through 268 removed outlier: 6.820A pdb=" N ALA E 263 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N PHE E 300 " --> pdb=" O ALA E 263 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE E 265 " --> pdb=" O PHE E 300 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ASP E 302 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL E 267 " --> pdb=" O ASP E 302 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N CYS E 297 " --> pdb=" O VAL E 344 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU E 346 " --> pdb=" O CYS E 297 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE E 299 " --> pdb=" O LEU E 346 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ALA E 348 " --> pdb=" O ILE E 299 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU E 301 " --> pdb=" O ALA E 348 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 562 through 566 removed outlier: 6.503A pdb=" N ASN E 562 " --> pdb=" O ILE E 597 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N PHE E 599 " --> pdb=" O ASN E 562 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE E 564 " --> pdb=" O PHE E 599 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N CYS E 596 " --> pdb=" O TYR E 639 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE E 641 " --> pdb=" O CYS E 596 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU E 598 " --> pdb=" O ILE E 641 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ALA E 643 " --> pdb=" O LEU E 598 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N PHE E 600 " --> pdb=" O ALA E 643 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE E 538 " --> pdb=" O GLY E 642 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N THR E 644 " --> pdb=" O ILE E 538 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU E 540 " --> pdb=" O THR E 644 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR E 662 " --> pdb=" O GLY E 537 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 264 through 267 removed outlier: 7.764A pdb=" N ILE F 265 " --> pdb=" O PHE F 300 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ASP F 302 " --> pdb=" O ILE F 265 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL F 267 " --> pdb=" O ASP F 302 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE F 299 " --> pdb=" O LEU F 346 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA F 348 " --> pdb=" O ILE F 299 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU F 301 " --> pdb=" O ALA F 348 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU F 240 " --> pdb=" O ILE F 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 492 through 493 removed outlier: 6.477A pdb=" N ASN F 562 " --> pdb=" O ILE F 597 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N PHE F 599 " --> pdb=" O ASN F 562 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE F 564 " --> pdb=" O PHE F 599 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASP F 601 " --> pdb=" O ILE F 564 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE F 566 " --> pdb=" O ASP F 601 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N CYS F 596 " --> pdb=" O TYR F 639 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ILE F 641 " --> pdb=" O CYS F 596 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU F 598 " --> pdb=" O ILE F 641 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ALA F 643 " --> pdb=" O LEU F 598 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N PHE F 600 " --> pdb=" O ALA F 643 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE F 538 " --> pdb=" O VAL F 640 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY F 642 " --> pdb=" O ILE F 538 " (cutoff:3.500A) 1314 hydrogen bonds defined for protein. 3687 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.02 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8888 1.34 - 1.46: 4625 1.46 - 1.58: 13055 1.58 - 1.69: 51 1.69 - 1.81: 206 Bond restraints: 26825 Sorted by residual: bond pdb=" O5' ATP E 902 " pdb=" PA ATP E 902 " ideal model delta sigma weight residual 1.579 1.610 -0.031 1.10e-02 8.26e+03 7.78e+00 bond pdb=" O5' ATP B 901 " pdb=" PA ATP B 901 " ideal model delta sigma weight residual 1.579 1.609 -0.030 1.10e-02 8.26e+03 7.32e+00 bond pdb=" O5' ATP D 902 " pdb=" PA ATP D 902 " ideal model delta sigma weight residual 1.579 1.608 -0.029 1.10e-02 8.26e+03 6.97e+00 bond pdb=" O5' ATP D 901 " pdb=" PA ATP D 901 " ideal model delta sigma weight residual 1.579 1.608 -0.029 1.10e-02 8.26e+03 6.96e+00 bond pdb=" O5' ATP A 902 " pdb=" PA ATP A 902 " ideal model delta sigma weight residual 1.579 1.608 -0.029 1.10e-02 8.26e+03 6.87e+00 ... (remaining 26820 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.70: 36181 3.70 - 7.40: 157 7.40 - 11.10: 3 11.10 - 14.80: 12 14.80 - 18.50: 8 Bond angle restraints: 36361 Sorted by residual: angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 121.37 18.50 1.00e+00 1.00e+00 3.42e+02 angle pdb=" PA ATP B 901 " pdb=" O3A ATP B 901 " pdb=" PB ATP B 901 " ideal model delta sigma weight residual 136.83 118.58 18.25 1.00e+00 1.00e+00 3.33e+02 angle pdb=" PB ATP B 902 " pdb=" O3B ATP B 902 " pdb=" PG ATP B 902 " ideal model delta sigma weight residual 139.87 123.01 16.86 1.00e+00 1.00e+00 2.84e+02 angle pdb=" PA ATP D 901 " pdb=" O3A ATP D 901 " pdb=" PB ATP D 901 " ideal model delta sigma weight residual 136.83 121.16 15.67 1.00e+00 1.00e+00 2.45e+02 angle pdb=" PA ATP A 901 " pdb=" O3A ATP A 901 " pdb=" PB ATP A 901 " ideal model delta sigma weight residual 136.83 121.21 15.62 1.00e+00 1.00e+00 2.44e+02 ... (remaining 36356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.86: 16207 25.86 - 51.72: 389 51.72 - 77.58: 83 77.58 - 103.44: 3 103.44 - 129.29: 3 Dihedral angle restraints: 16685 sinusoidal: 6946 harmonic: 9739 Sorted by residual: dihedral pdb=" C5' ADP F 901 " pdb=" O5' ADP F 901 " pdb=" PA ADP F 901 " pdb=" O2A ADP F 901 " ideal model delta sinusoidal sigma weight residual 300.00 170.71 129.29 1 2.00e+01 2.50e-03 3.92e+01 dihedral pdb=" O1B ADP E 901 " pdb=" O3A ADP E 901 " pdb=" PB ADP E 901 " pdb=" PA ADP E 901 " ideal model delta sinusoidal sigma weight residual -60.00 63.78 -123.78 1 2.00e+01 2.50e-03 3.73e+01 dihedral pdb=" O1B ADP F 901 " pdb=" O3A ADP F 901 " pdb=" PB ADP F 901 " pdb=" PA ADP F 901 " ideal model delta sinusoidal sigma weight residual -60.00 61.71 -121.72 1 2.00e+01 2.50e-03 3.66e+01 ... (remaining 16682 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2498 0.032 - 0.065: 1137 0.065 - 0.097: 354 0.097 - 0.129: 152 0.129 - 0.162: 24 Chirality restraints: 4165 Sorted by residual: chirality pdb=" C3' ATP E 902 " pdb=" C2' ATP E 902 " pdb=" C4' ATP E 902 " pdb=" O3' ATP E 902 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CA ILE E 495 " pdb=" N ILE E 495 " pdb=" C ILE E 495 " pdb=" CB ILE E 495 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" C3' ATP D 902 " pdb=" C2' ATP D 902 " pdb=" C4' ATP D 902 " pdb=" O3' ATP D 902 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.16 2.00e-01 2.50e+01 6.27e-01 ... (remaining 4162 not shown) Planarity restraints: 4679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 568 " -0.035 5.00e-02 4.00e+02 5.34e-02 4.55e+00 pdb=" N PRO F 569 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO F 569 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 569 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 356 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO A 357 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 357 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 357 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 356 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.08e+00 pdb=" N PRO F 357 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO F 357 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 357 " 0.020 5.00e-02 4.00e+02 ... (remaining 4676 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 200 2.47 - 3.07: 18162 3.07 - 3.68: 39490 3.68 - 4.29: 59913 4.29 - 4.90: 99451 Nonbonded interactions: 217216 Sorted by model distance: nonbonded pdb=" O1B ATP A 902 " pdb="MG MG A 904 " model vdw 1.857 2.170 nonbonded pdb=" O1B ATP B 901 " pdb="MG MG B 903 " model vdw 1.890 2.170 nonbonded pdb=" O2G ATP C 902 " pdb="MG MG C 904 " model vdw 1.892 2.170 nonbonded pdb=" O1B ATP C 901 " pdb="MG MG C 903 " model vdw 1.898 2.170 nonbonded pdb=" O1B ATP D 902 " pdb="MG MG D 904 " model vdw 1.907 2.170 ... (remaining 217211 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 193 through 460 or (resid 461 through 463 and (name N or n \ ame CA or name C or name O or name CB )) or resid 464 through 487 or resid 493 t \ hrough 573 or (resid 574 through 576 and (name N or name CA or name C or name O \ or name CB )) or resid 577 or (resid 578 and (name N or name CA or name C or nam \ e O or name CB )) or resid 579 through 631 or resid 637 through 754 or (resid 75 \ 5 through 757 and (name N or name CA or name C or name O or name CB )) or resid \ 773 through 790)) selection = (chain 'B' and (resid 193 through 338 or (resid 339 and (name N or name CA or na \ me C or name O or name CB )) or resid 340 or (resid 341 and (name N or name CA o \ r name C or name O or name CB )) or resid 342 through 460 or (resid 461 through \ 463 and (name N or name CA or name C or name O or name CB )) or resid 464 throug \ h 487 or resid 493 through 573 or (resid 574 through 576 and (name N or name CA \ or name C or name O or name CB )) or resid 577 or (resid 578 and (name N or name \ CA or name C or name O or name CB )) or resid 579 through 631 or resid 637 thro \ ugh 754 or (resid 755 through 757 and (name N or name CA or name C or name O or \ name CB )) or resid 773 through 790)) selection = (chain 'C' and (resid 193 through 338 or (resid 339 and (name N or name CA or na \ me C or name O or name CB )) or resid 340 or (resid 341 and (name N or name CA o \ r name C or name O or name CB )) or resid 342 through 460 or (resid 461 through \ 463 and (name N or name CA or name C or name O or name CB )) or resid 464 throug \ h 487 or resid 493 through 573 or (resid 574 through 576 and (name N or name CA \ or name C or name O or name CB )) or resid 577 or (resid 578 and (name N or name \ CA or name C or name O or name CB )) or resid 579 through 631 or resid 637 thro \ ugh 754 or (resid 755 through 757 and (name N or name CA or name C or name O or \ name CB )) or resid 773 through 790)) selection = (chain 'D' and (resid 193 through 338 or (resid 339 and (name N or name CA or na \ me C or name O or name CB )) or resid 340 or (resid 341 and (name N or name CA o \ r name C or name O or name CB )) or resid 342 through 460 or (resid 461 through \ 463 and (name N or name CA or name C or name O or name CB )) or resid 464 throug \ h 487 or resid 493 through 573 or (resid 574 through 576 and (name N or name CA \ or name C or name O or name CB )) or resid 577 or (resid 578 and (name N or name \ CA or name C or name O or name CB )) or resid 579 through 631 or resid 637 thro \ ugh 754 or (resid 755 through 757 and (name N or name CA or name C or name O or \ name CB )) or resid 773 through 790)) selection = (chain 'E' and (resid 193 through 338 or (resid 339 and (name N or name CA or na \ me C or name O or name CB )) or resid 340 or (resid 341 and (name N or name CA o \ r name C or name O or name CB )) or resid 342 through 573 or (resid 574 through \ 576 and (name N or name CA or name C or name O or name CB )) or resid 577 or (re \ sid 578 and (name N or name CA or name C or name O or name CB )) or resid 579 th \ rough 790)) selection = (chain 'F' and (resid 193 through 338 or (resid 339 and (name N or name CA or na \ me C or name O or name CB )) or resid 340 or (resid 341 and (name N or name CA o \ r name C or name O or name CB )) or resid 342 through 460 or (resid 461 through \ 463 and (name N or name CA or name C or name O or name CB )) or resid 464 throug \ h 487 or resid 493 through 631 or resid 637 through 754 or (resid 755 through 75 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 773 through \ 790)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.900 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 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 : 0.004 0.053 26825 Z= 0.191 Angle : 0.726 18.497 36361 Z= 0.474 Chirality : 0.043 0.162 4165 Planarity : 0.004 0.053 4679 Dihedral : 11.583 129.295 10373 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.01 % Favored : 95.84 % Rotamer: Outliers : 1.71 % Allowed : 3.02 % Favored : 95.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: -0.13 (0.15), residues: 3343 helix: -0.33 (0.12), residues: 1786 sheet: 0.70 (0.26), residues: 402 loop : 0.37 (0.20), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 361 TYR 0.017 0.001 TYR B 752 PHE 0.017 0.002 PHE B 600 TRP 0.019 0.002 TRP E 500 HIS 0.003 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00410 (26825) covalent geometry : angle 0.72623 (36361) hydrogen bonds : bond 0.27120 ( 1314) hydrogen bonds : angle 7.56523 ( 3687) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 814 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 VAL cc_start: 0.8414 (t) cc_final: 0.8181 (p) REVERT: A 508 ASP cc_start: 0.8354 (t70) cc_final: 0.7946 (t0) REVERT: A 795 GLU cc_start: 0.8101 (mp0) cc_final: 0.7689 (mp0) REVERT: A 798 MET cc_start: 0.4504 (ptt) cc_final: 0.3980 (tpp) REVERT: A 799 HIS cc_start: 0.5790 (m170) cc_final: 0.4712 (t70) REVERT: B 294 LEU cc_start: 0.9236 (tp) cc_final: 0.8890 (tp) REVERT: B 472 THR cc_start: 0.7875 (p) cc_final: 0.7660 (m) REVERT: B 530 VAL cc_start: 0.8971 (m) cc_final: 0.8753 (t) REVERT: B 578 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7891 (tp30) REVERT: C 201 ILE cc_start: 0.9145 (tp) cc_final: 0.8943 (tp) REVERT: C 538 ILE cc_start: 0.8748 (mm) cc_final: 0.8399 (tt) REVERT: C 754 GLN cc_start: 0.8039 (mt0) cc_final: 0.7798 (mm110) REVERT: D 321 ARG cc_start: 0.7877 (mtm110) cc_final: 0.7523 (mtm-85) REVERT: D 431 LEU cc_start: 0.8904 (mt) cc_final: 0.8590 (tt) REVERT: D 472 THR cc_start: 0.7915 (m) cc_final: 0.7354 (p) REVERT: D 511 LYS cc_start: 0.8041 (mtpt) cc_final: 0.7762 (ttmm) REVERT: D 584 ARG cc_start: 0.7866 (mtm110) cc_final: 0.7382 (mtm110) REVERT: D 739 LEU cc_start: 0.8857 (tp) cc_final: 0.8652 (tt) REVERT: E 350 ASN cc_start: 0.7588 (p0) cc_final: 0.7348 (p0) REVERT: F 368 ASP cc_start: 0.6158 (t0) cc_final: 0.5779 (p0) REVERT: F 402 MET cc_start: 0.7646 (ptp) cc_final: 0.6792 (mmm) REVERT: F 508 ASP cc_start: 0.7508 (t0) cc_final: 0.6872 (m-30) REVERT: F 515 MET cc_start: 0.8455 (ttp) cc_final: 0.8162 (ttm) REVERT: F 601 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.6995 (m-30) REVERT: F 718 ASP cc_start: 0.7270 (m-30) cc_final: 0.6770 (m-30) outliers start: 48 outliers final: 10 residues processed: 850 average time/residue: 0.1942 time to fit residues: 250.7180 Evaluate side-chains 449 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 438 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 645 ASN Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 601 ASP Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain G residue 23 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.0870 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 8.9990 overall best weight: 5.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 HIS A 459 HIS A 557 ASN B 426 ASN B 756 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 ASN C 602 GLN C 684 ASN D 212 GLN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 459 HIS D 585 GLN ** D 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 ASN E 741 GLN F 242 HIS F 438 HIS F 557 ASN F 645 ASN ** F 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.139307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.107692 restraints weight = 52520.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.107040 restraints weight = 31612.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.107942 restraints weight = 24482.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.108603 restraints weight = 22812.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.108783 restraints weight = 19961.997| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26825 Z= 0.187 Angle : 0.682 9.950 36361 Z= 0.346 Chirality : 0.046 0.297 4165 Planarity : 0.006 0.070 4679 Dihedral : 11.620 117.878 4022 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.83 % Favored : 96.11 % Rotamer: Outliers : 3.02 % Allowed : 11.28 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: 0.39 (0.15), residues: 3343 helix: 0.32 (0.12), residues: 1822 sheet: 0.32 (0.25), residues: 400 loop : 0.48 (0.21), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 334 TYR 0.020 0.001 TYR E 682 PHE 0.021 0.002 PHE B 731 TRP 0.012 0.001 TRP C 219 HIS 0.007 0.001 HIS B 459 Details of bonding type rmsd covalent geometry : bond 0.00427 (26825) covalent geometry : angle 0.68185 (36361) hydrogen bonds : bond 0.05365 ( 1314) hydrogen bonds : angle 4.95642 ( 3687) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 472 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 726 LEU cc_start: 0.8473 (pt) cc_final: 0.8267 (mt) REVERT: A 798 MET cc_start: 0.4861 (ptt) cc_final: 0.4297 (tpp) REVERT: A 799 HIS cc_start: 0.5676 (m170) cc_final: 0.4582 (t-170) REVERT: B 294 LEU cc_start: 0.9241 (tp) cc_final: 0.8837 (tp) REVERT: B 359 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8092 (tt) REVERT: B 402 MET cc_start: 0.7873 (ptm) cc_final: 0.7601 (ttt) REVERT: B 735 ASP cc_start: 0.7140 (m-30) cc_final: 0.6853 (m-30) REVERT: C 482 LEU cc_start: 0.8895 (mm) cc_final: 0.8649 (tp) REVERT: C 724 LEU cc_start: 0.8129 (tp) cc_final: 0.7928 (tt) REVERT: C 754 GLN cc_start: 0.8016 (mt0) cc_final: 0.7757 (mm-40) REVERT: D 318 MET cc_start: 0.7755 (tpp) cc_final: 0.7036 (tpp) REVERT: D 431 LEU cc_start: 0.8853 (mt) cc_final: 0.8632 (tt) REVERT: D 511 LYS cc_start: 0.8237 (mtpt) cc_final: 0.8031 (ttmm) REVERT: D 585 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.7085 (tp40) REVERT: D 740 MET cc_start: 0.8306 (ttp) cc_final: 0.7920 (ttt) REVERT: E 350 ASN cc_start: 0.7724 (p0) cc_final: 0.7416 (p0) REVERT: E 718 ASP cc_start: 0.8029 (m-30) cc_final: 0.7765 (t0) REVERT: E 752 TYR cc_start: 0.6895 (m-10) cc_final: 0.6627 (m-80) REVERT: E 777 MET cc_start: 0.8276 (tmm) cc_final: 0.8075 (tmm) REVERT: E 780 TRP cc_start: 0.8274 (m100) cc_final: 0.7900 (m100) REVERT: F 212 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8594 (pp30) REVERT: F 254 HIS cc_start: 0.7285 (m90) cc_final: 0.7082 (m90) REVERT: F 515 MET cc_start: 0.9023 (ttp) cc_final: 0.8659 (ttt) REVERT: F 652 GLU cc_start: 0.7802 (pm20) cc_final: 0.7580 (mp0) REVERT: F 786 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7946 (pm20) outliers start: 85 outliers final: 48 residues processed: 532 average time/residue: 0.1721 time to fit residues: 143.5043 Evaluate side-chains 416 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 365 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 433 GLN Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 585 GLN Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain D residue 747 CYS Chi-restraints excluded: chain E residue 297 CYS Chi-restraints excluded: chain E residue 327 MET Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 591 LYS Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 212 GLN Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 632 VAL Chi-restraints excluded: chain F residue 650 ILE Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain F residue 753 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 23 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 186 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 324 optimal weight: 7.9990 chunk 174 optimal weight: 3.9990 chunk 223 optimal weight: 20.0000 chunk 206 optimal weight: 6.9990 chunk 234 optimal weight: 50.0000 chunk 128 optimal weight: 10.0000 chunk 8 optimal weight: 50.0000 chunk 56 optimal weight: 40.0000 chunk 281 optimal weight: 30.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN B 395 ASN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 HIS ** D 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 741 GLN ** D 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 GLN F 242 HIS F 438 HIS F 459 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.138972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.106159 restraints weight = 52380.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.108221 restraints weight = 30798.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.109948 restraints weight = 21756.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.110482 restraints weight = 17076.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.110513 restraints weight = 16194.763| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26825 Z= 0.184 Angle : 0.654 8.658 36361 Z= 0.325 Chirality : 0.045 0.239 4165 Planarity : 0.005 0.063 4679 Dihedral : 11.374 120.992 4018 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.86 % Favored : 96.05 % Rotamer: Outliers : 3.27 % Allowed : 13.34 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: 0.52 (0.15), residues: 3343 helix: 0.52 (0.12), residues: 1810 sheet: 0.03 (0.25), residues: 396 loop : 0.48 (0.21), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 362 TYR 0.020 0.001 TYR E 682 PHE 0.019 0.002 PHE E 354 TRP 0.017 0.001 TRP E 453 HIS 0.004 0.001 HIS F 438 Details of bonding type rmsd covalent geometry : bond 0.00428 (26825) covalent geometry : angle 0.65380 (36361) hydrogen bonds : bond 0.04307 ( 1314) hydrogen bonds : angle 4.64377 ( 3687) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 383 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 VAL cc_start: 0.8655 (t) cc_final: 0.8414 (p) REVERT: A 330 MET cc_start: 0.7977 (mtt) cc_final: 0.7673 (mtm) REVERT: A 466 TRP cc_start: 0.7415 (m-90) cc_final: 0.6913 (m-90) REVERT: A 798 MET cc_start: 0.4492 (ptt) cc_final: 0.4112 (tpp) REVERT: A 799 HIS cc_start: 0.5645 (m170) cc_final: 0.4560 (t-170) REVERT: B 294 LEU cc_start: 0.9274 (tp) cc_final: 0.9038 (tp) REVERT: B 359 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7899 (tt) REVERT: B 402 MET cc_start: 0.7906 (ptm) cc_final: 0.7677 (ttt) REVERT: B 515 MET cc_start: 0.7164 (ttp) cc_final: 0.6515 (ttp) REVERT: B 731 PHE cc_start: 0.7995 (m-80) cc_final: 0.7417 (m-80) REVERT: B 735 ASP cc_start: 0.6919 (m-30) cc_final: 0.6451 (m-30) REVERT: B 740 MET cc_start: 0.6763 (tmm) cc_final: 0.6402 (tmm) REVERT: C 349 THR cc_start: 0.9303 (OUTLIER) cc_final: 0.9052 (t) REVERT: C 360 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.8107 (ttt-90) REVERT: C 754 GLN cc_start: 0.7991 (mt0) cc_final: 0.7769 (mm-40) REVERT: D 318 MET cc_start: 0.7224 (tpp) cc_final: 0.6736 (tpp) REVERT: D 431 LEU cc_start: 0.8941 (mt) cc_final: 0.8646 (tt) REVERT: E 350 ASN cc_start: 0.7961 (p0) cc_final: 0.7672 (p0) REVERT: E 527 PHE cc_start: 0.7030 (OUTLIER) cc_final: 0.6805 (t80) REVERT: E 603 MET cc_start: 0.8510 (ttp) cc_final: 0.8223 (ttm) REVERT: E 718 ASP cc_start: 0.8032 (m-30) cc_final: 0.7714 (t0) REVERT: E 752 TYR cc_start: 0.6987 (m-10) cc_final: 0.6635 (m-80) REVERT: E 777 MET cc_start: 0.8258 (tmm) cc_final: 0.8021 (tmm) REVERT: E 780 TRP cc_start: 0.8267 (m100) cc_final: 0.7888 (m100) REVERT: F 212 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8568 (pp30) REVERT: F 254 HIS cc_start: 0.7380 (m90) cc_final: 0.7141 (m90) REVERT: F 318 MET cc_start: 0.4072 (tpp) cc_final: 0.3818 (tpt) REVERT: F 330 MET cc_start: 0.7237 (mpp) cc_final: 0.6617 (mpp) REVERT: F 515 MET cc_start: 0.9186 (ttp) cc_final: 0.8819 (ttt) REVERT: F 603 MET cc_start: 0.8917 (ttp) cc_final: 0.8410 (tpp) REVERT: F 620 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8006 (mtp-110) REVERT: F 652 GLU cc_start: 0.8383 (pm20) cc_final: 0.8055 (mp0) REVERT: F 786 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8152 (pm20) outliers start: 92 outliers final: 59 residues processed: 449 average time/residue: 0.1671 time to fit residues: 119.8776 Evaluate side-chains 391 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 326 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain D residue 747 CYS Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 518 ILE Chi-restraints excluded: chain E residue 527 PHE Chi-restraints excluded: chain E residue 591 LYS Chi-restraints excluded: chain E residue 645 ASN Chi-restraints excluded: chain E residue 662 THR Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 212 GLN Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 620 ARG Chi-restraints excluded: chain F residue 632 VAL Chi-restraints excluded: chain F residue 650 ILE Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain F residue 753 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 306 optimal weight: 10.0000 chunk 159 optimal weight: 4.9990 chunk 180 optimal weight: 0.8980 chunk 182 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 227 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 269 optimal weight: 20.0000 chunk 322 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN B 328 ASN B 379 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 ASN ** D 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 438 HIS F 459 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.139631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.107130 restraints weight = 52537.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.109342 restraints weight = 31709.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.110668 restraints weight = 23341.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.111400 restraints weight = 18307.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.111516 restraints weight = 17091.188| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26825 Z= 0.155 Angle : 0.606 8.816 36361 Z= 0.299 Chirality : 0.044 0.227 4165 Planarity : 0.005 0.076 4679 Dihedral : 11.139 125.288 4018 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.83 % Favored : 96.11 % Rotamer: Outliers : 3.31 % Allowed : 13.70 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: 0.61 (0.15), residues: 3343 helix: 0.68 (0.12), residues: 1819 sheet: -0.15 (0.25), residues: 396 loop : 0.44 (0.21), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 362 TYR 0.018 0.001 TYR E 682 PHE 0.014 0.001 PHE D 288 TRP 0.025 0.001 TRP E 453 HIS 0.005 0.001 HIS F 438 Details of bonding type rmsd covalent geometry : bond 0.00364 (26825) covalent geometry : angle 0.60614 (36361) hydrogen bonds : bond 0.03753 ( 1314) hydrogen bonds : angle 4.39166 ( 3687) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 367 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 VAL cc_start: 0.8661 (t) cc_final: 0.8423 (p) REVERT: A 573 ASN cc_start: 0.8772 (OUTLIER) cc_final: 0.8513 (t0) REVERT: A 795 GLU cc_start: 0.8340 (mp0) cc_final: 0.8002 (mp0) REVERT: A 798 MET cc_start: 0.4460 (ptt) cc_final: 0.4237 (tpp) REVERT: A 799 HIS cc_start: 0.5639 (m170) cc_final: 0.4592 (t-170) REVERT: B 217 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7792 (mt-10) REVERT: B 294 LEU cc_start: 0.9193 (tp) cc_final: 0.8971 (tp) REVERT: B 359 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8180 (tt) REVERT: B 402 MET cc_start: 0.7972 (ptm) cc_final: 0.7515 (ttt) REVERT: B 515 MET cc_start: 0.6999 (ttp) cc_final: 0.6437 (ttp) REVERT: B 731 PHE cc_start: 0.7986 (m-80) cc_final: 0.7334 (m-80) REVERT: B 735 ASP cc_start: 0.6801 (m-30) cc_final: 0.6382 (m-30) REVERT: B 740 MET cc_start: 0.6740 (tmm) cc_final: 0.6366 (tmm) REVERT: C 349 THR cc_start: 0.9267 (OUTLIER) cc_final: 0.9020 (t) REVERT: C 523 ASN cc_start: 0.8454 (OUTLIER) cc_final: 0.7932 (p0) REVERT: C 754 GLN cc_start: 0.7956 (mt0) cc_final: 0.7695 (mm-40) REVERT: D 318 MET cc_start: 0.7521 (tpp) cc_final: 0.7096 (tpp) REVERT: D 360 ARG cc_start: 0.8633 (ttm-80) cc_final: 0.8345 (ttm-80) REVERT: D 431 LEU cc_start: 0.8884 (mt) cc_final: 0.8617 (tt) REVERT: D 782 LYS cc_start: 0.8603 (mmmt) cc_final: 0.8311 (mmmm) REVERT: E 350 ASN cc_start: 0.7875 (p0) cc_final: 0.7576 (p0) REVERT: E 603 MET cc_start: 0.8492 (ttp) cc_final: 0.8207 (ttm) REVERT: E 649 MET cc_start: 0.6090 (mmt) cc_final: 0.5830 (mmt) REVERT: E 718 ASP cc_start: 0.8103 (m-30) cc_final: 0.7797 (t0) REVERT: E 752 TYR cc_start: 0.6816 (m-10) cc_final: 0.6400 (m-10) REVERT: E 780 TRP cc_start: 0.8303 (m100) cc_final: 0.7925 (m100) REVERT: F 254 HIS cc_start: 0.7438 (m90) cc_final: 0.7166 (m90) REVERT: F 330 MET cc_start: 0.7401 (mpp) cc_final: 0.6615 (mpp) REVERT: F 473 MET cc_start: 0.8485 (tmm) cc_final: 0.7965 (tpp) REVERT: F 515 MET cc_start: 0.9255 (ttp) cc_final: 0.8931 (ttt) REVERT: F 652 GLU cc_start: 0.8448 (pm20) cc_final: 0.8128 (mp0) REVERT: F 786 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8144 (pm20) outliers start: 93 outliers final: 64 residues processed: 432 average time/residue: 0.1555 time to fit residues: 110.2040 Evaluate side-chains 398 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 330 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 523 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 297 CYS Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 518 ILE Chi-restraints excluded: chain E residue 591 LYS Chi-restraints excluded: chain E residue 645 ASN Chi-restraints excluded: chain E residue 662 THR Chi-restraints excluded: chain E residue 748 LEU Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 353 GLU Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 620 ARG Chi-restraints excluded: chain F residue 621 VAL Chi-restraints excluded: chain F residue 650 ILE Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 18 optimal weight: 5.9990 chunk 193 optimal weight: 30.0000 chunk 98 optimal weight: 9.9990 chunk 162 optimal weight: 30.0000 chunk 247 optimal weight: 30.0000 chunk 2 optimal weight: 9.9990 chunk 20 optimal weight: 0.5980 chunk 151 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 250 optimal weight: 50.0000 chunk 97 optimal weight: 20.0000 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 738 ASN B 328 ASN B 379 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS F 438 HIS F 557 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.137718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.106332 restraints weight = 52783.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.107597 restraints weight = 30190.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.108163 restraints weight = 22215.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.108988 restraints weight = 21083.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.109025 restraints weight = 18014.421| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3539 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3539 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26825 Z= 0.174 Angle : 0.619 9.396 36361 Z= 0.305 Chirality : 0.044 0.249 4165 Planarity : 0.005 0.056 4679 Dihedral : 10.960 130.695 4016 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.19 % Favored : 95.75 % Rotamer: Outliers : 3.49 % Allowed : 15.19 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: 0.71 (0.15), residues: 3343 helix: 0.81 (0.12), residues: 1794 sheet: -0.29 (0.24), residues: 396 loop : 0.48 (0.21), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 362 TYR 0.012 0.001 TYR F 406 PHE 0.014 0.002 PHE A 600 TRP 0.023 0.001 TRP E 453 HIS 0.006 0.001 HIS F 438 Details of bonding type rmsd covalent geometry : bond 0.00411 (26825) covalent geometry : angle 0.61878 (36361) hydrogen bonds : bond 0.03649 ( 1314) hydrogen bonds : angle 4.32968 ( 3687) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 360 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 VAL cc_start: 0.8720 (t) cc_final: 0.8497 (p) REVERT: A 330 MET cc_start: 0.8181 (mtm) cc_final: 0.7584 (mpp) REVERT: A 578 GLU cc_start: 0.8011 (pt0) cc_final: 0.7696 (mp0) REVERT: A 795 GLU cc_start: 0.8419 (mp0) cc_final: 0.8076 (mp0) REVERT: A 798 MET cc_start: 0.4558 (ptt) cc_final: 0.4314 (tpp) REVERT: A 799 HIS cc_start: 0.5536 (m170) cc_final: 0.4499 (t-170) REVERT: B 217 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7788 (mt-10) REVERT: B 294 LEU cc_start: 0.9277 (tp) cc_final: 0.9058 (tp) REVERT: B 359 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8184 (tt) REVERT: B 402 MET cc_start: 0.8052 (ptm) cc_final: 0.7721 (ttt) REVERT: B 515 MET cc_start: 0.7139 (ttp) cc_final: 0.6563 (ttp) REVERT: B 731 PHE cc_start: 0.8227 (m-80) cc_final: 0.7404 (m-80) REVERT: B 735 ASP cc_start: 0.6952 (m-30) cc_final: 0.6466 (m-30) REVERT: B 740 MET cc_start: 0.6856 (tmm) cc_final: 0.6415 (tmm) REVERT: C 349 THR cc_start: 0.9285 (OUTLIER) cc_final: 0.9059 (t) REVERT: C 754 GLN cc_start: 0.8037 (mt0) cc_final: 0.7773 (mm-40) REVERT: C 792 LYS cc_start: 0.8022 (mmtm) cc_final: 0.7659 (mppt) REVERT: D 318 MET cc_start: 0.7739 (tpp) cc_final: 0.7340 (tpp) REVERT: D 360 ARG cc_start: 0.8665 (ttm-80) cc_final: 0.8390 (ttm-80) REVERT: D 431 LEU cc_start: 0.8879 (mt) cc_final: 0.8552 (tt) REVERT: D 782 LYS cc_start: 0.8670 (mmmt) cc_final: 0.8257 (mmtm) REVERT: E 231 MET cc_start: 0.6177 (tpp) cc_final: 0.5928 (tpp) REVERT: E 350 ASN cc_start: 0.7942 (p0) cc_final: 0.7620 (p0) REVERT: E 541 TRP cc_start: 0.7897 (p-90) cc_final: 0.7545 (p-90) REVERT: E 603 MET cc_start: 0.8485 (ttp) cc_final: 0.8193 (ttm) REVERT: E 649 MET cc_start: 0.6285 (mmt) cc_final: 0.6050 (mmt) REVERT: E 731 PHE cc_start: 0.7403 (m-10) cc_final: 0.7168 (m-10) REVERT: E 752 TYR cc_start: 0.7002 (m-10) cc_final: 0.6613 (m-10) REVERT: E 777 MET cc_start: 0.8310 (tmm) cc_final: 0.7596 (tmm) REVERT: F 330 MET cc_start: 0.7420 (mpp) cc_final: 0.7176 (mpp) REVERT: F 353 GLU cc_start: 0.5874 (OUTLIER) cc_final: 0.5263 (tp30) REVERT: F 515 MET cc_start: 0.9160 (ttp) cc_final: 0.8909 (ttt) REVERT: F 652 GLU cc_start: 0.8433 (pm20) cc_final: 0.8114 (mp0) REVERT: F 786 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8027 (pm20) outliers start: 98 outliers final: 70 residues processed: 428 average time/residue: 0.1542 time to fit residues: 106.5940 Evaluate side-chains 400 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 327 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 297 CYS Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 297 CYS Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 591 LYS Chi-restraints excluded: chain E residue 662 THR Chi-restraints excluded: chain E residue 748 LEU Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 353 GLU Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 621 VAL Chi-restraints excluded: chain F residue 650 ILE Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 61 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 103 optimal weight: 0.0570 chunk 227 optimal weight: 8.9990 chunk 43 optimal weight: 40.0000 chunk 10 optimal weight: 9.9990 chunk 323 optimal weight: 50.0000 chunk 83 optimal weight: 8.9990 chunk 314 optimal weight: 20.0000 chunk 113 optimal weight: 7.9990 chunk 184 optimal weight: 7.9990 overall best weight: 4.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 ASN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 756 GLN F 242 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.139177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.106898 restraints weight = 52487.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.108799 restraints weight = 32304.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.109429 restraints weight = 22101.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.110231 restraints weight = 20783.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.110452 restraints weight = 18248.545| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26825 Z= 0.153 Angle : 0.600 10.108 36361 Z= 0.295 Chirality : 0.043 0.191 4165 Planarity : 0.004 0.091 4679 Dihedral : 10.854 133.428 4016 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.95 % Favored : 95.99 % Rotamer: Outliers : 3.24 % Allowed : 15.47 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: 0.79 (0.15), residues: 3343 helix: 0.92 (0.12), residues: 1796 sheet: -0.38 (0.24), residues: 396 loop : 0.50 (0.21), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 375 TYR 0.018 0.001 TYR F 665 PHE 0.013 0.001 PHE D 288 TRP 0.035 0.001 TRP E 453 HIS 0.003 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00364 (26825) covalent geometry : angle 0.59952 (36361) hydrogen bonds : bond 0.03424 ( 1314) hydrogen bonds : angle 4.24040 ( 3687) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 360 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 VAL cc_start: 0.8755 (t) cc_final: 0.8520 (p) REVERT: A 330 MET cc_start: 0.8213 (mtm) cc_final: 0.7598 (mpp) REVERT: A 515 MET cc_start: 0.7282 (mtm) cc_final: 0.7016 (mtm) REVERT: A 578 GLU cc_start: 0.7885 (pt0) cc_final: 0.7646 (mp0) REVERT: A 795 GLU cc_start: 0.8481 (mp0) cc_final: 0.8049 (mp0) REVERT: A 799 HIS cc_start: 0.5568 (m170) cc_final: 0.4528 (t-170) REVERT: B 217 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7736 (mt-10) REVERT: B 294 LEU cc_start: 0.9235 (tp) cc_final: 0.9010 (tp) REVERT: B 321 ARG cc_start: 0.7914 (mtm180) cc_final: 0.7403 (ptp-170) REVERT: B 353 GLU cc_start: 0.7763 (mp0) cc_final: 0.7541 (mp0) REVERT: B 359 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8249 (tt) REVERT: B 402 MET cc_start: 0.8011 (ptm) cc_final: 0.7607 (ttt) REVERT: B 515 MET cc_start: 0.7157 (ttp) cc_final: 0.6594 (ttp) REVERT: B 731 PHE cc_start: 0.8103 (m-80) cc_final: 0.7379 (m-80) REVERT: B 735 ASP cc_start: 0.6873 (m-30) cc_final: 0.6454 (m-30) REVERT: B 740 MET cc_start: 0.6766 (tmm) cc_final: 0.6330 (tmm) REVERT: C 349 THR cc_start: 0.9243 (OUTLIER) cc_final: 0.9010 (t) REVERT: C 402 MET cc_start: 0.8359 (ptp) cc_final: 0.8119 (ptm) REVERT: C 523 ASN cc_start: 0.8487 (OUTLIER) cc_final: 0.7947 (p0) REVERT: C 754 GLN cc_start: 0.7995 (mt0) cc_final: 0.7757 (mm-40) REVERT: C 792 LYS cc_start: 0.8085 (mmtm) cc_final: 0.7734 (mppt) REVERT: D 318 MET cc_start: 0.7837 (tpp) cc_final: 0.7496 (tpp) REVERT: D 351 ARG cc_start: 0.8089 (ttp-110) cc_final: 0.7786 (ttp-110) REVERT: D 431 LEU cc_start: 0.8827 (mt) cc_final: 0.8532 (tt) REVERT: D 782 LYS cc_start: 0.8646 (mmmt) cc_final: 0.8429 (mmmm) REVERT: D 798 MET cc_start: 0.7265 (mmm) cc_final: 0.7006 (mmt) REVERT: E 350 ASN cc_start: 0.7866 (p0) cc_final: 0.7478 (p0) REVERT: E 541 TRP cc_start: 0.7910 (p-90) cc_final: 0.7567 (p-90) REVERT: E 603 MET cc_start: 0.8464 (ttp) cc_final: 0.8172 (ttm) REVERT: E 625 LEU cc_start: 0.8737 (tt) cc_final: 0.8520 (tp) REVERT: E 649 MET cc_start: 0.6371 (mmt) cc_final: 0.6165 (mmt) REVERT: E 752 TYR cc_start: 0.7081 (m-10) cc_final: 0.6695 (m-10) REVERT: F 215 LEU cc_start: 0.7632 (tt) cc_final: 0.7399 (pp) REVERT: F 330 MET cc_start: 0.7383 (mpp) cc_final: 0.7160 (mpp) REVERT: F 515 MET cc_start: 0.9170 (ttp) cc_final: 0.8966 (ttt) REVERT: F 650 ILE cc_start: 0.4447 (OUTLIER) cc_final: 0.3487 (tp) REVERT: F 652 GLU cc_start: 0.8455 (pm20) cc_final: 0.8081 (mp0) REVERT: F 786 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8053 (pm20) outliers start: 91 outliers final: 67 residues processed: 423 average time/residue: 0.1532 time to fit residues: 104.8678 Evaluate side-chains 400 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 329 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 523 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 297 CYS Chi-restraints excluded: chain E residue 316 LYS Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 591 LYS Chi-restraints excluded: chain E residue 645 ASN Chi-restraints excluded: chain E residue 748 LEU Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 650 ILE Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 55 optimal weight: 7.9990 chunk 242 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 69 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 192 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 313 optimal weight: 30.0000 chunk 58 optimal weight: 5.9990 chunk 165 optimal weight: 20.0000 chunk 244 optimal weight: 5.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 303 GLN B 328 ASN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 785 ASN E 412 GLN F 242 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.137188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.104638 restraints weight = 51859.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.107739 restraints weight = 29646.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.108390 restraints weight = 18075.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.109265 restraints weight = 17272.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.109366 restraints weight = 14888.559| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26825 Z= 0.164 Angle : 0.622 10.811 36361 Z= 0.304 Chirality : 0.044 0.262 4165 Planarity : 0.004 0.058 4679 Dihedral : 10.774 133.622 4016 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.13 % Favored : 95.81 % Rotamer: Outliers : 3.77 % Allowed : 15.40 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: 0.77 (0.15), residues: 3343 helix: 0.94 (0.12), residues: 1803 sheet: -0.47 (0.24), residues: 396 loop : 0.45 (0.21), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 362 TYR 0.017 0.001 TYR F 665 PHE 0.013 0.001 PHE D 288 TRP 0.030 0.002 TRP B 466 HIS 0.004 0.001 HIS E 254 Details of bonding type rmsd covalent geometry : bond 0.00390 (26825) covalent geometry : angle 0.62199 (36361) hydrogen bonds : bond 0.03385 ( 1314) hydrogen bonds : angle 4.19926 ( 3687) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 361 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 MET cc_start: 0.8121 (mtm) cc_final: 0.7484 (mpp) REVERT: A 799 HIS cc_start: 0.5486 (m170) cc_final: 0.4669 (t70) REVERT: B 217 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7757 (mt-10) REVERT: B 294 LEU cc_start: 0.9273 (tp) cc_final: 0.9066 (tp) REVERT: B 321 ARG cc_start: 0.7883 (mtm180) cc_final: 0.7275 (ptp-170) REVERT: B 353 GLU cc_start: 0.8010 (mp0) cc_final: 0.7684 (mp0) REVERT: B 359 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8075 (tt) REVERT: B 402 MET cc_start: 0.8122 (ptm) cc_final: 0.7830 (ttt) REVERT: B 515 MET cc_start: 0.7214 (ttp) cc_final: 0.6653 (ttp) REVERT: B 731 PHE cc_start: 0.8324 (m-80) cc_final: 0.7453 (m-80) REVERT: B 735 ASP cc_start: 0.6964 (m-30) cc_final: 0.6415 (m-30) REVERT: B 740 MET cc_start: 0.6923 (tmm) cc_final: 0.6443 (tmm) REVERT: C 349 THR cc_start: 0.9302 (OUTLIER) cc_final: 0.9068 (t) REVERT: C 402 MET cc_start: 0.8558 (ptp) cc_final: 0.8316 (ptm) REVERT: C 523 ASN cc_start: 0.8572 (OUTLIER) cc_final: 0.7979 (p0) REVERT: C 754 GLN cc_start: 0.8004 (mt0) cc_final: 0.7768 (mm110) REVERT: C 792 LYS cc_start: 0.8121 (mmtm) cc_final: 0.7736 (mppt) REVERT: D 318 MET cc_start: 0.7627 (tpp) cc_final: 0.7244 (tpp) REVERT: D 351 ARG cc_start: 0.8144 (ttp-110) cc_final: 0.7879 (ttp-110) REVERT: D 431 LEU cc_start: 0.8942 (mt) cc_final: 0.8655 (tt) REVERT: D 782 LYS cc_start: 0.8819 (mmmt) cc_final: 0.8427 (mmtm) REVERT: D 798 MET cc_start: 0.7188 (mmm) cc_final: 0.6939 (mmt) REVERT: E 350 ASN cc_start: 0.7924 (p0) cc_final: 0.7529 (p0) REVERT: E 498 THR cc_start: 0.8655 (m) cc_final: 0.8283 (p) REVERT: E 515 MET cc_start: 0.8280 (ptt) cc_final: 0.8010 (ptp) REVERT: E 541 TRP cc_start: 0.7952 (p-90) cc_final: 0.7607 (p-90) REVERT: E 603 MET cc_start: 0.8488 (ttp) cc_final: 0.8199 (ttm) REVERT: E 649 MET cc_start: 0.6557 (mmt) cc_final: 0.6304 (mmm) REVERT: E 752 TYR cc_start: 0.7155 (m-10) cc_final: 0.6807 (m-10) REVERT: F 330 MET cc_start: 0.7386 (mpp) cc_final: 0.7074 (mpp) REVERT: F 603 MET cc_start: 0.8663 (mmm) cc_final: 0.8291 (mmm) REVERT: F 650 ILE cc_start: 0.4630 (OUTLIER) cc_final: 0.3662 (tp) REVERT: F 652 GLU cc_start: 0.8496 (pm20) cc_final: 0.8101 (mp0) REVERT: F 786 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8074 (pm20) outliers start: 106 outliers final: 81 residues processed: 437 average time/residue: 0.1573 time to fit residues: 111.0332 Evaluate side-chains 418 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 333 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 433 GLN Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 523 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 297 CYS Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 297 CYS Chi-restraints excluded: chain E residue 316 LYS Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 591 LYS Chi-restraints excluded: chain E residue 662 THR Chi-restraints excluded: chain E residue 748 LEU Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 629 LEU Chi-restraints excluded: chain F residue 650 ILE Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 149 optimal weight: 10.0000 chunk 258 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 75 optimal weight: 0.3980 chunk 120 optimal weight: 30.0000 chunk 178 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 ASN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.136864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.106044 restraints weight = 52238.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.106383 restraints weight = 30459.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.107992 restraints weight = 21782.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.110001 restraints weight = 17443.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.110035 restraints weight = 14982.667| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26825 Z= 0.127 Angle : 0.604 11.711 36361 Z= 0.295 Chirality : 0.043 0.186 4165 Planarity : 0.004 0.057 4679 Dihedral : 10.630 131.882 4016 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.98 % Favored : 95.96 % Rotamer: Outliers : 2.77 % Allowed : 16.54 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: 0.87 (0.15), residues: 3343 helix: 1.03 (0.12), residues: 1818 sheet: -0.50 (0.25), residues: 390 loop : 0.49 (0.21), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 759 TYR 0.014 0.001 TYR E 682 PHE 0.013 0.001 PHE D 288 TRP 0.034 0.001 TRP B 466 HIS 0.002 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00303 (26825) covalent geometry : angle 0.60382 (36361) hydrogen bonds : bond 0.03167 ( 1314) hydrogen bonds : angle 4.07594 ( 3687) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 374 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 MET cc_start: 0.8059 (mtm) cc_final: 0.7486 (mpp) REVERT: A 515 MET cc_start: 0.7508 (mtm) cc_final: 0.7307 (mtm) REVERT: A 795 GLU cc_start: 0.8131 (tp30) cc_final: 0.7866 (tp30) REVERT: A 799 HIS cc_start: 0.6084 (m170) cc_final: 0.5267 (t70) REVERT: B 217 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7687 (mt-10) REVERT: B 321 ARG cc_start: 0.7850 (mtm180) cc_final: 0.7271 (ptp-170) REVERT: B 353 GLU cc_start: 0.7935 (mp0) cc_final: 0.7644 (mp0) REVERT: B 359 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8137 (tt) REVERT: B 402 MET cc_start: 0.8064 (ptm) cc_final: 0.7819 (ttt) REVERT: B 515 MET cc_start: 0.7163 (ttp) cc_final: 0.6601 (ttp) REVERT: B 731 PHE cc_start: 0.8267 (m-80) cc_final: 0.7434 (m-80) REVERT: B 735 ASP cc_start: 0.6922 (m-30) cc_final: 0.6406 (m-30) REVERT: B 740 MET cc_start: 0.6848 (tmm) cc_final: 0.6377 (tmm) REVERT: C 351 ARG cc_start: 0.8290 (tpp-160) cc_final: 0.8021 (tpp-160) REVERT: C 402 MET cc_start: 0.8512 (ptp) cc_final: 0.8162 (ptm) REVERT: C 473 MET cc_start: 0.8633 (tpp) cc_final: 0.8283 (tpp) REVERT: C 523 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.7922 (p0) REVERT: C 754 GLN cc_start: 0.7989 (mt0) cc_final: 0.7769 (mm110) REVERT: C 792 LYS cc_start: 0.8108 (mmtm) cc_final: 0.7892 (mppt) REVERT: D 318 MET cc_start: 0.7550 (tpp) cc_final: 0.7313 (tpp) REVERT: D 351 ARG cc_start: 0.8101 (ttp-110) cc_final: 0.7760 (ttp-110) REVERT: D 360 ARG cc_start: 0.8703 (ttm-80) cc_final: 0.8451 (ttm-80) REVERT: D 431 LEU cc_start: 0.9056 (mt) cc_final: 0.8162 (tt) REVERT: D 782 LYS cc_start: 0.8773 (mmmt) cc_final: 0.8393 (mmtm) REVERT: E 350 ASN cc_start: 0.7796 (p0) cc_final: 0.7183 (t0) REVERT: E 355 LEU cc_start: 0.8627 (mm) cc_final: 0.8380 (mt) REVERT: E 498 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8230 (p) REVERT: E 515 MET cc_start: 0.8269 (ptt) cc_final: 0.8001 (ptp) REVERT: E 541 TRP cc_start: 0.7946 (p-90) cc_final: 0.7596 (p-90) REVERT: E 603 MET cc_start: 0.8498 (ttp) cc_final: 0.8231 (ttm) REVERT: E 649 MET cc_start: 0.6430 (mmt) cc_final: 0.6184 (mmm) REVERT: E 752 TYR cc_start: 0.7002 (m-10) cc_final: 0.6361 (m-10) REVERT: F 330 MET cc_start: 0.7390 (mpp) cc_final: 0.7121 (mpp) REVERT: F 369 MET cc_start: 0.4673 (mtm) cc_final: 0.4385 (mtm) REVERT: F 603 MET cc_start: 0.8641 (mmm) cc_final: 0.8299 (mmm) REVERT: F 650 ILE cc_start: 0.4655 (OUTLIER) cc_final: 0.3794 (tp) REVERT: F 652 GLU cc_start: 0.8440 (pm20) cc_final: 0.8040 (mp0) REVERT: F 786 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8048 (pm20) outliers start: 78 outliers final: 65 residues processed: 432 average time/residue: 0.1612 time to fit residues: 112.1230 Evaluate side-chains 417 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 348 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 523 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 297 CYS Chi-restraints excluded: chain E residue 316 LYS Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 591 LYS Chi-restraints excluded: chain E residue 662 THR Chi-restraints excluded: chain E residue 748 LEU Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 650 ILE Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 219 optimal weight: 5.9990 chunk 318 optimal weight: 50.0000 chunk 66 optimal weight: 0.3980 chunk 163 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 275 optimal weight: 50.0000 chunk 10 optimal weight: 0.0010 chunk 261 optimal weight: 1.9990 chunk 285 optimal weight: 0.0060 chunk 175 optimal weight: 2.9990 overall best weight: 0.6804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 ASN B 395 ASN B 412 GLN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 GLN F 242 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.140980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.106871 restraints weight = 52526.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.109978 restraints weight = 29979.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.112086 restraints weight = 20762.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.113385 restraints weight = 16290.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.114279 restraints weight = 13998.505| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3647 r_free = 0.3647 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3647 r_free = 0.3647 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26825 Z= 0.110 Angle : 0.614 11.762 36361 Z= 0.297 Chirality : 0.043 0.175 4165 Planarity : 0.004 0.074 4679 Dihedral : 10.392 129.737 4016 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.95 % Favored : 95.99 % Rotamer: Outliers : 2.03 % Allowed : 18.04 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: 0.99 (0.15), residues: 3343 helix: 1.14 (0.12), residues: 1830 sheet: -0.40 (0.25), residues: 390 loop : 0.50 (0.21), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 477 TYR 0.012 0.001 TYR F 665 PHE 0.016 0.001 PHE C 354 TRP 0.038 0.001 TRP B 466 HIS 0.002 0.000 HIS A 502 Details of bonding type rmsd covalent geometry : bond 0.00252 (26825) covalent geometry : angle 0.61356 (36361) hydrogen bonds : bond 0.03041 ( 1314) hydrogen bonds : angle 3.98817 ( 3687) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 394 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 MET cc_start: 0.7909 (mtm) cc_final: 0.7312 (mpp) REVERT: A 515 MET cc_start: 0.7459 (mtm) cc_final: 0.7246 (mtm) REVERT: A 795 GLU cc_start: 0.7973 (tp30) cc_final: 0.7618 (tp30) REVERT: A 799 HIS cc_start: 0.6250 (m170) cc_final: 0.5461 (t-170) REVERT: B 294 LEU cc_start: 0.9063 (tp) cc_final: 0.8851 (tp) REVERT: B 321 ARG cc_start: 0.7828 (mtm180) cc_final: 0.7347 (ptp-170) REVERT: B 353 GLU cc_start: 0.7764 (mp0) cc_final: 0.7523 (mp0) REVERT: B 361 ARG cc_start: 0.8246 (ptt90) cc_final: 0.7577 (tmm160) REVERT: B 402 MET cc_start: 0.7804 (ptm) cc_final: 0.7512 (ttt) REVERT: B 515 MET cc_start: 0.7094 (ttp) cc_final: 0.6496 (ttp) REVERT: B 731 PHE cc_start: 0.7932 (m-80) cc_final: 0.7236 (m-80) REVERT: B 735 ASP cc_start: 0.6787 (m-30) cc_final: 0.6426 (m-30) REVERT: B 740 MET cc_start: 0.6692 (tmm) cc_final: 0.6253 (tmm) REVERT: C 402 MET cc_start: 0.8174 (ptp) cc_final: 0.7965 (ptm) REVERT: C 523 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.7899 (p0) REVERT: C 792 LYS cc_start: 0.7974 (mmtm) cc_final: 0.7757 (mppt) REVERT: D 318 MET cc_start: 0.7701 (tpp) cc_final: 0.7488 (tpp) REVERT: D 726 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8717 (tp) REVERT: D 782 LYS cc_start: 0.8602 (mmmt) cc_final: 0.8301 (mmtm) REVERT: E 350 ASN cc_start: 0.7715 (p0) cc_final: 0.7119 (t0) REVERT: E 355 LEU cc_start: 0.8563 (mm) cc_final: 0.8352 (mt) REVERT: E 498 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.8169 (p) REVERT: E 515 MET cc_start: 0.8147 (ptt) cc_final: 0.7898 (ptp) REVERT: E 541 TRP cc_start: 0.7945 (p-90) cc_final: 0.7627 (p-90) REVERT: E 603 MET cc_start: 0.8443 (ttp) cc_final: 0.8206 (ttm) REVERT: F 369 MET cc_start: 0.4360 (mtm) cc_final: 0.4082 (mtm) REVERT: F 402 MET cc_start: 0.7149 (ptt) cc_final: 0.5967 (ppp) REVERT: F 603 MET cc_start: 0.8640 (mmm) cc_final: 0.8276 (mmm) REVERT: F 652 GLU cc_start: 0.8435 (pm20) cc_final: 0.8057 (mp0) REVERT: F 745 GLN cc_start: 0.8187 (mt0) cc_final: 0.7956 (mt0) REVERT: F 786 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8082 (pm20) outliers start: 57 outliers final: 46 residues processed: 431 average time/residue: 0.1552 time to fit residues: 109.0003 Evaluate side-chains 401 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 352 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 433 GLN Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 523 ASN Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 297 CYS Chi-restraints excluded: chain E residue 316 LYS Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 591 LYS Chi-restraints excluded: chain E residue 654 ILE Chi-restraints excluded: chain E residue 662 THR Chi-restraints excluded: chain E residue 748 LEU Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 214 optimal weight: 7.9990 chunk 275 optimal weight: 50.0000 chunk 48 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 141 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 50 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 ASN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS F 328 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.135138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.104322 restraints weight = 52521.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.105259 restraints weight = 30104.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.106229 restraints weight = 22612.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.106635 restraints weight = 20098.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.107507 restraints weight = 16673.546| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3517 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3517 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26825 Z= 0.186 Angle : 0.676 14.794 36361 Z= 0.328 Chirality : 0.045 0.171 4165 Planarity : 0.005 0.059 4679 Dihedral : 10.429 129.092 4016 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.25 % Favored : 95.72 % Rotamer: Outliers : 2.13 % Allowed : 19.00 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: 0.84 (0.15), residues: 3343 helix: 1.04 (0.12), residues: 1804 sheet: -0.42 (0.25), residues: 377 loop : 0.35 (0.20), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 489 TYR 0.020 0.001 TYR E 639 PHE 0.025 0.002 PHE B 600 TRP 0.050 0.002 TRP B 466 HIS 0.003 0.001 HIS E 254 Details of bonding type rmsd covalent geometry : bond 0.00447 (26825) covalent geometry : angle 0.67593 (36361) hydrogen bonds : bond 0.03388 ( 1314) hydrogen bonds : angle 4.19148 ( 3687) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 353 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 MET cc_start: 0.7937 (mtm) cc_final: 0.7332 (mpp) REVERT: A 515 MET cc_start: 0.7475 (mtm) cc_final: 0.7231 (mtm) REVERT: B 321 ARG cc_start: 0.7914 (mtm180) cc_final: 0.7235 (ptp-170) REVERT: B 402 MET cc_start: 0.8126 (ptm) cc_final: 0.7894 (ttt) REVERT: B 515 MET cc_start: 0.7243 (ttp) cc_final: 0.6709 (ttp) REVERT: B 731 PHE cc_start: 0.8320 (m-80) cc_final: 0.7477 (m-80) REVERT: B 735 ASP cc_start: 0.6998 (m-30) cc_final: 0.6400 (m-30) REVERT: B 740 MET cc_start: 0.6959 (tmm) cc_final: 0.6475 (tmm) REVERT: C 402 MET cc_start: 0.8432 (ptp) cc_final: 0.8218 (ptm) REVERT: C 603 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7275 (ppp) REVERT: C 792 LYS cc_start: 0.8108 (mmtm) cc_final: 0.7888 (mppt) REVERT: C 798 MET cc_start: 0.6765 (tmm) cc_final: 0.6109 (mtp) REVERT: D 318 MET cc_start: 0.7532 (tpp) cc_final: 0.7158 (tpp) REVERT: D 410 ASP cc_start: 0.7580 (m-30) cc_final: 0.7328 (t0) REVERT: D 726 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8665 (tt) REVERT: D 727 ARG cc_start: 0.8543 (mtm180) cc_final: 0.8128 (mtm180) REVERT: D 782 LYS cc_start: 0.8800 (mmmt) cc_final: 0.8574 (mmmm) REVERT: D 798 MET cc_start: 0.6991 (mmm) cc_final: 0.6720 (ptm) REVERT: E 350 ASN cc_start: 0.7859 (p0) cc_final: 0.7258 (t0) REVERT: E 498 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8240 (p) REVERT: E 515 MET cc_start: 0.8313 (ptt) cc_final: 0.8049 (ptp) REVERT: E 541 TRP cc_start: 0.8058 (p-90) cc_final: 0.7700 (p-90) REVERT: E 603 MET cc_start: 0.8502 (ttp) cc_final: 0.8266 (ttm) REVERT: E 649 MET cc_start: 0.6554 (mmt) cc_final: 0.6310 (mmm) REVERT: F 369 MET cc_start: 0.4676 (mtm) cc_final: 0.4377 (mtm) REVERT: F 402 MET cc_start: 0.7252 (ptt) cc_final: 0.6108 (ppp) REVERT: F 508 ASP cc_start: 0.8044 (t0) cc_final: 0.7433 (m-30) REVERT: F 603 MET cc_start: 0.8611 (mmm) cc_final: 0.8301 (mmm) REVERT: F 652 GLU cc_start: 0.8497 (pm20) cc_final: 0.8084 (mp0) REVERT: F 745 GLN cc_start: 0.8268 (mt0) cc_final: 0.7978 (mt0) outliers start: 60 outliers final: 53 residues processed: 395 average time/residue: 0.1527 time to fit residues: 97.7757 Evaluate side-chains 391 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 335 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 433 GLN Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain D residue 747 CYS Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 297 CYS Chi-restraints excluded: chain E residue 316 LYS Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 591 LYS Chi-restraints excluded: chain E residue 662 THR Chi-restraints excluded: chain E residue 748 LEU Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 632 VAL Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 45 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 227 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 241 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 259 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 ASN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.136369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.104006 restraints weight = 52146.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.106776 restraints weight = 30148.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.107481 restraints weight = 19197.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.108001 restraints weight = 17971.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.108232 restraints weight = 15723.603| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26825 Z= 0.149 Angle : 0.662 14.760 36361 Z= 0.319 Chirality : 0.044 0.197 4165 Planarity : 0.004 0.058 4679 Dihedral : 10.404 126.008 4016 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.13 % Favored : 95.84 % Rotamer: Outliers : 2.17 % Allowed : 19.03 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: 0.86 (0.15), residues: 3343 helix: 1.09 (0.12), residues: 1793 sheet: -0.46 (0.26), residues: 378 loop : 0.34 (0.20), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 360 TYR 0.014 0.001 TYR D 406 PHE 0.028 0.002 PHE B 600 TRP 0.040 0.001 TRP B 466 HIS 0.006 0.001 HIS F 254 Details of bonding type rmsd covalent geometry : bond 0.00358 (26825) covalent geometry : angle 0.66187 (36361) hydrogen bonds : bond 0.03252 ( 1314) hydrogen bonds : angle 4.15117 ( 3687) =============================================================================== Job complete usr+sys time: 4203.85 seconds wall clock time: 73 minutes 27.19 seconds (4407.19 seconds total)