Starting phenix.real_space_refine on Mon Jun 23 01:04:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t0v_25582/06_2025/7t0v_25582.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t0v_25582/06_2025/7t0v_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_25582/06_2025/7t0v_25582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t0v_25582/06_2025/7t0v_25582.map" model { file = "/net/cci-nas-00/data/ceres_data/7t0v_25582/06_2025/7t0v_25582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t0v_25582/06_2025/7t0v_25582.cif" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 3, 'ARG:plan': 1} 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: {'GLU:plan': 1, 'ARG: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: {'GLU:plan': 3, 'ARG:plan': 1} 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: {'GLU:plan': 3, 'ARG:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} 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: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} 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: 15.76, per 1000 atoms: 0.60 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: 6.49 Conformation dependent library (CDL) restraints added in 3.8 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: 2.84 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: 10.00 Time building geometry restraints manager: 7.76 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: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.200 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 59.650 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.130 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.400 ------------------------------------------------------------------------------- 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 : 10.12 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (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 TRP 0.019 0.002 TRP E 500 HIS 0.003 0.001 HIS C 254 PHE 0.017 0.002 PHE B 600 TYR 0.017 0.001 TYR B 752 ARG 0.007 0.001 ARG D 361 Details of bonding type rmsd hydrogen bonds : bond 0.27120 ( 1314) hydrogen bonds : angle 7.56523 ( 3687) covalent geometry : bond 0.00410 (26825) covalent geometry : angle 0.72623 (36361) *********************** 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 : 3.244 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: 0.7645 (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: 0.4400 time to fit residues: 564.9154 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 : 3.308 ------------------------------------------------------------------------------- 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 284 optimal weight: 40.0000 chunk 255 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 172 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 chunk 264 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 160 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 306 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.140202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.108442 restraints weight = 52220.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.108049 restraints weight = 31116.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.109011 restraints weight = 25038.387| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 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 = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 26825 Z= 0.171 Angle : 0.686 11.885 36361 Z= 0.347 Chirality : 0.046 0.314 4165 Planarity : 0.006 0.073 4679 Dihedral : 11.651 118.483 4022 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.77 % Favored : 96.17 % Rotamer: Outliers : 2.81 % Allowed : 11.21 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.15), residues: 3343 helix: 0.34 (0.12), residues: 1827 sheet: 0.36 (0.25), residues: 400 loop : 0.48 (0.21), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 219 HIS 0.008 0.001 HIS B 459 PHE 0.021 0.002 PHE B 731 TYR 0.022 0.001 TYR E 682 ARG 0.012 0.001 ARG A 362 Details of bonding type rmsd hydrogen bonds : bond 0.05170 ( 1314) hydrogen bonds : angle 4.95544 ( 3687) covalent geometry : bond 0.00393 (26825) covalent geometry : angle 0.68614 (36361) *********************** 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 561 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 482 time to evaluate : 3.392 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: 0.8510 (pt) cc_final: 0.8302 (mt) REVERT: A 798 MET cc_start: 0.4809 (ptt) cc_final: 0.4217 (tpp) REVERT: A 799 HIS cc_start: 0.5641 (m170) cc_final: 0.4555 (t-170) REVERT: B 294 LEU cc_start: 0.9207 (tp) cc_final: 0.8815 (tp) REVERT: B 390 LEU cc_start: 0.8153 (mp) cc_final: 0.7935 (tp) REVERT: B 402 MET cc_start: 0.7891 (ptm) cc_final: 0.7637 (ttt) REVERT: B 731 PHE cc_start: 0.7734 (m-80) cc_final: 0.7350 (m-80) REVERT: B 735 ASP cc_start: 0.7199 (m-30) cc_final: 0.6830 (m-30) REVERT: C 482 LEU cc_start: 0.8872 (mm) cc_final: 0.8618 (tp) REVERT: C 754 GLN cc_start: 0.8002 (mt0) cc_final: 0.7740 (mm-40) REVERT: D 222 LEU cc_start: 0.9233 (mt) cc_final: 0.8944 (mp) REVERT: D 318 MET cc_start: 0.7706 (tpp) cc_final: 0.6810 (tpp) REVERT: D 431 LEU cc_start: 0.8915 (mt) cc_final: 0.8687 (tt) REVERT: D 585 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.7003 (tp40) REVERT: D 740 MET cc_start: 0.8255 (ttp) cc_final: 0.7868 (ttt) REVERT: E 350 ASN cc_start: 0.7713 (p0) cc_final: 0.7402 (p0) REVERT: E 603 MET cc_start: 0.8307 (ttp) cc_final: 0.8089 (ttm) REVERT: E 718 ASP cc_start: 0.8005 (m-30) cc_final: 0.7763 (t0) REVERT: E 752 TYR cc_start: 0.6882 (m-10) cc_final: 0.6636 (m-80) REVERT: E 780 TRP cc_start: 0.8265 (m100) cc_final: 0.7901 (m100) REVERT: F 212 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8563 (pp30) REVERT: F 515 MET cc_start: 0.8992 (ttp) cc_final: 0.8632 (ttt) REVERT: F 652 GLU cc_start: 0.7889 (pm20) cc_final: 0.7685 (mp0) REVERT: F 786 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8009 (pm20) outliers start: 79 outliers final: 46 residues processed: 537 average time/residue: 0.4601 time to fit residues: 388.2270 Evaluate side-chains 408 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 360 time to evaluate : 3.190 ------------------------------------------------------------------------------- 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 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 433 GLN Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 517 ILE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 571 LEU 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 E residue 297 CYS 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 304 ILE Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 362 ARG 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 132 optimal weight: 0.0030 chunk 192 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 333 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 79 optimal weight: 0.0270 chunk 82 optimal weight: 5.9990 chunk 285 optimal weight: 8.9990 chunk 111 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 overall best weight: 4.2054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN B 242 HIS ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 HIS D 426 ASN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.141214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.108686 restraints weight = 52382.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.110337 restraints weight = 34253.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.112383 restraints weight = 22906.135| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3674 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= 0.156 Angle : 0.631 8.467 36361 Z= 0.312 Chirality : 0.045 0.218 4165 Planarity : 0.005 0.065 4679 Dihedral : 11.326 120.252 4018 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.77 % Favored : 96.14 % Rotamer: Outliers : 3.02 % Allowed : 13.27 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.15), residues: 3343 helix: 0.57 (0.12), residues: 1831 sheet: 0.07 (0.25), residues: 396 loop : 0.48 (0.21), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 453 HIS 0.005 0.001 HIS F 254 PHE 0.018 0.002 PHE E 354 TYR 0.021 0.001 TYR E 682 ARG 0.007 0.001 ARG C 334 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 1314) hydrogen bonds : angle 4.56156 ( 3687) covalent geometry : bond 0.00360 (26825) covalent geometry : angle 0.63055 (36361) *********************** 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 478 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 393 time to evaluate : 3.139 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 272 VAL cc_start: 0.8636 (t) cc_final: 0.8358 (p) REVERT: A 466 TRP cc_start: 0.7310 (m-90) cc_final: 0.6877 (m-90) REVERT: A 798 MET cc_start: 0.4627 (ptt) cc_final: 0.4190 (tpp) REVERT: A 799 HIS cc_start: 0.5659 (m170) cc_final: 0.4588 (t-170) REVERT: B 294 LEU cc_start: 0.9217 (tp) cc_final: 0.8818 (tp) REVERT: B 515 MET cc_start: 0.7070 (ttp) cc_final: 0.6431 (ttp) REVERT: B 731 PHE cc_start: 0.7782 (m-80) cc_final: 0.7320 (m-80) REVERT: B 735 ASP cc_start: 0.6730 (m-30) cc_final: 0.6342 (m-30) REVERT: B 740 MET cc_start: 0.6792 (tmm) cc_final: 0.6441 (tmm) REVERT: C 349 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.9032 (t) REVERT: C 360 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8085 (ttt-90) REVERT: C 538 ILE cc_start: 0.8707 (tp) cc_final: 0.8395 (tt) REVERT: D 222 LEU cc_start: 0.9190 (mt) cc_final: 0.8962 (mp) REVERT: D 431 LEU cc_start: 0.8875 (mt) cc_final: 0.8593 (tt) REVERT: E 350 ASN cc_start: 0.7877 (p0) cc_final: 0.7565 (p0) REVERT: E 603 MET cc_start: 0.8497 (ttp) cc_final: 0.8217 (ttm) REVERT: E 752 TYR cc_start: 0.6951 (m-10) cc_final: 0.6642 (m-80) REVERT: E 777 MET cc_start: 0.8446 (tmm) cc_final: 0.8015 (tmm) REVERT: E 780 TRP cc_start: 0.8230 (m100) cc_final: 0.7918 (m100) REVERT: F 212 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8539 (pp30) REVERT: F 318 MET cc_start: 0.4185 (tpp) cc_final: 0.3858 (tpt) REVERT: F 515 MET cc_start: 0.9074 (ttp) cc_final: 0.8768 (ttt) REVERT: F 603 MET cc_start: 0.8803 (ttp) cc_final: 0.8560 (mtp) REVERT: F 620 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.8005 (mtp-110) REVERT: F 740 MET cc_start: 0.8683 (tpp) cc_final: 0.8369 (tpp) REVERT: F 786 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8110 (pm20) outliers start: 85 outliers final: 53 residues processed: 452 average time/residue: 0.4421 time to fit residues: 323.7586 Evaluate side-chains 389 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 332 time to evaluate : 3.573 ------------------------------------------------------------------------------- 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 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 473 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 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 422 SER Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 551 VAL 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 566 ILE 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 292 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 384 LEU 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 654 ILE 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 272 VAL Chi-restraints excluded: chain F residue 304 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 23 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 169 optimal weight: 0.0670 chunk 328 optimal weight: 30.0000 chunk 44 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 202 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 258 optimal weight: 30.0000 chunk 295 optimal weight: 20.0000 chunk 333 optimal weight: 40.0000 chunk 315 optimal weight: 9.9990 overall best weight: 5.8126 ------------------------------------------------------------------------------- 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** C 684 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 = 0.3992 r_free = 0.3992 target = 0.139255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.106248 restraints weight = 53230.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.109108 restraints weight = 32124.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.110517 restraints weight = 21454.319| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 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 = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4047 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= 0.177 Angle : 0.627 9.721 36361 Z= 0.309 Chirality : 0.044 0.232 4165 Planarity : 0.005 0.078 4679 Dihedral : 11.092 121.449 4018 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.07 % Favored : 95.87 % Rotamer: Outliers : 3.42 % Allowed : 13.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.15), residues: 3343 helix: 0.74 (0.12), residues: 1817 sheet: -0.13 (0.24), residues: 396 loop : 0.49 (0.21), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 466 HIS 0.005 0.001 HIS F 438 PHE 0.015 0.002 PHE A 600 TYR 0.017 0.001 TYR E 682 ARG 0.007 0.001 ARG B 375 Details of bonding type rmsd hydrogen bonds : bond 0.03810 ( 1314) hydrogen bonds : angle 4.40817 ( 3687) covalent geometry : bond 0.00416 (26825) covalent geometry : angle 0.62666 (36361) *********************** 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 464 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 368 time to evaluate : 3.182 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 272 VAL cc_start: 0.8660 (t) cc_final: 0.8410 (p) REVERT: A 330 MET cc_start: 0.8284 (mtm) cc_final: 0.7722 (mpp) REVERT: A 578 GLU cc_start: 0.8061 (pt0) cc_final: 0.7780 (mp0) REVERT: A 630 ASP cc_start: 0.7682 (m-30) cc_final: 0.7100 (m-30) REVERT: A 795 GLU cc_start: 0.8434 (mp0) cc_final: 0.8103 (mp0) REVERT: A 798 MET cc_start: 0.4661 (ptt) cc_final: 0.4355 (tpp) REVERT: A 799 HIS cc_start: 0.5614 (m170) cc_final: 0.4564 (t-170) REVERT: B 294 LEU cc_start: 0.9253 (tp) cc_final: 0.9033 (tp) REVERT: B 321 ARG cc_start: 0.7936 (mtm110) cc_final: 0.7274 (ptp-170) REVERT: B 515 MET cc_start: 0.7027 (ttp) cc_final: 0.6467 (ttp) REVERT: B 731 PHE cc_start: 0.8008 (m-80) cc_final: 0.7412 (m-80) REVERT: B 735 ASP cc_start: 0.6882 (m-30) cc_final: 0.6502 (m-30) REVERT: B 740 MET cc_start: 0.6803 (tmm) cc_final: 0.6423 (tmm) REVERT: C 349 THR cc_start: 0.9270 (OUTLIER) cc_final: 0.9027 (t) REVERT: C 523 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.7959 (p0) REVERT: C 724 LEU cc_start: 0.8174 (tp) cc_final: 0.7954 (tt) REVERT: D 390 LEU cc_start: 0.8267 (mp) cc_final: 0.8016 (mt) REVERT: D 431 LEU cc_start: 0.8877 (mt) cc_final: 0.8604 (tt) REVERT: D 585 GLN cc_start: 0.7565 (tp40) cc_final: 0.7076 (tp-100) REVERT: D 782 LYS cc_start: 0.8602 (mmmt) cc_final: 0.8311 (mmmm) REVERT: E 350 ASN cc_start: 0.7887 (p0) cc_final: 0.7586 (p0) REVERT: E 603 MET cc_start: 0.8559 (ttp) cc_final: 0.8250 (ttm) REVERT: E 752 TYR cc_start: 0.6939 (m-10) cc_final: 0.6532 (m-10) REVERT: F 240 LEU cc_start: 0.7959 (tp) cc_final: 0.7200 (pp) REVERT: F 330 MET cc_start: 0.8006 (mpp) cc_final: 0.7698 (mpp) REVERT: F 515 MET cc_start: 0.9225 (ttp) cc_final: 0.8924 (ttt) REVERT: F 786 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8092 (pm20) outliers start: 96 outliers final: 64 residues processed: 433 average time/residue: 0.3648 time to fit residues: 254.8461 Evaluate side-chains 397 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 331 time to evaluate : 3.447 ------------------------------------------------------------------------------- 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 482 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 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 774 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 383 SER 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 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 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 346 LEU Chi-restraints excluded: chain D residue 351 ARG 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 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 518 ILE 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 346 LEU 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 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 217 optimal weight: 20.0000 chunk 241 optimal weight: 5.9990 chunk 224 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 240 optimal weight: 40.0000 chunk 335 optimal weight: 7.9990 chunk 177 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 198 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 325 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 GLN ** D 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 785 ASN F 242 HIS F 438 HIS F 557 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.138719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.108180 restraints weight = 52806.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.107868 restraints weight = 31006.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.108765 restraints weight = 24820.454| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26825 Z= 0.168 Angle : 0.612 9.123 36361 Z= 0.300 Chirality : 0.044 0.246 4165 Planarity : 0.004 0.056 4679 Dihedral : 10.932 126.612 4016 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.95 % Favored : 95.99 % Rotamer: Outliers : 3.49 % Allowed : 14.98 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.15), residues: 3343 helix: 0.85 (0.12), residues: 1808 sheet: -0.28 (0.25), residues: 394 loop : 0.50 (0.21), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 453 HIS 0.005 0.001 HIS F 438 PHE 0.013 0.002 PHE D 288 TYR 0.026 0.001 TYR E 682 ARG 0.006 0.001 ARG E 360 Details of bonding type rmsd hydrogen bonds : bond 0.03615 ( 1314) hydrogen bonds : angle 4.28955 ( 3687) covalent geometry : bond 0.00394 (26825) covalent geometry : angle 0.61185 (36361) *********************** 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 457 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 359 time to evaluate : 2.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 VAL cc_start: 0.8715 (t) cc_final: 0.8486 (p) REVERT: A 330 MET cc_start: 0.8204 (mtm) cc_final: 0.7505 (mpp) REVERT: A 466 TRP cc_start: 0.7457 (m-90) cc_final: 0.7248 (m-90) REVERT: A 578 GLU cc_start: 0.8001 (pt0) cc_final: 0.7665 (mp0) REVERT: A 795 GLU cc_start: 0.8473 (mp0) cc_final: 0.8111 (mp0) REVERT: A 798 MET cc_start: 0.4746 (ptt) cc_final: 0.4425 (tpp) REVERT: A 799 HIS cc_start: 0.5558 (m170) cc_final: 0.4523 (t-170) REVERT: B 294 LEU cc_start: 0.9236 (tp) cc_final: 0.9009 (tp) REVERT: B 402 MET cc_start: 0.8006 (ptm) cc_final: 0.7583 (ttt) REVERT: B 515 MET cc_start: 0.7027 (ttp) cc_final: 0.6452 (ttp) REVERT: B 731 PHE cc_start: 0.8141 (m-80) cc_final: 0.7381 (m-80) REVERT: B 735 ASP cc_start: 0.6955 (m-30) cc_final: 0.6513 (m-30) REVERT: B 740 MET cc_start: 0.6865 (tmm) cc_final: 0.6451 (tmm) REVERT: C 349 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.9008 (t) REVERT: C 523 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.7963 (p0) REVERT: C 792 LYS cc_start: 0.8046 (mmtm) cc_final: 0.7702 (mppt) REVERT: D 390 LEU cc_start: 0.8218 (mp) cc_final: 0.7924 (mt) REVERT: D 431 LEU cc_start: 0.8896 (mt) cc_final: 0.8581 (tt) REVERT: D 585 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.7009 (tp-100) REVERT: D 782 LYS cc_start: 0.8638 (mmmt) cc_final: 0.8216 (mmtm) REVERT: E 316 LYS cc_start: 0.7547 (ttpt) cc_final: 0.7328 (ptpp) REVERT: E 350 ASN cc_start: 0.7902 (p0) cc_final: 0.7577 (p0) REVERT: E 541 TRP cc_start: 0.7915 (p-90) cc_final: 0.7559 (p-90) REVERT: E 603 MET cc_start: 0.8547 (ttp) cc_final: 0.8228 (ttm) REVERT: E 649 MET cc_start: 0.6336 (mmt) cc_final: 0.6117 (mmt) REVERT: E 731 PHE cc_start: 0.7294 (m-10) cc_final: 0.7058 (m-10) REVERT: E 752 TYR cc_start: 0.6999 (m-10) cc_final: 0.6632 (m-10) REVERT: F 330 MET cc_start: 0.8168 (mpp) cc_final: 0.7487 (mpp) REVERT: F 515 MET cc_start: 0.9095 (ttp) cc_final: 0.8876 (ttt) REVERT: F 650 ILE cc_start: 0.3847 (OUTLIER) cc_final: 0.2921 (tp) REVERT: F 786 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8028 (pm20) outliers start: 98 outliers final: 72 residues processed: 428 average time/residue: 0.3678 time to fit residues: 253.3074 Evaluate side-chains 403 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 327 time to evaluate : 2.986 ------------------------------------------------------------------------------- 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 482 LEU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 603 MET 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 320 SER Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 369 MET 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 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 349 THR Chi-restraints excluded: chain C residue 353 GLU 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 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 429 SER Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 585 GLN 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 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 472 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 106 optimal weight: 20.0000 chunk 77 optimal weight: 7.9990 chunk 211 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 124 optimal weight: 30.0000 chunk 277 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 146 optimal weight: 0.9990 chunk 194 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 412 GLN F 242 HIS F 328 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.138730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.106458 restraints weight = 52567.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.108045 restraints weight = 32248.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.108815 restraints weight = 22369.078| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3518 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3518 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4504 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= 0.170 Angle : 0.615 10.089 36361 Z= 0.301 Chirality : 0.044 0.205 4165 Planarity : 0.005 0.089 4679 Dihedral : 10.862 128.667 4016 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.10 % Favored : 95.84 % Rotamer: Outliers : 3.49 % Allowed : 15.12 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.15), residues: 3343 helix: 0.90 (0.12), residues: 1808 sheet: -0.36 (0.25), residues: 396 loop : 0.50 (0.21), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP E 453 HIS 0.007 0.001 HIS F 254 PHE 0.012 0.002 PHE A 600 TYR 0.017 0.001 TYR F 665 ARG 0.015 0.001 ARG B 375 Details of bonding type rmsd hydrogen bonds : bond 0.03565 ( 1314) hydrogen bonds : angle 4.26365 ( 3687) covalent geometry : bond 0.00405 (26825) covalent geometry : angle 0.61511 (36361) *********************** 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 454 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 356 time to evaluate : 4.994 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: 0.8181 (mtm) cc_final: 0.7423 (mpp) REVERT: A 466 TRP cc_start: 0.7416 (m-90) cc_final: 0.6868 (m-90) REVERT: A 578 GLU cc_start: 0.8038 (pt0) cc_final: 0.7785 (mp0) REVERT: A 795 GLU cc_start: 0.8501 (mp0) cc_final: 0.8126 (mp0) REVERT: A 798 MET cc_start: 0.4624 (ptt) cc_final: 0.4364 (tpp) REVERT: A 799 HIS cc_start: 0.5533 (m170) cc_final: 0.4495 (t-170) REVERT: B 294 LEU cc_start: 0.9291 (tp) cc_final: 0.9072 (tp) REVERT: B 353 GLU cc_start: 0.7795 (mp0) cc_final: 0.7548 (mp0) REVERT: B 402 MET cc_start: 0.8012 (ptm) cc_final: 0.7763 (ttp) REVERT: B 515 MET cc_start: 0.7146 (ttp) cc_final: 0.6581 (ttp) REVERT: B 731 PHE cc_start: 0.8128 (m-80) cc_final: 0.7395 (m-80) REVERT: B 735 ASP cc_start: 0.6914 (m-30) cc_final: 0.6496 (m-30) REVERT: B 740 MET cc_start: 0.6867 (tmm) cc_final: 0.6413 (tmm) REVERT: C 349 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.9033 (t) REVERT: C 402 MET cc_start: 0.8413 (ptp) cc_final: 0.8167 (ptm) REVERT: C 523 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8005 (p0) REVERT: C 792 LYS cc_start: 0.8128 (mmtm) cc_final: 0.7764 (mppt) REVERT: D 351 ARG cc_start: 0.8124 (ttp-110) cc_final: 0.7737 (ttp-110) REVERT: D 390 LEU cc_start: 0.8222 (mp) cc_final: 0.7926 (mt) REVERT: D 431 LEU cc_start: 0.8861 (mt) cc_final: 0.8613 (tt) REVERT: D 727 ARG cc_start: 0.8371 (mtm180) cc_final: 0.7974 (mtm180) REVERT: D 782 LYS cc_start: 0.8749 (mmmt) cc_final: 0.8528 (mmmm) REVERT: D 798 MET cc_start: 0.7247 (mmm) cc_final: 0.6932 (mmt) REVERT: E 350 ASN cc_start: 0.7911 (p0) cc_final: 0.7534 (p0) REVERT: E 541 TRP cc_start: 0.7906 (p-90) cc_final: 0.7560 (p-90) REVERT: E 603 MET cc_start: 0.8517 (ttp) cc_final: 0.8206 (ttm) REVERT: E 752 TYR cc_start: 0.7051 (m-10) cc_final: 0.6614 (m-10) REVERT: F 330 MET cc_start: 0.8043 (mpp) cc_final: 0.7367 (mpp) REVERT: F 515 MET cc_start: 0.9277 (ttp) cc_final: 0.9009 (ttt) REVERT: F 650 ILE cc_start: 0.3821 (OUTLIER) cc_final: 0.2977 (tp) REVERT: F 652 GLU cc_start: 0.8415 (pm20) cc_final: 0.8176 (mp0) REVERT: F 778 GLU cc_start: 0.8662 (tp30) cc_final: 0.8430 (tm-30) REVERT: F 786 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8076 (pm20) outliers start: 98 outliers final: 75 residues processed: 426 average time/residue: 0.4444 time to fit residues: 314.7327 Evaluate side-chains 411 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 333 time to evaluate : 3.267 ------------------------------------------------------------------------------- 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 482 LEU 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 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 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 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 523 ASN 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 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 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 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 472 THR Chi-restraints excluded: chain E residue 532 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 65 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 172 optimal weight: 30.0000 chunk 90 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 302 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 13 optimal weight: 40.0000 chunk 47 optimal weight: 30.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 ASN B 379 GLN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 HIS ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 756 GLN F 242 HIS ** F 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.140009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.106415 restraints weight = 52281.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.109326 restraints weight = 30538.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.111301 restraints weight = 21500.234| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26825 Z= 0.131 Angle : 0.611 11.078 36361 Z= 0.296 Chirality : 0.043 0.230 4165 Planarity : 0.004 0.056 4679 Dihedral : 10.718 128.791 4016 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.98 % Favored : 95.96 % Rotamer: Outliers : 3.02 % Allowed : 16.33 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.15), residues: 3343 helix: 0.95 (0.12), residues: 1835 sheet: -0.36 (0.25), residues: 396 loop : 0.54 (0.21), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 466 HIS 0.007 0.001 HIS F 254 PHE 0.013 0.001 PHE D 288 TYR 0.017 0.001 TYR F 665 ARG 0.007 0.000 ARG C 351 Details of bonding type rmsd hydrogen bonds : bond 0.03306 ( 1314) hydrogen bonds : angle 4.12223 ( 3687) covalent geometry : bond 0.00310 (26825) covalent geometry : angle 0.61114 (36361) *********************** 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 460 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 375 time to evaluate : 2.926 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: 0.8062 (mtm) cc_final: 0.7358 (mpp) REVERT: A 795 GLU cc_start: 0.8335 (mp0) cc_final: 0.7935 (mp0) REVERT: A 799 HIS cc_start: 0.5637 (m170) cc_final: 0.4605 (t70) REVERT: B 294 LEU cc_start: 0.9205 (tp) cc_final: 0.9005 (tp) REVERT: B 353 GLU cc_start: 0.7791 (mp0) cc_final: 0.7555 (mp0) REVERT: B 359 ILE cc_start: 0.8528 (tt) cc_final: 0.8284 (tt) REVERT: B 402 MET cc_start: 0.7941 (ptm) cc_final: 0.7443 (ttt) REVERT: B 515 MET cc_start: 0.7122 (ttp) cc_final: 0.6535 (ttp) REVERT: B 731 PHE cc_start: 0.8025 (m-80) cc_final: 0.7309 (m-80) REVERT: B 735 ASP cc_start: 0.6848 (m-30) cc_final: 0.6450 (m-30) REVERT: B 740 MET cc_start: 0.6797 (tmm) cc_final: 0.6361 (tmm) REVERT: C 402 MET cc_start: 0.8299 (ptp) cc_final: 0.7986 (ptm) REVERT: C 523 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.7903 (p0) REVERT: C 792 LYS cc_start: 0.8048 (mmtm) cc_final: 0.7614 (mppt) REVERT: D 390 LEU cc_start: 0.8095 (mp) cc_final: 0.7702 (mt) REVERT: D 431 LEU cc_start: 0.8962 (mt) cc_final: 0.7958 (tt) REVERT: D 538 ILE cc_start: 0.8954 (mp) cc_final: 0.8750 (mt) REVERT: D 727 ARG cc_start: 0.8333 (mtm180) cc_final: 0.8033 (mtm180) REVERT: D 782 LYS cc_start: 0.8631 (mmmt) cc_final: 0.8302 (mmtm) REVERT: E 350 ASN cc_start: 0.7724 (p0) cc_final: 0.7297 (p0) REVERT: E 453 TRP cc_start: 0.7118 (m100) cc_final: 0.6910 (m100) REVERT: E 498 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8293 (p) REVERT: E 515 MET cc_start: 0.8085 (ptt) cc_final: 0.7808 (ptp) REVERT: E 541 TRP cc_start: 0.7928 (p-90) cc_final: 0.7584 (p-90) REVERT: E 603 MET cc_start: 0.8548 (ttp) cc_final: 0.8258 (ttm) REVERT: E 752 TYR cc_start: 0.7079 (m-10) cc_final: 0.6783 (m-10) REVERT: F 330 MET cc_start: 0.7945 (mpp) cc_final: 0.7343 (mpp) REVERT: F 351 ARG cc_start: 0.8071 (mmm160) cc_final: 0.7787 (tpt170) REVERT: F 508 ASP cc_start: 0.8218 (t0) cc_final: 0.7575 (m-30) REVERT: F 603 MET cc_start: 0.8706 (mmm) cc_final: 0.8381 (mmm) REVERT: F 620 ARG cc_start: 0.8283 (mtp180) cc_final: 0.8030 (mtp-110) REVERT: F 650 ILE cc_start: 0.4392 (OUTLIER) cc_final: 0.3590 (tp) REVERT: F 652 GLU cc_start: 0.8475 (pm20) cc_final: 0.8237 (mp0) REVERT: F 779 ASP cc_start: 0.6833 (m-30) cc_final: 0.5585 (m-30) REVERT: F 786 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8029 (pm20) outliers start: 85 outliers final: 65 residues processed: 433 average time/residue: 0.3661 time to fit residues: 254.7453 Evaluate side-chains 403 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 335 time to evaluate : 3.434 ------------------------------------------------------------------------------- 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 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 322 ILE Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 579 SER 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 798 MET Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 286 ASP 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 433 GLN 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 346 LEU 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 654 ILE Chi-restraints excluded: chain E residue 714 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 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 68 optimal weight: 30.0000 chunk 255 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 259 optimal weight: 8.9990 chunk 166 optimal weight: 1.9990 chunk 332 optimal weight: 30.0000 chunk 117 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 330 optimal weight: 30.0000 chunk 281 optimal weight: 50.0000 chunk 245 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS ** F 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.138713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.106807 restraints weight = 51846.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.108881 restraints weight = 30200.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.109983 restraints weight = 19498.497| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26825 Z= 0.139 Angle : 0.621 11.479 36361 Z= 0.301 Chirality : 0.043 0.169 4165 Planarity : 0.004 0.058 4679 Dihedral : 10.591 128.176 4016 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.16 % Favored : 95.78 % Rotamer: Outliers : 2.85 % Allowed : 17.11 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.15), residues: 3343 helix: 0.95 (0.12), residues: 1842 sheet: -0.35 (0.25), residues: 396 loop : 0.55 (0.21), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 466 HIS 0.006 0.001 HIS F 254 PHE 0.014 0.001 PHE D 288 TYR 0.014 0.001 TYR F 406 ARG 0.008 0.000 ARG C 477 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 1314) hydrogen bonds : angle 4.12236 ( 3687) covalent geometry : bond 0.00332 (26825) covalent geometry : angle 0.62084 (36361) *********************** 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 438 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 358 time to evaluate : 3.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 MET cc_start: 0.8150 (mtm) cc_final: 0.7430 (mpp) REVERT: A 515 MET cc_start: 0.7603 (mtm) cc_final: 0.6738 (mtm) REVERT: A 799 HIS cc_start: 0.5463 (m170) cc_final: 0.4580 (t70) REVERT: B 353 GLU cc_start: 0.8000 (mp0) cc_final: 0.7685 (mp0) REVERT: B 359 ILE cc_start: 0.8416 (tt) cc_final: 0.8139 (tt) REVERT: B 515 MET cc_start: 0.7176 (ttp) cc_final: 0.6621 (ttp) REVERT: B 731 PHE cc_start: 0.8249 (m-80) cc_final: 0.7421 (m-80) REVERT: B 735 ASP cc_start: 0.7004 (m-30) cc_final: 0.6514 (m-30) REVERT: B 740 MET cc_start: 0.6888 (tmm) cc_final: 0.6424 (tmm) REVERT: C 349 THR cc_start: 0.9287 (OUTLIER) cc_final: 0.9050 (t) REVERT: C 402 MET cc_start: 0.8444 (ptp) cc_final: 0.8203 (ptm) REVERT: C 523 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.7962 (p0) REVERT: C 792 LYS cc_start: 0.8124 (mmtm) cc_final: 0.7915 (mppt) REVERT: D 390 LEU cc_start: 0.8130 (mp) cc_final: 0.7780 (mt) REVERT: D 431 LEU cc_start: 0.8741 (mt) cc_final: 0.8539 (tt) REVERT: D 727 ARG cc_start: 0.8488 (mtm180) cc_final: 0.8076 (mtm180) REVERT: D 740 MET cc_start: 0.8377 (tmm) cc_final: 0.8105 (ppp) REVERT: D 782 LYS cc_start: 0.8807 (mmmt) cc_final: 0.8591 (mmmm) REVERT: D 798 MET cc_start: 0.7113 (mmm) cc_final: 0.6851 (ptm) REVERT: E 350 ASN cc_start: 0.7895 (p0) cc_final: 0.7280 (t0) REVERT: E 498 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.8198 (p) REVERT: E 515 MET cc_start: 0.8276 (ptt) cc_final: 0.8019 (ptp) REVERT: E 541 TRP cc_start: 0.7960 (p-90) cc_final: 0.7610 (p-90) REVERT: E 603 MET cc_start: 0.8490 (ttp) cc_final: 0.8193 (ttm) REVERT: F 330 MET cc_start: 0.8002 (mpp) cc_final: 0.7334 (mpp) REVERT: F 351 ARG cc_start: 0.8038 (mmm160) cc_final: 0.7728 (tpt170) REVERT: F 508 ASP cc_start: 0.8134 (t0) cc_final: 0.7507 (m-30) REVERT: F 515 MET cc_start: 0.9049 (ttt) cc_final: 0.8802 (tpt) REVERT: F 603 MET cc_start: 0.8669 (mmm) cc_final: 0.8271 (mmm) REVERT: F 620 ARG cc_start: 0.8322 (mtp180) cc_final: 0.8111 (mtp-110) REVERT: F 650 ILE cc_start: 0.4405 (OUTLIER) cc_final: 0.3692 (tp) REVERT: F 652 GLU cc_start: 0.8470 (pm20) cc_final: 0.8249 (mp0) REVERT: F 745 GLN cc_start: 0.8239 (mt0) cc_final: 0.7763 (mt0) REVERT: F 786 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8054 (pm20) outliers start: 80 outliers final: 66 residues processed: 414 average time/residue: 0.3714 time to fit residues: 247.3053 Evaluate side-chains 403 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 333 time to evaluate : 2.895 ------------------------------------------------------------------------------- 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 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 551 VAL Chi-restraints excluded: chain B residue 579 SER 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 798 MET 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 433 GLN 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 346 LEU 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 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 714 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 234 optimal weight: 9.9990 chunk 150 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 277 optimal weight: 9.9990 chunk 243 optimal weight: 0.0370 chunk 7 optimal weight: 8.9990 chunk 199 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 251 optimal weight: 9.9990 overall best weight: 2.3862 ------------------------------------------------------------------------------- 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 ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS ** F 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.139850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.108369 restraints weight = 52526.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.108963 restraints weight = 33780.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.109344 restraints weight = 24387.163| |-----------------------------------------------------------------------------| 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: 3 | |-----------------------------------------------------------------------------| |-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: 2 | |-----------------------------------------------------------------------------| r_final: 0.3559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26825 Z= 0.119 Angle : 0.615 12.168 36361 Z= 0.297 Chirality : 0.043 0.181 4165 Planarity : 0.004 0.059 4679 Dihedral : 10.415 125.837 4016 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.01 % Favored : 95.93 % Rotamer: Outliers : 2.45 % Allowed : 17.82 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.15), residues: 3343 helix: 1.13 (0.12), residues: 1821 sheet: -0.30 (0.25), residues: 393 loop : 0.56 (0.21), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 466 HIS 0.006 0.001 HIS F 254 PHE 0.016 0.001 PHE A 220 TYR 0.013 0.001 TYR F 406 ARG 0.006 0.000 ARG D 589 Details of bonding type rmsd hydrogen bonds : bond 0.03103 ( 1314) hydrogen bonds : angle 4.01665 ( 3687) covalent geometry : bond 0.00284 (26825) covalent geometry : angle 0.61495 (36361) *********************** 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 434 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 365 time to evaluate : 2.968 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: 0.8138 (mtm) cc_final: 0.7455 (mpp) REVERT: A 515 MET cc_start: 0.7489 (mtm) cc_final: 0.7050 (mtm) REVERT: A 639 TYR cc_start: 0.8257 (m-80) cc_final: 0.7990 (m-80) REVERT: A 799 HIS cc_start: 0.6025 (m170) cc_final: 0.4938 (t-170) REVERT: B 353 GLU cc_start: 0.7763 (mp0) cc_final: 0.7544 (mp0) REVERT: B 359 ILE cc_start: 0.8535 (tt) cc_final: 0.8264 (tt) REVERT: B 402 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7663 (ttt) REVERT: B 424 GLN cc_start: 0.8367 (tm-30) cc_final: 0.8147 (tm-30) REVERT: B 515 MET cc_start: 0.7136 (ttp) cc_final: 0.6549 (ttp) REVERT: B 731 PHE cc_start: 0.8074 (m-80) cc_final: 0.7295 (m-80) REVERT: B 735 ASP cc_start: 0.7019 (m-30) cc_final: 0.6604 (m-30) REVERT: B 740 MET cc_start: 0.6835 (tmm) cc_final: 0.6388 (tmm) REVERT: C 349 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.8983 (t) REVERT: C 351 ARG cc_start: 0.8191 (tpp-160) cc_final: 0.7938 (tpp-160) REVERT: C 402 MET cc_start: 0.8241 (ptp) cc_final: 0.8037 (ptm) REVERT: C 523 ASN cc_start: 0.8424 (OUTLIER) cc_final: 0.7888 (p0) REVERT: C 792 LYS cc_start: 0.8124 (mmtm) cc_final: 0.7901 (mppt) REVERT: D 431 LEU cc_start: 0.8695 (mt) cc_final: 0.8463 (tt) REVERT: D 726 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8650 (tt) REVERT: D 727 ARG cc_start: 0.8481 (mtm180) cc_final: 0.8153 (mtm180) REVERT: D 782 LYS cc_start: 0.8763 (mmmt) cc_final: 0.8368 (mmtm) REVERT: E 350 ASN cc_start: 0.7850 (p0) cc_final: 0.7225 (t0) REVERT: E 515 MET cc_start: 0.8298 (ptt) cc_final: 0.8048 (ptp) REVERT: E 541 TRP cc_start: 0.7948 (p-90) cc_final: 0.7620 (p-90) REVERT: E 603 MET cc_start: 0.8474 (ttp) cc_final: 0.8183 (ttm) REVERT: E 752 TYR cc_start: 0.7151 (m-10) cc_final: 0.6636 (m-10) REVERT: F 215 LEU cc_start: 0.7585 (tt) cc_final: 0.7364 (pp) REVERT: F 240 LEU cc_start: 0.7966 (tp) cc_final: 0.7240 (pp) REVERT: F 330 MET cc_start: 0.7954 (mpp) cc_final: 0.7641 (mpp) REVERT: F 508 ASP cc_start: 0.8193 (t0) cc_final: 0.7561 (m-30) REVERT: F 603 MET cc_start: 0.8631 (mmm) cc_final: 0.8291 (mmm) REVERT: F 620 ARG cc_start: 0.8331 (mtp180) cc_final: 0.7968 (mtp-110) REVERT: F 650 ILE cc_start: 0.4492 (OUTLIER) cc_final: 0.3715 (tp) REVERT: F 652 GLU cc_start: 0.8467 (pm20) cc_final: 0.8215 (mp0) REVERT: F 786 GLU cc_start: 0.8257 (mm-30) cc_final: 0.8017 (pm20) outliers start: 69 outliers final: 60 residues processed: 412 average time/residue: 0.3538 time to fit residues: 236.6769 Evaluate side-chains 400 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 335 time to evaluate : 2.970 ------------------------------------------------------------------------------- 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 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 320 SER Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 349 THR 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 433 GLN Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 523 ASN 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 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 92 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 124 optimal weight: 30.0000 chunk 269 optimal weight: 30.0000 chunk 97 optimal weight: 20.0000 chunk 115 optimal weight: 2.9990 chunk 219 optimal weight: 7.9990 chunk 325 optimal weight: 0.0670 chunk 123 optimal weight: 9.9990 chunk 8 optimal weight: 50.0000 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 ASN B 379 GLN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS ** F 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.136322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.104162 restraints weight = 52147.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.106512 restraints weight = 31800.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.107587 restraints weight = 20092.985| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 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 = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26825 Z= 0.149 Angle : 0.642 13.657 36361 Z= 0.309 Chirality : 0.044 0.272 4165 Planarity : 0.004 0.058 4679 Dihedral : 10.355 123.643 4016 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.16 % Favored : 95.81 % Rotamer: Outliers : 2.70 % Allowed : 18.07 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.15), residues: 3343 helix: 1.16 (0.12), residues: 1801 sheet: -0.33 (0.25), residues: 393 loop : 0.48 (0.21), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 466 HIS 0.006 0.001 HIS F 254 PHE 0.020 0.001 PHE A 220 TYR 0.014 0.001 TYR F 406 ARG 0.008 0.000 ARG F 489 Details of bonding type rmsd hydrogen bonds : bond 0.03207 ( 1314) hydrogen bonds : angle 4.06977 ( 3687) covalent geometry : bond 0.00358 (26825) covalent geometry : angle 0.64232 (36361) ********************** 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 425 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 349 time to evaluate : 3.175 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: 0.8168 (mtm) cc_final: 0.7462 (mpp) REVERT: A 515 MET cc_start: 0.7639 (mtm) cc_final: 0.7159 (mtm) REVERT: A 795 GLU cc_start: 0.8380 (tp30) cc_final: 0.7881 (tp30) REVERT: B 353 GLU cc_start: 0.7939 (mp0) cc_final: 0.7645 (mp0) REVERT: B 402 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7854 (ttt) REVERT: B 515 MET cc_start: 0.7181 (ttp) cc_final: 0.6623 (ttp) REVERT: B 731 PHE cc_start: 0.8230 (m-80) cc_final: 0.7407 (m-80) REVERT: B 735 ASP cc_start: 0.7108 (m-30) cc_final: 0.6561 (m-30) REVERT: B 740 MET cc_start: 0.6889 (tmm) cc_final: 0.6417 (tmm) REVERT: C 349 THR cc_start: 0.9278 (OUTLIER) cc_final: 0.9033 (t) REVERT: C 351 ARG cc_start: 0.8269 (tpp-160) cc_final: 0.8058 (tpp-160) REVERT: C 402 MET cc_start: 0.8413 (ptp) cc_final: 0.8185 (ptm) REVERT: C 523 ASN cc_start: 0.8523 (OUTLIER) cc_final: 0.7968 (p0) REVERT: C 792 LYS cc_start: 0.8083 (mmtm) cc_final: 0.7857 (mppt) REVERT: C 794 PRO cc_start: 0.8220 (Cg_exo) cc_final: 0.7750 (Cg_endo) REVERT: C 798 MET cc_start: 0.6545 (tmm) cc_final: 0.5939 (mtp) REVERT: D 431 LEU cc_start: 0.8739 (mt) cc_final: 0.8497 (tt) REVERT: D 726 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8659 (tt) REVERT: D 727 ARG cc_start: 0.8544 (mtm180) cc_final: 0.8177 (mtm180) REVERT: D 782 LYS cc_start: 0.8824 (mmmt) cc_final: 0.8609 (mmmm) REVERT: E 350 ASN cc_start: 0.7882 (p0) cc_final: 0.7277 (t0) REVERT: E 515 MET cc_start: 0.8334 (ptt) cc_final: 0.8060 (ptp) REVERT: E 541 TRP cc_start: 0.8004 (p-90) cc_final: 0.7672 (p-90) REVERT: E 603 MET cc_start: 0.8501 (ttp) cc_final: 0.8244 (ttm) REVERT: E 682 TYR cc_start: 0.7951 (t80) cc_final: 0.7602 (t80) REVERT: F 215 LEU cc_start: 0.7795 (tt) cc_final: 0.7475 (pp) REVERT: F 330 MET cc_start: 0.7967 (mpp) cc_final: 0.7599 (mpp) REVERT: F 508 ASP cc_start: 0.8184 (t0) cc_final: 0.7535 (m-30) REVERT: F 603 MET cc_start: 0.8681 (mmm) cc_final: 0.8271 (mmm) REVERT: F 650 ILE cc_start: 0.4785 (OUTLIER) cc_final: 0.4045 (tp) REVERT: F 652 GLU cc_start: 0.8556 (pm20) cc_final: 0.8327 (mp0) REVERT: F 786 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8116 (pm20) outliers start: 76 outliers final: 58 residues processed: 404 average time/residue: 0.3504 time to fit residues: 231.4692 Evaluate side-chains 399 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 336 time to evaluate : 3.138 ------------------------------------------------------------------------------- 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 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 402 MET Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 349 THR 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 433 GLN Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 494 THR 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 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 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 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 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 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 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 285 optimal weight: 50.0000 chunk 46 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 chunk 209 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 chunk 334 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 193 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 ASN B 412 GLN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS ** F 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.139138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.104963 restraints weight = 52490.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.107978 restraints weight = 30331.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.110003 restraints weight = 21145.103| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26825 Z= 0.117 Angle : 0.632 13.454 36361 Z= 0.301 Chirality : 0.043 0.193 4165 Planarity : 0.004 0.058 4679 Dihedral : 10.211 118.843 4016 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.07 % Favored : 95.90 % Rotamer: Outliers : 2.35 % Allowed : 18.75 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.15), residues: 3343 helix: 1.23 (0.12), residues: 1811 sheet: -0.38 (0.25), residues: 387 loop : 0.50 (0.21), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 466 HIS 0.006 0.001 HIS F 254 PHE 0.018 0.001 PHE C 354 TYR 0.012 0.001 TYR F 406 ARG 0.007 0.000 ARG A 435 Details of bonding type rmsd hydrogen bonds : bond 0.02992 ( 1314) hydrogen bonds : angle 3.98891 ( 3687) covalent geometry : bond 0.00279 (26825) covalent geometry : angle 0.63220 (36361) =============================================================================== Job complete usr+sys time: 9235.93 seconds wall clock time: 163 minutes 3.78 seconds (9783.78 seconds total)