Starting phenix.real_space_refine on Sun Jul 5 08:01:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7t0v_25582/07_2026/7t0v_25582.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t0v_25582/07_2026/7t0v_25582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7t0v_25582/07_2026/7t0v_25582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t0v_25582/07_2026/7t0v_25582.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t0v_25582/07_2026/7t0v_25582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t0v_25582/07_2026/7t0v_25582.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7t0v_25582/07_2026/7t0v_25582.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7t0v_25582/07_2026/7t0v_25582.cif" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.048 sd= 0.158 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 31 5.49 5 Mg 9 5.21 5 S 124 5.16 5 C 16462 2.51 5 N 4698 2.21 5 O 5073 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26397 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4365 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 536} Chain breaks: 3 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 4387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4387 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 537} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 4385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4385 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 538} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 4385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4385 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 538} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 4121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4121 Classifications: {'peptide': 540} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 509} Chain breaks: 5 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 29 Chain: "F" Number of atoms: 4251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4251 Classifications: {'peptide': 557} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 526} Chain breaks: 3 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 29 Chain: "G" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 161 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.08, per 1000 atoms: 0.19 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: 1.94 Conformation dependent library (CDL) restraints added in 1.1 seconds 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6312 Finding SS restraints... Secondary structure from input PDB file: 191 helices and 12 sheets defined 60.4% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 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: 4.55 Time building geometry restraints manager: 2.47 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: 16100 25.86 - 51.72: 283 51.72 - 77.58: 19 77.58 - 103.44: 1 103.44 - 129.29: 3 Dihedral angle restraints: 16406 sinusoidal: 6667 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 16403 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2498 0.032 - 0.065: 1137 0.065 - 0.097: 354 0.097 - 0.129: 152 0.129 - 0.162: 24 Chirality restraints: 4165 Sorted by residual: chirality pdb=" C3' ATP E 902 " pdb=" C2' ATP E 902 " pdb=" C4' ATP E 902 " pdb=" O3' ATP E 902 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CA ILE E 495 " pdb=" N ILE E 495 " pdb=" C ILE E 495 " pdb=" CB ILE E 495 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" C3' ATP D 902 " pdb=" C2' ATP D 902 " pdb=" C4' ATP D 902 " pdb=" O3' ATP D 902 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.16 2.00e-01 2.50e+01 6.27e-01 ... (remaining 4162 not shown) Planarity restraints: 4679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 568 " -0.035 5.00e-02 4.00e+02 5.34e-02 4.55e+00 pdb=" N PRO F 569 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO F 569 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 569 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 356 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO A 357 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 357 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 357 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 356 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.08e+00 pdb=" N PRO F 357 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO F 357 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 357 " 0.020 5.00e-02 4.00e+02 ... (remaining 4676 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 200 2.47 - 3.07: 18162 3.07 - 3.68: 39490 3.68 - 4.29: 59913 4.29 - 4.90: 99451 Nonbonded interactions: 217216 Sorted by model distance: nonbonded pdb=" O1B ATP A 902 " pdb="MG MG A 904 " model vdw 1.857 2.170 nonbonded pdb=" O1B ATP B 901 " pdb="MG MG B 903 " model vdw 1.890 2.170 nonbonded pdb=" O2G ATP C 902 " pdb="MG MG C 904 " model vdw 1.892 2.170 nonbonded pdb=" O1B ATP C 901 " pdb="MG MG C 903 " model vdw 1.898 2.170 nonbonded pdb=" O1B ATP D 902 " pdb="MG MG D 904 " model vdw 1.907 2.170 ... (remaining 217211 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 193 through 460 or (resid 461 through 463 and (name N or n \ ame CA or name C or name O or name CB )) or resid 464 through 487 or resid 493 t \ hrough 573 or (resid 574 through 576 and (name N or name CA or name C or name O \ or name CB )) or resid 577 or (resid 578 and (name N or name CA or name C or nam \ e O or name CB )) or resid 579 through 631 or resid 637 through 754 or (resid 75 \ 5 through 757 and (name N or name CA or name C or name O or name CB )) or resid \ 773 through 790)) selection = (chain 'B' and (resid 193 through 338 or (resid 339 and (name N or name CA or na \ me C or name O or name CB )) or resid 340 or (resid 341 and (name N or name CA o \ r name C or name O or name CB )) or resid 342 through 460 or (resid 461 through \ 463 and (name N or name CA or name C or name O or name CB )) or resid 464 throug \ h 487 or resid 493 through 573 or (resid 574 through 576 and (name N or name CA \ or name C or name O or name CB )) or resid 577 or (resid 578 and (name N or name \ CA or name C or name O or name CB )) or resid 579 through 631 or resid 637 thro \ ugh 754 or (resid 755 through 757 and (name N or name CA or name C or name O or \ name CB )) or resid 773 through 790)) selection = (chain 'C' and (resid 193 through 338 or (resid 339 and (name N or name CA or na \ me C or name O or name CB )) or resid 340 or (resid 341 and (name N or name CA o \ r name C or name O or name CB )) or resid 342 through 460 or (resid 461 through \ 463 and (name N or name CA or name C or name O or name CB )) or resid 464 throug \ h 487 or resid 493 through 573 or (resid 574 through 576 and (name N or name CA \ or name C or name O or name CB )) or resid 577 or (resid 578 and (name N or name \ CA or name C or name O or name CB )) or resid 579 through 631 or resid 637 thro \ ugh 754 or (resid 755 through 757 and (name N or name CA or name C or name O or \ name CB )) or resid 773 through 790)) selection = (chain 'D' and (resid 193 through 338 or (resid 339 and (name N or name CA or na \ me C or name O or name CB )) or resid 340 or (resid 341 and (name N or name CA o \ r name C or name O or name CB )) or resid 342 through 460 or (resid 461 through \ 463 and (name N or name CA or name C or name O or name CB )) or resid 464 throug \ h 487 or resid 493 through 573 or (resid 574 through 576 and (name N or name CA \ or name C or name O or name CB )) or resid 577 or (resid 578 and (name N or name \ CA or name C or name O or name CB )) or resid 579 through 631 or resid 637 thro \ ugh 754 or (resid 755 through 757 and (name N or name CA or name C or name O or \ name CB )) or resid 773 through 790)) selection = (chain 'E' and (resid 193 through 338 or (resid 339 and (name N or name CA or na \ me C or name O or name CB )) or resid 340 or (resid 341 and (name N or name CA o \ r name C or name O or name CB )) or resid 342 through 573 or (resid 574 through \ 576 and (name N or name CA or name C or name O or name CB )) or resid 577 or (re \ sid 578 and (name N or name CA or name C or name O or name CB )) or resid 579 th \ rough 790)) selection = (chain 'F' and (resid 193 through 338 or (resid 339 and (name N or name CA or na \ me C or name O or name CB )) or resid 340 or (resid 341 and (name N or name CA o \ r name C or name O or name CB )) or resid 342 through 460 or (resid 461 through \ 463 and (name N or name CA or name C or name O or name CB )) or resid 464 throug \ h 487 or resid 493 through 631 or resid 637 through 754 or (resid 755 through 75 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 773 through \ 790)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 22.030 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 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 : 9.802 129.295 10094 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.01 % Favored : 95.84 % Rotamer: Outliers : 1.71 % Allowed : 3.02 % Favored : 95.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.15), residues: 3343 helix: -0.33 (0.12), residues: 1786 sheet: 0.70 (0.26), residues: 402 loop : 0.37 (0.20), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 361 TYR 0.017 0.001 TYR B 752 PHE 0.017 0.002 PHE B 600 TRP 0.019 0.002 TRP E 500 HIS 0.003 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 (26825) covalent geometry : angle 0.72623 / 0.47 (36361) hydrogen bonds : bond 0.27120 / 18.62 ( 1314) hydrogen bonds : angle 7.56523 / 5.50 ( 3687) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 814 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 VAL cc_start: 0.8414 (t) cc_final: 0.8181 (p) REVERT: A 508 ASP cc_start: 0.8354 (t70) cc_final: 0.7946 (t0) REVERT: A 795 GLU cc_start: 0.8101 (mp0) cc_final: 0.7689 (mp0) REVERT: A 798 MET cc_start: 0.4504 (ptt) cc_final: 0.3980 (tpp) REVERT: A 799 HIS cc_start: 0.5790 (m170) cc_final: 0.4712 (t70) REVERT: B 294 LEU cc_start: 0.9236 (tp) cc_final: 0.8890 (tp) REVERT: B 472 THR cc_start: 0.7875 (p) cc_final: 0.7660 (m) REVERT: B 530 VAL cc_start: 0.8971 (m) cc_final: 0.8753 (t) REVERT: B 578 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7891 (tp30) REVERT: C 201 ILE cc_start: 0.9145 (tp) cc_final: 0.8943 (tp) REVERT: C 538 ILE cc_start: 0.8748 (mm) cc_final: 0.8399 (tt) REVERT: C 754 GLN cc_start: 0.8039 (mt0) cc_final: 0.7798 (mm110) REVERT: D 321 ARG cc_start: 0.7877 (mtm110) cc_final: 0.7523 (mtm-85) REVERT: D 431 LEU cc_start: 0.8904 (mt) cc_final: 0.8590 (tt) REVERT: D 472 THR cc_start: 0.7915 (m) cc_final: 0.7354 (p) REVERT: D 511 LYS cc_start: 0.8041 (mtpt) cc_final: 0.7762 (ttmm) REVERT: D 584 ARG cc_start: 0.7866 (mtm110) cc_final: 0.7382 (mtm110) REVERT: D 739 LEU cc_start: 0.8857 (tp) cc_final: 0.8652 (tt) REVERT: E 350 ASN cc_start: 0.7588 (p0) cc_final: 0.7348 (p0) REVERT: F 368 ASP cc_start: 0.6158 (t0) cc_final: 0.5779 (p0) REVERT: F 402 MET cc_start: 0.7646 (ptp) cc_final: 0.6792 (mmm) REVERT: F 508 ASP cc_start: 0.7508 (t0) cc_final: 0.6872 (m-30) REVERT: F 515 MET cc_start: 0.8455 (ttp) cc_final: 0.8162 (ttm) REVERT: F 601 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.6995 (m-30) REVERT: F 718 ASP cc_start: 0.7270 (m-30) cc_final: 0.6770 (m-30) outliers start: 48 outliers final: 10 residues processed: 850 average time/residue: 0.2057 time to fit residues: 266.0281 Evaluate side-chains 449 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 438 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 645 ASN Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 601 ASP Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain G residue 23 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.0870 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 8.9990 overall best weight: 5.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 438 HIS A 459 HIS A 557 ASN B 395 ASN B 426 ASN B 756 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 ASN C 602 GLN C 684 ASN D 212 GLN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 459 HIS D 475 GLN 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 459 HIS F 557 ASN F 645 ASN ** F 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.139371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.108065 restraints weight = 52508.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.107374 restraints weight = 31154.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.108500 restraints weight = 24201.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.108977 restraints weight = 20948.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.109110 restraints weight = 19792.460| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3584 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 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 = 0.3582 r_free = 0.3582 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3582 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 26825 Z= 0.187 Angle : 0.683 11.220 36361 Z= 0.344 Chirality : 0.046 0.299 4165 Planarity : 0.006 0.075 4679 Dihedral : 6.572 117.909 3743 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.86 % Favored : 96.08 % Rotamer: Outliers : 2.92 % Allowed : 11.42 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.15), residues: 3343 helix: 0.27 (0.12), residues: 1822 sheet: 0.31 (0.25), residues: 401 loop : 0.48 (0.21), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 362 TYR 0.021 0.001 TYR E 682 PHE 0.020 0.002 PHE B 731 TRP 0.013 0.001 TRP C 219 HIS 0.007 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (26825) covalent geometry : angle 0.68294 / 0.34 (36361) hydrogen bonds : bond 0.05404 / 3.69 ( 1314) hydrogen bonds : angle 4.96526 / 3.61 ( 3687) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 477 time to evaluate : 1.113 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 318 MET cc_start: 0.7464 (ttp) cc_final: 0.7249 (ttt) REVERT: A 798 MET cc_start: 0.4832 (ptt) cc_final: 0.4282 (tpp) REVERT: A 799 HIS cc_start: 0.5677 (m170) cc_final: 0.4585 (t-170) REVERT: B 294 LEU cc_start: 0.9245 (tp) cc_final: 0.8842 (tp) REVERT: B 402 MET cc_start: 0.7871 (ptm) cc_final: 0.7603 (ttt) REVERT: B 731 PHE cc_start: 0.7811 (m-80) cc_final: 0.7436 (m-80) REVERT: B 735 ASP cc_start: 0.7121 (m-30) cc_final: 0.6692 (m-30) REVERT: C 482 LEU cc_start: 0.8893 (mm) cc_final: 0.8649 (tp) REVERT: C 754 GLN cc_start: 0.8004 (mt0) cc_final: 0.7745 (mm-40) REVERT: D 318 MET cc_start: 0.7753 (tpp) cc_final: 0.7007 (tpp) REVERT: D 431 LEU cc_start: 0.8835 (mt) cc_final: 0.8622 (tt) REVERT: D 452 ASP cc_start: 0.6644 (m-30) cc_final: 0.6436 (m-30) REVERT: D 585 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.7079 (tp40) REVERT: D 740 MET cc_start: 0.8292 (ttp) cc_final: 0.7900 (ttt) REVERT: E 350 ASN cc_start: 0.7711 (p0) cc_final: 0.7403 (p0) REVERT: E 718 ASP cc_start: 0.7949 (m-30) cc_final: 0.7741 (t0) REVERT: E 752 TYR cc_start: 0.6939 (m-10) cc_final: 0.6694 (m-80) REVERT: E 780 TRP cc_start: 0.8253 (m100) cc_final: 0.7923 (m100) REVERT: F 212 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8550 (pp30) REVERT: F 515 MET cc_start: 0.8941 (ttp) cc_final: 0.8612 (ttt) REVERT: F 652 GLU cc_start: 0.7791 (pm20) cc_final: 0.7573 (mp0) REVERT: F 786 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7947 (pm20) outliers start: 82 outliers final: 46 residues processed: 534 average time/residue: 0.1832 time to fit residues: 153.8266 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 : 1.036 ------------------------------------------------------------------------------- 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 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 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 551 VAL Chi-restraints excluded: chain D residue 585 GLN Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain D residue 747 CYS Chi-restraints excluded: chain E residue 297 CYS Chi-restraints excluded: chain E residue 327 MET Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 591 LYS Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 212 GLN Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 632 VAL Chi-restraints excluded: chain F residue 650 ILE Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain F residue 753 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 23 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 186 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 324 optimal weight: 20.0000 chunk 174 optimal weight: 5.9990 chunk 223 optimal weight: 30.0000 chunk 206 optimal weight: 8.9990 chunk 234 optimal weight: 50.0000 chunk 128 optimal weight: 4.9990 chunk 8 optimal weight: 50.0000 chunk 56 optimal weight: 40.0000 chunk 281 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 GLN B 328 ASN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 HIS ** D 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 GLN 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 = 0.4010 r_free = 0.4010 target = 0.139118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.106791 restraints weight = 52488.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.108062 restraints weight = 32065.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.108965 restraints weight = 22937.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.110615 restraints weight = 19822.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.110378 restraints weight = 17070.117| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3560 r_free = 0.3560 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 26825 Z= 0.183 Angle : 0.650 8.316 36361 Z= 0.322 Chirality : 0.045 0.243 4165 Planarity : 0.005 0.062 4679 Dihedral : 6.453 118.136 3739 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 3.34 % Allowed : 13.23 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.15), residues: 3343 helix: 0.52 (0.12), residues: 1811 sheet: 0.02 (0.25), residues: 396 loop : 0.49 (0.21), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 362 TYR 0.019 0.001 TYR E 682 PHE 0.020 0.002 PHE E 354 TRP 0.017 0.001 TRP E 453 HIS 0.005 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (26825) covalent geometry : angle 0.64973 / 0.32 (36361) hydrogen bonds : bond 0.04313 / 2.96 ( 1314) hydrogen bonds : angle 4.64091 / 3.38 ( 3687) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 383 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 VAL cc_start: 0.8658 (t) cc_final: 0.8418 (p) REVERT: A 466 TRP cc_start: 0.7393 (m-90) cc_final: 0.6889 (m-90) REVERT: A 798 MET cc_start: 0.4578 (ptt) cc_final: 0.4167 (tpp) REVERT: A 799 HIS cc_start: 0.5676 (m170) cc_final: 0.4585 (t-170) REVERT: B 294 LEU cc_start: 0.9248 (tp) cc_final: 0.9013 (tp) REVERT: B 402 MET cc_start: 0.7877 (ptm) cc_final: 0.7630 (ttt) REVERT: B 515 MET cc_start: 0.7120 (ttp) cc_final: 0.6474 (ttp) REVERT: B 731 PHE cc_start: 0.7938 (m-80) cc_final: 0.7376 (m-80) REVERT: B 735 ASP cc_start: 0.6923 (m-30) cc_final: 0.6471 (m-30) REVERT: B 740 MET cc_start: 0.6773 (tmm) cc_final: 0.6416 (tmm) REVERT: C 349 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.9023 (t) REVERT: C 360 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8129 (ttt-90) REVERT: C 538 ILE cc_start: 0.8738 (tp) cc_final: 0.8445 (tt) REVERT: D 318 MET cc_start: 0.7465 (tpp) cc_final: 0.6972 (tpp) REVERT: D 431 LEU cc_start: 0.8891 (mt) cc_final: 0.8674 (tt) REVERT: D 452 ASP cc_start: 0.6728 (m-30) cc_final: 0.6519 (m-30) REVERT: E 350 ASN cc_start: 0.7948 (p0) cc_final: 0.7651 (p0) REVERT: E 603 MET cc_start: 0.8526 (ttp) cc_final: 0.8226 (ttm) REVERT: E 752 TYR cc_start: 0.7017 (m-10) cc_final: 0.6696 (m-80) REVERT: E 777 MET cc_start: 0.8475 (tmm) cc_final: 0.8037 (tmm) REVERT: E 780 TRP cc_start: 0.8282 (m100) cc_final: 0.7970 (m100) REVERT: F 212 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8521 (pp30) REVERT: F 231 MET cc_start: 0.5863 (tpp) cc_final: 0.5593 (tpp) REVERT: F 330 MET cc_start: 0.7198 (mpp) cc_final: 0.6646 (mpp) REVERT: F 515 MET cc_start: 0.9093 (ttp) cc_final: 0.8777 (ttt) REVERT: F 603 MET cc_start: 0.8845 (ttp) cc_final: 0.8377 (tpp) REVERT: F 652 GLU cc_start: 0.8340 (pm20) cc_final: 0.8019 (mp0) REVERT: F 786 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8114 (pm20) outliers start: 94 outliers final: 60 residues processed: 450 average time/residue: 0.1774 time to fit residues: 127.9777 Evaluate side-chains 391 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 328 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 518 ILE Chi-restraints excluded: chain E residue 591 LYS Chi-restraints excluded: chain E residue 645 ASN Chi-restraints excluded: chain E residue 662 THR Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 212 GLN Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 620 ARG Chi-restraints excluded: chain F residue 632 VAL Chi-restraints excluded: chain F residue 650 ILE Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain F residue 753 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 306 optimal weight: 9.9990 chunk 159 optimal weight: 0.5980 chunk 180 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 114 optimal weight: 0.7980 chunk 227 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 269 optimal weight: 8.9990 chunk 322 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 overall best weight: 4.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 GLN 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 426 ASN ** D 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 438 HIS F 459 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.139722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.106657 restraints weight = 52735.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.109426 restraints weight = 32082.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.110887 restraints weight = 21445.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.111317 restraints weight = 17891.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.111404 restraints weight = 17103.895| |-----------------------------------------------------------------------------| 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) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26825 Z= 0.155 Angle : 0.601 8.847 36361 Z= 0.297 Chirality : 0.044 0.230 4165 Planarity : 0.005 0.074 4679 Dihedral : 6.404 120.775 3739 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.86 % Favored : 96.08 % Rotamer: Outliers : 3.45 % Allowed : 13.55 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.15), residues: 3343 helix: 0.69 (0.12), residues: 1818 sheet: -0.16 (0.24), residues: 396 loop : 0.47 (0.21), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 362 TYR 0.018 0.001 TYR E 682 PHE 0.018 0.002 PHE D 354 TRP 0.026 0.001 TRP E 453 HIS 0.006 0.001 HIS F 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (26825) covalent geometry : angle 0.60134 / 0.30 (36361) hydrogen bonds : bond 0.03720 / 2.54 ( 1314) hydrogen bonds : angle 4.36457 / 3.18 ( 3687) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 367 time to evaluate : 1.055 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: 0.8674 (t) cc_final: 0.8417 (p) REVERT: A 330 MET cc_start: 0.8175 (mtm) cc_final: 0.7726 (mpp) REVERT: A 573 ASN cc_start: 0.8768 (OUTLIER) cc_final: 0.8498 (t0) REVERT: A 795 GLU cc_start: 0.8354 (mp0) cc_final: 0.8019 (mp0) REVERT: A 798 MET cc_start: 0.4564 (ptt) cc_final: 0.4347 (tpp) REVERT: A 799 HIS cc_start: 0.5627 (m170) cc_final: 0.4578 (t-170) REVERT: B 217 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7809 (mt-10) REVERT: B 294 LEU cc_start: 0.9186 (tp) cc_final: 0.8965 (tp) REVERT: B 321 ARG cc_start: 0.7918 (mtm110) cc_final: 0.7263 (ptp-170) REVERT: B 359 ILE cc_start: 0.8473 (tt) cc_final: 0.8217 (tt) REVERT: B 402 MET cc_start: 0.7958 (ptm) cc_final: 0.7612 (ttt) REVERT: B 515 MET cc_start: 0.7003 (ttp) cc_final: 0.6446 (ttp) REVERT: B 731 PHE cc_start: 0.7958 (m-80) cc_final: 0.7282 (m-80) REVERT: B 735 ASP cc_start: 0.6890 (m-30) cc_final: 0.6484 (m-30) REVERT: B 740 MET cc_start: 0.6746 (tmm) cc_final: 0.6361 (tmm) REVERT: C 349 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.9030 (t) REVERT: C 523 ASN cc_start: 0.8447 (OUTLIER) cc_final: 0.7930 (p0) REVERT: C 724 LEU cc_start: 0.8163 (tp) cc_final: 0.7944 (tt) REVERT: D 318 MET cc_start: 0.7514 (tpp) cc_final: 0.7032 (tpp) REVERT: D 360 ARG cc_start: 0.8637 (ttm-80) cc_final: 0.8345 (ttm-80) REVERT: D 452 ASP cc_start: 0.6692 (m-30) cc_final: 0.6490 (m-30) REVERT: E 350 ASN cc_start: 0.7870 (p0) cc_final: 0.7561 (p0) REVERT: E 603 MET cc_start: 0.8497 (ttp) cc_final: 0.8197 (ttm) REVERT: E 752 TYR cc_start: 0.6878 (m-10) cc_final: 0.6489 (m-10) REVERT: F 330 MET cc_start: 0.7530 (mpp) cc_final: 0.6767 (mpp) REVERT: F 473 MET cc_start: 0.8497 (tmm) cc_final: 0.8046 (tpp) REVERT: F 515 MET cc_start: 0.9211 (ttp) cc_final: 0.8916 (ttt) REVERT: F 603 MET cc_start: 0.8871 (ttp) cc_final: 0.8580 (mtp) REVERT: F 620 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.8000 (mtp-110) REVERT: F 652 GLU cc_start: 0.8439 (pm20) cc_final: 0.8124 (mp0) REVERT: F 786 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8096 (pm20) outliers start: 97 outliers final: 69 residues processed: 431 average time/residue: 0.1699 time to fit residues: 119.7723 Evaluate side-chains 401 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 328 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 757 GLN 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 473 MET Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain B residue 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 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 483 VAL Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 523 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain D residue 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 645 ASN Chi-restraints excluded: chain E residue 662 THR Chi-restraints excluded: chain E residue 748 LEU Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 620 ARG Chi-restraints excluded: chain F residue 621 VAL Chi-restraints excluded: chain F residue 650 ILE Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 18 optimal weight: 5.9990 chunk 193 optimal weight: 40.0000 chunk 98 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 247 optimal weight: 40.0000 chunk 2 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 250 optimal weight: 40.0000 chunk 97 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 738 ASN B 328 ASN B 379 GLN B 395 ASN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS F 438 HIS F 557 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.138434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.106717 restraints weight = 53108.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.107536 restraints weight = 32460.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.109264 restraints weight = 23646.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.110089 restraints weight = 19057.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.109887 restraints weight = 17175.787| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 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 = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4342 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= 0.177 Angle : 0.612 9.392 36361 Z= 0.301 Chirality : 0.044 0.200 4165 Planarity : 0.005 0.057 4679 Dihedral : 6.338 126.880 3737 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.13 % Favored : 95.81 % Rotamer: Outliers : 3.70 % Allowed : 14.59 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.15), residues: 3343 helix: 0.76 (0.12), residues: 1809 sheet: -0.30 (0.24), residues: 396 loop : 0.50 (0.21), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 362 TYR 0.025 0.001 TYR E 682 PHE 0.013 0.002 PHE A 600 TRP 0.031 0.001 TRP E 453 HIS 0.005 0.001 HIS F 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (26825) covalent geometry : angle 0.61227 / 0.30 (36361) hydrogen bonds : bond 0.03646 / 2.49 ( 1314) hydrogen bonds : angle 4.32336 / 3.15 ( 3687) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 358 time to evaluate : 1.171 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: 0.8718 (t) cc_final: 0.8504 (p) REVERT: A 330 MET cc_start: 0.8269 (mtm) cc_final: 0.7633 (mpp) REVERT: A 466 TRP cc_start: 0.7483 (m-90) cc_final: 0.7280 (m-90) REVERT: A 578 GLU cc_start: 0.7975 (pt0) cc_final: 0.7752 (pt0) REVERT: A 795 GLU cc_start: 0.8410 (mp0) cc_final: 0.8072 (mp0) REVERT: A 798 MET cc_start: 0.4575 (ptt) cc_final: 0.4348 (tpp) REVERT: A 799 HIS cc_start: 0.5553 (m170) cc_final: 0.4519 (t-170) REVERT: B 294 LEU cc_start: 0.9253 (tp) cc_final: 0.9038 (tp) REVERT: B 359 ILE cc_start: 0.8496 (tt) cc_final: 0.8247 (tt) REVERT: B 402 MET cc_start: 0.7988 (ptm) cc_final: 0.7654 (ttt) REVERT: B 515 MET cc_start: 0.7058 (ttp) cc_final: 0.6511 (ttp) REVERT: B 731 PHE cc_start: 0.8141 (m-80) cc_final: 0.7412 (m-80) REVERT: B 735 ASP cc_start: 0.6975 (m-30) cc_final: 0.6566 (m-30) REVERT: B 740 MET cc_start: 0.6821 (tmm) cc_final: 0.6407 (tmm) REVERT: C 349 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.9020 (t) REVERT: D 318 MET cc_start: 0.7825 (tpp) cc_final: 0.7236 (tpp) REVERT: D 360 ARG cc_start: 0.8675 (ttm-80) cc_final: 0.8398 (ttm-80) REVERT: D 782 LYS cc_start: 0.8502 (mmmm) cc_final: 0.8194 (mmtm) REVERT: E 350 ASN cc_start: 0.7952 (p0) cc_final: 0.7638 (p0) REVERT: E 541 TRP cc_start: 0.7911 (p-90) cc_final: 0.7566 (p-90) REVERT: E 603 MET cc_start: 0.8498 (ttp) cc_final: 0.8187 (ttm) REVERT: E 649 MET cc_start: 0.6268 (mmt) cc_final: 0.6035 (mmt) REVERT: E 731 PHE cc_start: 0.7468 (m-10) cc_final: 0.7219 (m-10) REVERT: E 752 TYR cc_start: 0.7000 (m-10) cc_final: 0.6588 (m-10) REVERT: F 215 LEU cc_start: 0.7837 (tt) cc_final: 0.7495 (pp) REVERT: F 330 MET cc_start: 0.7425 (mpp) cc_final: 0.7158 (mpp) REVERT: F 515 MET cc_start: 0.9207 (ttp) cc_final: 0.8930 (ttt) REVERT: F 620 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7856 (mtp-110) REVERT: F 652 GLU cc_start: 0.8472 (pm20) cc_final: 0.8131 (mp0) REVERT: F 786 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8068 (pm20) outliers start: 104 outliers final: 73 residues processed: 433 average time/residue: 0.1741 time to fit residues: 122.8123 Evaluate side-chains 401 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 326 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 757 GLN 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 320 SER 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 645 ASN Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 326 ILE 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 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 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 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 596 CYS Chi-restraints excluded: chain F residue 620 ARG Chi-restraints excluded: chain F residue 650 ILE Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 61 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 43 optimal weight: 40.0000 chunk 10 optimal weight: 8.9990 chunk 323 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 314 optimal weight: 30.0000 chunk 113 optimal weight: 6.9990 chunk 184 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 328 ASN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 756 GLN D 785 ASN F 242 HIS F 328 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.136283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.103662 restraints weight = 52881.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.104640 restraints weight = 33028.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.105899 restraints weight = 23751.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.106799 restraints weight = 19785.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.106768 restraints weight = 17330.204| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4567 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= 0.183 Angle : 0.623 10.088 36361 Z= 0.306 Chirality : 0.044 0.273 4165 Planarity : 0.005 0.083 4679 Dihedral : 6.391 131.397 3737 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.34 % Favored : 95.60 % Rotamer: Outliers : 3.63 % Allowed : 15.15 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.15), residues: 3343 helix: 0.84 (0.12), residues: 1809 sheet: -0.42 (0.24), residues: 396 loop : 0.48 (0.21), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 375 TYR 0.026 0.001 TYR E 682 PHE 0.013 0.002 PHE A 600 TRP 0.025 0.001 TRP B 466 HIS 0.005 0.001 HIS F 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (26825) covalent geometry : angle 0.62327 / 0.31 (36361) hydrogen bonds : bond 0.03564 / 2.43 ( 1314) hydrogen bonds : angle 4.29995 / 3.13 ( 3687) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 355 time to evaluate : 1.034 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: 0.8769 (t) cc_final: 0.8533 (p) REVERT: A 330 MET cc_start: 0.8254 (mtm) cc_final: 0.7604 (mpp) REVERT: A 578 GLU cc_start: 0.7900 (pt0) cc_final: 0.7661 (mp0) REVERT: A 795 GLU cc_start: 0.8483 (mp0) cc_final: 0.8130 (mp0) REVERT: A 798 MET cc_start: 0.4521 (ptt) cc_final: 0.4306 (tpp) REVERT: A 799 HIS cc_start: 0.5522 (m170) cc_final: 0.4494 (t-170) REVERT: B 294 LEU cc_start: 0.9265 (tp) cc_final: 0.9052 (tp) REVERT: B 321 ARG cc_start: 0.7941 (mtm180) cc_final: 0.7404 (ptp-170) REVERT: B 353 GLU cc_start: 0.7850 (mp0) cc_final: 0.7584 (mp0) REVERT: B 402 MET cc_start: 0.8038 (ptm) cc_final: 0.7731 (ttt) REVERT: B 515 MET cc_start: 0.7208 (ttp) cc_final: 0.6672 (ttp) REVERT: B 731 PHE cc_start: 0.8249 (m-80) cc_final: 0.7433 (m-80) REVERT: B 735 ASP cc_start: 0.7002 (m-30) cc_final: 0.6516 (m-30) REVERT: B 740 MET cc_start: 0.6878 (tmm) cc_final: 0.6412 (tmm) REVERT: C 349 THR cc_start: 0.9243 (OUTLIER) cc_final: 0.9015 (t) REVERT: C 402 MET cc_start: 0.8432 (ptp) cc_final: 0.8186 (ptm) REVERT: C 523 ASN cc_start: 0.8555 (OUTLIER) cc_final: 0.7989 (p0) REVERT: D 318 MET cc_start: 0.7852 (tpp) cc_final: 0.7306 (tpp) REVERT: D 782 LYS cc_start: 0.8673 (mmmm) cc_final: 0.8364 (mmtm) REVERT: D 798 MET cc_start: 0.7340 (mmm) cc_final: 0.7071 (mmt) REVERT: E 350 ASN cc_start: 0.7866 (p0) cc_final: 0.7465 (p0) REVERT: E 541 TRP cc_start: 0.7923 (p-90) cc_final: 0.7570 (p-90) REVERT: E 603 MET cc_start: 0.8492 (ttp) cc_final: 0.8185 (ttm) REVERT: E 649 MET cc_start: 0.6467 (mmt) cc_final: 0.6261 (mmt) REVERT: E 752 TYR cc_start: 0.7017 (m-10) cc_final: 0.6544 (m-10) REVERT: F 215 LEU cc_start: 0.8050 (tt) cc_final: 0.7626 (pp) REVERT: F 330 MET cc_start: 0.7459 (mpp) cc_final: 0.7115 (mpp) REVERT: F 515 MET cc_start: 0.9316 (ttp) cc_final: 0.9034 (ttt) REVERT: F 603 MET cc_start: 0.8846 (ttp) cc_final: 0.8588 (mtp) REVERT: F 620 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7940 (mtp180) REVERT: F 650 ILE cc_start: 0.4708 (OUTLIER) cc_final: 0.3764 (tp) REVERT: F 652 GLU cc_start: 0.8466 (pm20) cc_final: 0.8065 (mp0) REVERT: F 778 GLU cc_start: 0.8728 (tp30) cc_final: 0.8480 (tm-30) REVERT: F 786 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8086 (pm20) outliers start: 102 outliers final: 77 residues processed: 424 average time/residue: 0.1721 time to fit residues: 119.3612 Evaluate side-chains 407 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 326 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 523 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 297 CYS Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 297 CYS Chi-restraints excluded: chain E residue 316 LYS Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 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 359 ILE 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 596 CYS Chi-restraints excluded: chain F residue 620 ARG Chi-restraints excluded: chain F residue 650 ILE Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 55 optimal weight: 5.9990 chunk 242 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 192 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 313 optimal weight: 0.5980 chunk 58 optimal weight: 7.9990 chunk 165 optimal weight: 20.0000 chunk 244 optimal weight: 5.9990 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 303 GLN B 328 ASN B 395 ASN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 412 GLN F 242 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.137275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.105162 restraints weight = 51937.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.107734 restraints weight = 32413.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.108888 restraints weight = 19976.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.109917 restraints weight = 17049.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.109935 restraints weight = 15592.034| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4708 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= 0.159 Angle : 0.617 11.208 36361 Z= 0.300 Chirality : 0.044 0.252 4165 Planarity : 0.004 0.057 4679 Dihedral : 6.398 133.253 3737 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.19 % Favored : 95.75 % Rotamer: Outliers : 3.66 % Allowed : 15.51 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.15), residues: 3343 helix: 0.85 (0.12), residues: 1827 sheet: -0.44 (0.25), residues: 396 loop : 0.49 (0.21), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 683 TYR 0.016 0.001 TYR F 665 PHE 0.013 0.001 PHE D 288 TRP 0.030 0.001 TRP B 466 HIS 0.006 0.001 HIS F 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (26825) covalent geometry : angle 0.61665 / 0.30 (36361) hydrogen bonds : bond 0.03436 / 2.34 ( 1314) hydrogen bonds : angle 4.21608 / 3.07 ( 3687) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 360 time to evaluate : 1.113 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 330 MET cc_start: 0.8242 (mtm) cc_final: 0.7652 (mpp) REVERT: A 578 GLU cc_start: 0.7942 (pt0) cc_final: 0.7642 (mp0) REVERT: A 795 GLU cc_start: 0.8474 (mp0) cc_final: 0.8127 (mp0) REVERT: A 799 HIS cc_start: 0.5506 (m170) cc_final: 0.4479 (t-170) REVERT: B 321 ARG cc_start: 0.7894 (mtm180) cc_final: 0.7284 (ptp-170) REVERT: B 353 GLU cc_start: 0.7920 (mp0) cc_final: 0.7606 (mp0) REVERT: B 402 MET cc_start: 0.8046 (ptm) cc_final: 0.7754 (ttt) REVERT: B 515 MET cc_start: 0.7250 (ttp) cc_final: 0.6683 (ttp) REVERT: B 731 PHE cc_start: 0.8323 (m-80) cc_final: 0.7464 (m-80) REVERT: B 735 ASP cc_start: 0.7010 (m-30) cc_final: 0.6465 (m-30) REVERT: B 740 MET cc_start: 0.6937 (tmm) cc_final: 0.6468 (tmm) REVERT: C 402 MET cc_start: 0.8496 (ptp) cc_final: 0.8263 (ptm) REVERT: C 523 ASN cc_start: 0.8553 (OUTLIER) cc_final: 0.7962 (p0) REVERT: D 318 MET cc_start: 0.7690 (tpp) cc_final: 0.7155 (tpp) REVERT: D 431 LEU cc_start: 0.7900 (tt) cc_final: 0.7603 (tp) REVERT: D 727 ARG cc_start: 0.8392 (mtm180) cc_final: 0.7953 (mtm180) REVERT: D 798 MET cc_start: 0.7146 (mmm) cc_final: 0.6915 (mmt) REVERT: E 350 ASN cc_start: 0.7912 (p0) cc_final: 0.7533 (p0) REVERT: E 498 THR cc_start: 0.8508 (m) cc_final: 0.8170 (p) REVERT: E 515 MET cc_start: 0.8245 (ptt) cc_final: 0.7972 (ptp) REVERT: E 541 TRP cc_start: 0.7951 (p-90) cc_final: 0.7598 (p-90) REVERT: E 603 MET cc_start: 0.8519 (ttp) cc_final: 0.8215 (ttm) REVERT: E 649 MET cc_start: 0.6523 (mmt) cc_final: 0.6298 (mmt) REVERT: E 752 TYR cc_start: 0.7180 (m-10) cc_final: 0.6787 (m-10) REVERT: F 215 LEU cc_start: 0.7736 (tt) cc_final: 0.7469 (pp) REVERT: F 330 MET cc_start: 0.7432 (mpp) cc_final: 0.7001 (mpp) REVERT: F 351 ARG cc_start: 0.8032 (mmm160) cc_final: 0.7658 (tpt170) REVERT: F 603 MET cc_start: 0.8819 (ttp) cc_final: 0.8576 (mtp) REVERT: F 620 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7971 (mtp180) REVERT: F 650 ILE cc_start: 0.4790 (OUTLIER) cc_final: 0.3862 (tp) REVERT: F 652 GLU cc_start: 0.8450 (pm20) cc_final: 0.8035 (mp0) REVERT: F 779 ASP cc_start: 0.6784 (m-30) cc_final: 0.5595 (m-30) REVERT: F 786 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8046 (pm20) outliers start: 103 outliers final: 81 residues processed: 434 average time/residue: 0.1785 time to fit residues: 125.2258 Evaluate side-chains 420 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 336 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 483 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 757 GLN 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 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 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 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 297 CYS Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 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 343 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 591 LYS Chi-restraints excluded: chain E residue 662 THR Chi-restraints excluded: chain E residue 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 596 CYS Chi-restraints excluded: chain F residue 620 ARG Chi-restraints excluded: chain F residue 650 ILE Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 149 optimal weight: 10.0000 chunk 258 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 328 ASN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 GLN 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 = 0.3937 r_free = 0.3937 target = 0.134644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.101853 restraints weight = 52621.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.104591 restraints weight = 32174.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.105670 restraints weight = 19982.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.106053 restraints weight = 16905.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.106260 restraints weight = 15544.798| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3501 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3501 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26825 Z= 0.155 Angle : 0.616 11.209 36361 Z= 0.300 Chirality : 0.044 0.175 4165 Planarity : 0.004 0.059 4679 Dihedral : 6.401 133.383 3737 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.16 % Favored : 95.78 % Rotamer: Outliers : 3.38 % Allowed : 15.83 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.15), residues: 3343 helix: 0.91 (0.12), residues: 1824 sheet: -0.54 (0.25), residues: 391 loop : 0.44 (0.21), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 334 TYR 0.015 0.001 TYR F 665 PHE 0.013 0.001 PHE A 220 TRP 0.033 0.001 TRP B 466 HIS 0.007 0.001 HIS F 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 (26825) covalent geometry : angle 0.61642 / 0.30 (36361) hydrogen bonds : bond 0.03353 / 2.29 ( 1314) hydrogen bonds : angle 4.16621 / 3.03 ( 3687) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 355 time to evaluate : 1.124 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 330 MET cc_start: 0.8251 (mtm) cc_final: 0.7654 (mpp) REVERT: A 515 MET cc_start: 0.7780 (mtm) cc_final: 0.6980 (mtm) REVERT: A 578 GLU cc_start: 0.7936 (pt0) cc_final: 0.7647 (mp0) REVERT: A 799 HIS cc_start: 0.5477 (m170) cc_final: 0.4577 (t70) REVERT: B 294 LEU cc_start: 0.9218 (tp) cc_final: 0.8973 (tp) REVERT: B 321 ARG cc_start: 0.7902 (mtm180) cc_final: 0.7249 (ptp-170) REVERT: B 353 GLU cc_start: 0.7967 (mp0) cc_final: 0.7652 (mp0) REVERT: B 359 ILE cc_start: 0.8417 (tt) cc_final: 0.8132 (tt) REVERT: B 402 MET cc_start: 0.8069 (ptm) cc_final: 0.7813 (ttt) REVERT: B 515 MET cc_start: 0.7232 (ttp) cc_final: 0.6692 (ttp) REVERT: B 731 PHE cc_start: 0.8340 (m-80) cc_final: 0.7471 (m-80) REVERT: B 735 ASP cc_start: 0.7074 (m-30) cc_final: 0.6473 (m-30) REVERT: B 740 MET cc_start: 0.6934 (tmm) cc_final: 0.6450 (tmm) REVERT: C 349 THR cc_start: 0.9318 (OUTLIER) cc_final: 0.9072 (t) REVERT: C 402 MET cc_start: 0.8578 (ptp) cc_final: 0.8333 (ptm) REVERT: C 523 ASN cc_start: 0.8544 (OUTLIER) cc_final: 0.7972 (p0) REVERT: D 318 MET cc_start: 0.7503 (tpp) cc_final: 0.7001 (tpp) REVERT: D 360 ARG cc_start: 0.8750 (ttm-80) cc_final: 0.8435 (ttm-80) REVERT: D 727 ARG cc_start: 0.8461 (mtm180) cc_final: 0.7997 (mtm180) REVERT: E 350 ASN cc_start: 0.7890 (p0) cc_final: 0.7280 (t0) REVERT: E 498 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8212 (p) REVERT: E 515 MET cc_start: 0.8332 (ptt) cc_final: 0.8069 (ptp) REVERT: E 541 TRP cc_start: 0.7972 (p-90) cc_final: 0.7614 (p-90) REVERT: E 603 MET cc_start: 0.8501 (ttp) cc_final: 0.8204 (ttm) REVERT: F 330 MET cc_start: 0.7441 (mpp) cc_final: 0.7040 (mpp) REVERT: F 351 ARG cc_start: 0.8006 (mmm160) cc_final: 0.7723 (tpt170) REVERT: F 515 MET cc_start: 0.9031 (ttm) cc_final: 0.8750 (tpt) REVERT: F 603 MET cc_start: 0.8809 (ttp) cc_final: 0.8556 (mtp) REVERT: F 620 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7896 (mtp-110) REVERT: F 646 ARG cc_start: 0.5680 (tpm170) cc_final: 0.5445 (tpm170) REVERT: F 650 ILE cc_start: 0.4810 (OUTLIER) cc_final: 0.3970 (tp) REVERT: F 652 GLU cc_start: 0.8450 (pm20) cc_final: 0.8033 (mp0) REVERT: F 745 GLN cc_start: 0.8274 (mt0) cc_final: 0.7680 (mt0) REVERT: F 786 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8104 (pm20) outliers start: 95 outliers final: 81 residues processed: 422 average time/residue: 0.1771 time to fit residues: 120.8197 Evaluate side-chains 423 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 337 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 483 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 757 GLN 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 473 MET 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 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 201 ILE Chi-restraints excluded: chain C residue 212 GLN Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 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 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 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 415 VAL 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 343 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 591 LYS Chi-restraints excluded: chain E residue 662 THR Chi-restraints excluded: chain E residue 678 LEU 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 596 CYS Chi-restraints excluded: chain F residue 620 ARG Chi-restraints excluded: chain F residue 650 ILE Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 219 optimal weight: 10.0000 chunk 318 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 163 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 58 optimal weight: 0.7980 chunk 275 optimal weight: 50.0000 chunk 10 optimal weight: 0.6980 chunk 261 optimal weight: 3.9990 chunk 285 optimal weight: 7.9990 chunk 175 optimal weight: 9.9990 overall best weight: 4.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 328 ASN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** 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 = 0.3948 r_free = 0.3948 target = 0.136375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.102702 restraints weight = 52220.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.106055 restraints weight = 28333.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.108215 restraints weight = 18935.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.109721 restraints weight = 14595.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.110559 restraints weight = 12286.739| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3560 r_free = 0.3560 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3560 r_free = 0.3560 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26825 Z= 0.144 Angle : 0.625 11.977 36361 Z= 0.303 Chirality : 0.044 0.249 4165 Planarity : 0.004 0.059 4679 Dihedral : 6.380 131.455 3737 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.16 % Favored : 95.78 % Rotamer: Outliers : 3.27 % Allowed : 16.54 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.15), residues: 3343 helix: 1.00 (0.12), residues: 1820 sheet: -0.52 (0.26), residues: 375 loop : 0.41 (0.21), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 362 TYR 0.012 0.001 TYR F 665 PHE 0.017 0.001 PHE A 220 TRP 0.043 0.002 TRP B 466 HIS 0.006 0.001 HIS F 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (26825) covalent geometry : angle 0.62471 / 0.30 (36361) hydrogen bonds : bond 0.03267 / 2.23 ( 1314) hydrogen bonds : angle 4.12310 / 2.99 ( 3687) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 354 time to evaluate : 1.099 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: 0.8155 (mtm) cc_final: 0.7594 (mpp) REVERT: A 515 MET cc_start: 0.7675 (mtm) cc_final: 0.6782 (mtm) REVERT: A 639 TYR cc_start: 0.8276 (m-80) cc_final: 0.7953 (m-80) REVERT: A 799 HIS cc_start: 0.6095 (m170) cc_final: 0.4970 (t-170) REVERT: B 217 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7751 (mt-10) REVERT: B 294 LEU cc_start: 0.9189 (tp) cc_final: 0.8984 (tp) REVERT: B 321 ARG cc_start: 0.7885 (mtm180) cc_final: 0.7180 (ptp-170) REVERT: B 359 ILE cc_start: 0.8374 (tt) cc_final: 0.8098 (tt) REVERT: B 402 MET cc_start: 0.7955 (ptm) cc_final: 0.7612 (ttt) REVERT: B 515 MET cc_start: 0.7190 (ttp) cc_final: 0.6628 (ttp) REVERT: B 731 PHE cc_start: 0.8206 (m-80) cc_final: 0.7375 (m-80) REVERT: B 735 ASP cc_start: 0.7029 (m-30) cc_final: 0.6483 (m-30) REVERT: B 740 MET cc_start: 0.6897 (tmm) cc_final: 0.6416 (tmm) REVERT: C 349 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.9016 (t) REVERT: C 351 ARG cc_start: 0.8340 (tpp-160) cc_final: 0.7944 (tpp-160) REVERT: C 402 MET cc_start: 0.8497 (ptp) cc_final: 0.8255 (ptm) REVERT: C 523 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.7946 (p0) REVERT: D 318 MET cc_start: 0.7623 (tpp) cc_final: 0.7049 (tpp) REVERT: D 360 ARG cc_start: 0.8734 (ttm-80) cc_final: 0.8436 (ttm-80) REVERT: D 727 ARG cc_start: 0.8406 (mtm180) cc_final: 0.8030 (mtm180) REVERT: E 350 ASN cc_start: 0.7763 (p0) cc_final: 0.7204 (t0) REVERT: E 498 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8187 (p) REVERT: E 515 MET cc_start: 0.8245 (ptt) cc_final: 0.7959 (ptp) REVERT: E 541 TRP cc_start: 0.7969 (p-90) cc_final: 0.7604 (p-90) REVERT: E 603 MET cc_start: 0.8574 (ttp) cc_final: 0.8289 (ttm) REVERT: F 351 ARG cc_start: 0.8082 (mmm160) cc_final: 0.7866 (tpt170) REVERT: F 508 ASP cc_start: 0.8257 (t70) cc_final: 0.7634 (m-30) REVERT: F 515 MET cc_start: 0.9067 (ttm) cc_final: 0.8839 (tpt) REVERT: F 603 MET cc_start: 0.8766 (ttp) cc_final: 0.8520 (mtp) REVERT: F 620 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.8002 (mtp-110) REVERT: F 646 ARG cc_start: 0.5853 (tpm170) cc_final: 0.5642 (tpm170) REVERT: F 650 ILE cc_start: 0.4739 (OUTLIER) cc_final: 0.3900 (tp) REVERT: F 652 GLU cc_start: 0.8452 (pm20) cc_final: 0.8038 (mp0) REVERT: F 745 GLN cc_start: 0.8251 (mt0) cc_final: 0.7740 (mt0) REVERT: F 777 MET cc_start: 0.7886 (mmp) cc_final: 0.7600 (mmp) REVERT: F 786 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8066 (pm20) outliers start: 92 outliers final: 78 residues processed: 420 average time/residue: 0.1691 time to fit residues: 116.9849 Evaluate side-chains 421 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 338 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 483 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 757 GLN 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 320 SER Chi-restraints excluded: chain B residue 322 ILE 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 774 VAL Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain C residue 201 ILE 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 399 LEU 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 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 C residue 751 VAL Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 297 CYS Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 297 CYS Chi-restraints excluded: chain E residue 316 LYS Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 591 LYS Chi-restraints excluded: chain E residue 662 THR Chi-restraints excluded: chain E residue 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 620 ARG 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 214 optimal weight: 0.9990 chunk 275 optimal weight: 50.0000 chunk 48 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 141 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 50 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 328 ASN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** 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 = 0.3947 r_free = 0.3947 target = 0.137843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.106689 restraints weight = 51881.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.108367 restraints weight = 31430.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.109414 restraints weight = 20048.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.110315 restraints weight = 18487.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.110440 restraints weight = 15970.379| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26825 Z= 0.149 Angle : 0.651 12.758 36361 Z= 0.315 Chirality : 0.044 0.236 4165 Planarity : 0.004 0.058 4679 Dihedral : 6.396 129.068 3737 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.13 % Favored : 95.84 % Rotamer: Outliers : 3.20 % Allowed : 17.18 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.15), residues: 3343 helix: 1.03 (0.12), residues: 1807 sheet: -0.53 (0.26), residues: 375 loop : 0.42 (0.20), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 489 TYR 0.012 0.001 TYR F 665 PHE 0.021 0.001 PHE A 220 TRP 0.034 0.002 TRP B 466 HIS 0.007 0.001 HIS F 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (26825) covalent geometry : angle 0.65070 / 0.31 (36361) hydrogen bonds : bond 0.03298 / 2.25 ( 1314) hydrogen bonds : angle 4.19118 / 3.03 ( 3687) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6686 Ramachandran restraints generated. 3343 Oldfield, 0 Emsley, 3343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 344 time to evaluate : 1.355 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: 0.8191 (mtm) cc_final: 0.7618 (mpp) REVERT: A 515 MET cc_start: 0.7554 (mtm) cc_final: 0.6707 (mtm) REVERT: A 639 TYR cc_start: 0.8277 (m-80) cc_final: 0.7919 (m-80) REVERT: A 795 GLU cc_start: 0.8312 (tp30) cc_final: 0.7810 (tp30) REVERT: B 321 ARG cc_start: 0.7934 (mtm180) cc_final: 0.7187 (ptp-170) REVERT: B 359 ILE cc_start: 0.8440 (tt) cc_final: 0.8172 (tt) REVERT: B 424 GLN cc_start: 0.8341 (tm-30) cc_final: 0.8135 (tm-30) REVERT: B 515 MET cc_start: 0.7124 (ttp) cc_final: 0.6588 (ttp) REVERT: B 731 PHE cc_start: 0.8223 (m-80) cc_final: 0.7368 (m-80) REVERT: B 735 ASP cc_start: 0.7034 (m-30) cc_final: 0.6471 (m-30) REVERT: B 740 MET cc_start: 0.6938 (tmm) cc_final: 0.6463 (tmm) REVERT: C 349 THR cc_start: 0.9251 (OUTLIER) cc_final: 0.9002 (t) REVERT: C 351 ARG cc_start: 0.8322 (tpp-160) cc_final: 0.8034 (tpp-160) REVERT: C 402 MET cc_start: 0.8519 (ptp) cc_final: 0.8271 (ptm) REVERT: C 523 ASN cc_start: 0.8495 (OUTLIER) cc_final: 0.7942 (p0) REVERT: D 318 MET cc_start: 0.7582 (tpp) cc_final: 0.6930 (tpp) REVERT: D 726 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8654 (tt) REVERT: D 727 ARG cc_start: 0.8447 (mtm180) cc_final: 0.8232 (mtm180) REVERT: E 350 ASN cc_start: 0.7832 (p0) cc_final: 0.7176 (t0) REVERT: E 498 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.8292 (p) REVERT: E 515 MET cc_start: 0.8228 (ptt) cc_final: 0.7957 (ptp) REVERT: E 541 TRP cc_start: 0.8040 (p-90) cc_final: 0.7697 (p-90) REVERT: E 603 MET cc_start: 0.8503 (ttp) cc_final: 0.8221 (ttm) REVERT: F 402 MET cc_start: 0.7209 (ptt) cc_final: 0.5934 (ppp) REVERT: F 508 ASP cc_start: 0.7953 (t70) cc_final: 0.7411 (m-30) REVERT: F 649 MET cc_start: 0.6710 (OUTLIER) cc_final: 0.6054 (mmm) REVERT: F 650 ILE cc_start: 0.4899 (OUTLIER) cc_final: 0.3945 (tp) REVERT: F 652 GLU cc_start: 0.8477 (pm20) cc_final: 0.8044 (mp0) REVERT: F 745 GLN cc_start: 0.8244 (mt0) cc_final: 0.7701 (mt0) REVERT: F 777 MET cc_start: 0.7619 (mmp) cc_final: 0.7346 (mmp) REVERT: F 786 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8041 (pm20) outliers start: 90 outliers final: 77 residues processed: 409 average time/residue: 0.1695 time to fit residues: 114.3123 Evaluate side-chains 417 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 334 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 483 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 757 GLN 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 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 774 VAL Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain C residue 201 ILE 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 399 LEU 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 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 C residue 751 VAL Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 297 CYS Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 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 349 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 591 LYS Chi-restraints excluded: chain E residue 662 THR Chi-restraints excluded: chain E residue 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 649 MET 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 45 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 227 optimal weight: 40.0000 chunk 6 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 159 optimal weight: 5.9990 chunk 241 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 259 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 328 ASN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** 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 = 0.3965 r_free = 0.3965 target = 0.139151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.108049 restraints weight = 51275.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.110042 restraints weight = 31146.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.111037 restraints weight = 19258.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.111767 restraints weight = 17966.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.112028 restraints weight = 15222.857| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26825 Z= 0.125 Angle : 0.635 13.379 36361 Z= 0.307 Chirality : 0.043 0.179 4165 Planarity : 0.004 0.057 4679 Dihedral : 6.343 125.357 3737 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.25 % Favored : 95.72 % Rotamer: Outliers : 2.70 % Allowed : 17.64 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.15), residues: 3343 helix: 1.11 (0.12), residues: 1804 sheet: -0.57 (0.25), residues: 375 loop : 0.41 (0.20), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 489 TYR 0.013 0.001 TYR F 665 PHE 0.018 0.001 PHE C 354 TRP 0.031 0.001 TRP B 466 HIS 0.006 0.001 HIS F 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (26825) covalent geometry : angle 0.63536 / 0.31 (36361) hydrogen bonds : bond 0.03153 / 2.15 ( 1314) hydrogen bonds : angle 4.11018 / 2.96 ( 3687) =============================================================================== Job complete usr+sys time: 4597.20 seconds wall clock time: 96 minutes 37.39 seconds (5797.39 seconds total)