Starting phenix.real_space_refine on Fri Jul 3 08:23:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e8a_47713/07_2026/9e8a_47713.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e8a_47713/07_2026/9e8a_47713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e8a_47713/07_2026/9e8a_47713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e8a_47713/07_2026/9e8a_47713.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e8a_47713/07_2026/9e8a_47713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e8a_47713/07_2026/9e8a_47713.map" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.025 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: 7 Type Number sf(0) Gaussians Ca 7 9.91 5 Mg 1 5.21 5 S 99 5.16 5 C 7822 2.51 5 N 2139 2.21 5 O 2499 1.98 5 H 22 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s 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: 12589 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7002 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 915, 6994 Classifications: {'peptide': 915} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 853} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 915, 6994 Classifications: {'peptide': 915} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 853} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 7151 Chain: "B" Number of atoms: 5234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5234 Classifications: {'peptide': 683} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 649} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 42 Ad-hoc single atom residues: {' CA': 5} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 15 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' MG': 1, 'NAG': 1} Classifications: {'undetermined': 2} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.09, per 1000 atoms: 0.32 Number of scatterers: 12589 At special positions: 0 Unit cell: (96.3, 129.47, 135.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 7 19.99 S 99 16.00 Mg 1 11.99 O 2499 8.00 N 2139 7.00 C 7822 6.00 H 22 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 515 " distance=2.03 Simple disulfide: pdb=" SG CYS A 521 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 639 " distance=2.03 Simple disulfide: pdb=" SG CYS A 705 " - pdb=" SG CYS A 718 " distance=2.03 Simple disulfide: pdb=" SG CYS A 857 " - pdb=" SG CYS A 921 " distance=2.03 Simple disulfide: pdb=" SG CYS A 911 " - pdb=" SG CYS A 916 " distance=2.03 Simple disulfide: pdb=" SG CYS B 31 " - pdb=" SG CYS B 49 " distance=2.03 Simple disulfide: pdb=" SG CYS B 39 " - pdb=" SG CYS B 461 " distance=2.03 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 64 " distance=2.02 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 75 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 210 " distance=2.03 Simple disulfide: pdb=" SG CYS B 258 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 400 " - pdb=" SG CYS B 412 " distance=2.04 Simple disulfide: pdb=" SG CYS B 432 " - pdb=" SG CYS B 459 " distance=2.03 Simple disulfide: pdb=" SG CYS B 463 " - pdb=" SG CYS B 483 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 488 " - pdb=" SG CYS B 497 " distance=2.03 Simple disulfide: pdb=" SG CYS B 499 " - pdb=" SG CYS B 529 " distance=2.03 Simple disulfide: pdb=" SG CYS B 512 " - pdb=" SG CYS B 527 " distance=2.03 Simple disulfide: pdb=" SG CYS B 521 " - pdb=" SG CYS B 532 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 547 " distance=2.03 Simple disulfide: pdb=" SG CYS B 549 " - pdb=" SG CYS B 570 " distance=2.03 Simple disulfide: pdb=" SG CYS B 554 " - pdb=" SG CYS B 568 " distance=2.03 Simple disulfide: pdb=" SG CYS B 562 " - pdb=" SG CYS B 573 " distance=2.04 Simple disulfide: pdb=" SG CYS B 575 " - pdb=" SG CYS B 584 " distance=2.03 Simple disulfide: pdb=" SG CYS B 586 " - pdb=" SG CYS B 609 " distance=2.03 Simple disulfide: pdb=" SG CYS B 593 " - pdb=" SG CYS B 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 593 " - pdb=" SG CYS B 607 " distance=2.03 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 612 " distance=2.02 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 624 " distance=2.03 Simple disulfide: pdb=" SG CYS B 627 " - pdb=" SG CYS B 630 " distance=2.03 Simple disulfide: pdb=" SG CYS B 634 " - pdb=" SG CYS B 681 " distance=2.03 Simple disulfide: pdb=" SG CYS B 643 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 689 " - pdb=" SG CYS B 713 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " BMA J 2 " - " NAG J 3 " " NAG J 3 " - " NAG J 4 " BETA1-6 " BMA J 1 " - " BMA J 2 " NAG-ASN " NAG A1105 " - " ASN A 280 " " NAG A1108 " - " ASN A 711 " " NAG B 804 " - " ASN B 680 " " NAG E 1 " - " ASN B 125 " " NAG F 1 " - " ASN B 585 " " NAG G 1 " - " ASN A 962 " " NAG H 1 " - " ASN B 397 " " NAG I 1 " - " ASN B 346 " Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 989.2 milliseconds 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2934 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 27 sheets defined 14.4% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 182 through 189 removed outlier: 3.662A pdb=" N TYR A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 231 through 238 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 498 through 502 removed outlier: 3.804A pdb=" N LYS A 502 " --> pdb=" O PRO A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 609 removed outlier: 4.061A pdb=" N GLU A 608 " --> pdb=" O PRO A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 744 removed outlier: 3.600A pdb=" N GLU A 743 " --> pdb=" O ASN A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 947 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 38 through 44 removed outlier: 3.787A pdb=" N ALA B 44 " --> pdb=" O GLN B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 73 Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 150 through 157 removed outlier: 3.531A pdb=" N TRP B 155 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER B 156 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 169 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 201 through 207 removed outlier: 4.370A pdb=" N ASP B 205 " --> pdb=" O PRO B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 235 removed outlier: 4.073A pdb=" N PHE B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN B 230 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 258 removed outlier: 3.541A pdb=" N ALA B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 284 through 288 removed outlier: 3.777A pdb=" N ARG B 287 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 311 removed outlier: 4.494A pdb=" N THR B 311 " --> pdb=" O SER B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 329 Processing helix chain 'B' and resid 340 through 351 removed outlier: 3.562A pdb=" N LEU B 350 " --> pdb=" O ASN B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 378 Processing helix chain 'B' and resid 461 through 465 Processing helix chain 'B' and resid 519 through 523 Processing helix chain 'B' and resid 560 through 564 Processing helix chain 'B' and resid 599 through 604 Processing helix chain 'B' and resid 632 through 645 removed outlier: 3.777A pdb=" N PHE B 636 " --> pdb=" O ASP B 632 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLU B 639 " --> pdb=" O THR B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 660 Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 43 removed outlier: 6.236A pdb=" N ASP A 465 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A 455 " --> pdb=" O ASP A 465 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER A 451 " --> pdb=" O GLY A 469 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 58 removed outlier: 4.446A pdb=" N VAL A 84 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 110 Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 131 Processing sheet with id=AA5, first strand: chain 'A' and resid 203 through 206 removed outlier: 3.587A pdb=" N SER A 203 " --> pdb=" O GLY A 215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 270 through 273 removed outlier: 6.489A pdb=" N VAL A 298 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ARG A 310 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE A 300 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 327 removed outlier: 3.535A pdb=" N LEU A 376 " --> pdb=" O LEU A 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 345 through 347 Processing sheet with id=AA9, first strand: chain 'A' and resid 391 through 395 removed outlier: 6.276A pdb=" N ILE A 391 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ALA A 408 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ALA A 406 " --> pdb=" O PRO A 393 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A 395 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN A 436 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 425 through 426 Processing sheet with id=AB2, first strand: chain 'A' and resid 552 through 554 removed outlier: 4.332A pdb=" N SER A 514 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL A 485 " --> pdb=" O HIS A 618 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ASP A 620 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ALA A 487 " --> pdb=" O ASP A 620 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 496 through 497 Processing sheet with id=AB4, first strand: chain 'A' and resid 643 through 650 removed outlier: 3.596A pdb=" N MET A 734 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA A 728 " --> pdb=" O ASN A 670 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLY A 731 " --> pdb=" O SER A 695 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N SER A 695 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA A 733 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ALA A 693 " --> pdb=" O ALA A 733 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU A 735 " --> pdb=" O MET A 691 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.116A pdb=" N LEU A 654 " --> pdb=" O ARG A 774 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 751 " --> pdb=" O HIS A 683 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG A 714 " --> pdb=" O LEU A 684 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 675 through 676 Processing sheet with id=AB7, first strand: chain 'A' and resid 780 through 786 removed outlier: 6.525A pdb=" N MET A 933 " --> pdb=" O PRO A 851 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR A 935 " --> pdb=" O ILE A 849 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ILE A 849 " --> pdb=" O THR A 935 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU A 937 " --> pdb=" O LEU A 847 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 907 through 909 removed outlier: 6.414A pdb=" N VAL A 907 " --> pdb=" O VAL A 954 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN A 956 " --> pdb=" O VAL A 907 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL A 909 " --> pdb=" O GLN A 956 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N HIS A 958 " --> pdb=" O VAL A 909 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLN A 924 " --> pdb=" O GLY A 827 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N HIS A 829 " --> pdb=" O ASP A 922 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASP A 922 " --> pdb=" O HIS A 829 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER A 831 " --> pdb=" O GLN A 920 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N GLN A 920 " --> pdb=" O SER A 831 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N HIS A 833 " --> pdb=" O VAL A 918 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL A 918 " --> pdb=" O HIS A 833 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 907 through 909 removed outlier: 6.414A pdb=" N VAL A 907 " --> pdb=" O VAL A 954 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN A 956 " --> pdb=" O VAL A 907 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL A 909 " --> pdb=" O GLN A 956 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N HIS A 958 " --> pdb=" O VAL A 909 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 86 through 91 removed outlier: 6.746A pdb=" N ARG B 113 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE B 114 " --> pdb=" O GLN B 454 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N THR B 456 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 116 " --> pdb=" O THR B 456 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 109 through 110 Processing sheet with id=AC3, first strand: chain 'B' and resid 216 through 223 removed outlier: 6.514A pdb=" N PHE B 179 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N THR B 221 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ILE B 177 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR B 223 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU B 175 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N HIS B 270 " --> pdb=" O ASN B 331 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ILE B 333 " --> pdb=" O HIS B 270 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU B 272 " --> pdb=" O ILE B 333 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA B 335 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE B 274 " --> pdb=" O ALA B 335 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 467 through 468 Processing sheet with id=AC5, first strand: chain 'B' and resid 525 through 527 Processing sheet with id=AC6, first strand: chain 'B' and resid 566 through 569 Processing sheet with id=AC7, first strand: chain 'B' and resid 579 through 580 Processing sheet with id=AC8, first strand: chain 'B' and resid 606 through 608 Processing sheet with id=AC9, first strand: chain 'B' and resid 679 through 684 397 hydrogen bonds defined for protein. 1004 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.31 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.87 - 1.06: 22 1.06 - 1.25: 2081 1.25 - 1.44: 3374 1.44 - 1.63: 7240 1.63 - 1.82: 124 Bond restraints: 12841 Sorted by residual: bond pdb=" N ARG A 948 " pdb=" CA ARG A 948 " ideal model delta sigma weight residual 1.458 1.487 -0.029 7.40e-03 1.83e+04 1.57e+01 bond pdb=" N VAL A 602 " pdb=" CA VAL A 602 " ideal model delta sigma weight residual 1.459 1.508 -0.049 1.25e-02 6.40e+03 1.52e+01 bond pdb=" N VAL A 825 " pdb=" CA VAL A 825 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.14e-02 7.69e+03 1.05e+01 bond pdb=" N VAL A 963 " pdb=" CA VAL A 963 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.19e-02 7.06e+03 1.05e+01 bond pdb=" N GLY A 978 " pdb=" CA GLY A 978 " ideal model delta sigma weight residual 1.444 1.476 -0.033 1.02e-02 9.61e+03 1.02e+01 ... (remaining 12836 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 16755 1.95 - 3.89: 657 3.89 - 5.84: 51 5.84 - 7.78: 1 7.78 - 9.73: 1 Bond angle restraints: 17465 Sorted by residual: angle pdb=" C CYS B 593 " pdb=" CA CYS B 593 " pdb=" CB CYS B 593 " ideal model delta sigma weight residual 110.88 101.15 9.73 1.57e+00 4.06e-01 3.84e+01 angle pdb=" CA GLY B 581 " pdb=" C GLY B 581 " pdb=" O GLY B 581 " ideal model delta sigma weight residual 122.22 118.31 3.91 6.50e-01 2.37e+00 3.62e+01 angle pdb=" C ASN B 74 " pdb=" CA ASN B 74 " pdb=" CB ASN B 74 " ideal model delta sigma weight residual 116.63 110.84 5.79 1.16e+00 7.43e-01 2.49e+01 angle pdb=" CA GLY C 494 " pdb=" C GLY C 494 " pdb=" O GLY C 494 " ideal model delta sigma weight residual 122.24 117.75 4.49 1.08e+00 8.57e-01 1.73e+01 angle pdb=" C CYS B 601 " pdb=" CA CYS B 601 " pdb=" CB CYS B 601 " ideal model delta sigma weight residual 111.80 117.86 -6.06 1.46e+00 4.69e-01 1.72e+01 ... (remaining 17460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.24: 7813 23.24 - 46.48: 208 46.48 - 69.72: 46 69.72 - 92.96: 18 92.96 - 116.21: 33 Dihedral angle restraints: 8118 sinusoidal: 3534 harmonic: 4584 Sorted by residual: dihedral pdb=" CD ARG A 977 " pdb=" NE ARG A 977 " pdb=" CZ ARG A 977 " pdb=" NH1 ARG A 977 " ideal model delta sinusoidal sigma weight residual 0.00 47.81 -47.81 1 1.00e+01 1.00e-02 3.15e+01 dihedral pdb=" CB CYS B 627 " pdb=" SG CYS B 627 " pdb=" SG CYS B 630 " pdb=" CB CYS B 630 " ideal model delta sinusoidal sigma weight residual -86.00 -133.56 47.56 1 1.00e+01 1.00e-02 3.12e+01 dihedral pdb=" CB CYS B 203 " pdb=" SG CYS B 203 " pdb=" SG CYS B 210 " pdb=" CB CYS B 210 " ideal model delta sinusoidal sigma weight residual -86.00 -125.57 39.57 1 1.00e+01 1.00e-02 2.20e+01 ... (remaining 8115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.253: 1977 0.253 - 0.506: 6 0.506 - 0.759: 1 0.759 - 1.012: 0 1.012 - 1.265: 1 Chirality restraints: 1985 Sorted by residual: chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.13 -1.27 2.00e-02 2.50e+03 4.00e+03 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-02 2.50e+03 3.69e+02 chirality pdb=" C1 NAG J 4 " pdb=" O4 NAG J 3 " pdb=" C2 NAG J 4 " pdb=" O5 NAG J 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-02 2.50e+03 2.84e+02 ... (remaining 1982 not shown) Planarity restraints: 2291 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " -0.323 2.00e-02 2.50e+03 2.79e-01 9.75e+02 pdb=" C7 NAG G 1 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " -0.142 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " 0.498 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.297 2.00e-02 2.50e+03 2.55e-01 8.13e+02 pdb=" C7 NAG E 2 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.164 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.449 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " -0.272 2.00e-02 2.50e+03 2.33e-01 6.79e+02 pdb=" C7 NAG E 1 " 0.064 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.162 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " 0.407 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " -0.038 2.00e-02 2.50e+03 ... (remaining 2288 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.53: 182 2.53 - 3.05: 9013 3.05 - 3.57: 14712 3.57 - 4.08: 23396 4.08 - 4.60: 32826 Nonbonded interactions: 80129 Sorted by model distance: nonbonded pdb=" OD2 ASP B 152 " pdb="CA CA B 803 " model vdw 2.018 3.130 nonbonded pdb=" OD1 ASP B 152 " pdb="CA CA B 803 " model vdw 2.037 3.130 nonbonded pdb=" OD1 ASN B 241 " pdb="CA CA B 802 " model vdw 2.201 3.130 nonbonded pdb=" O ASP B 647 " pdb=" NH1 ARG B 648 " model vdw 2.205 2.950 nonbonded pdb=" OD1 ASP A 459 " pdb="CA CA A1104 " model vdw 2.206 3.130 ... (remaining 80124 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 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 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: 0.140 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.980 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 0.006 0.049 12875 Z= 0.390 Angle : 0.797 15.756 17546 Z= 0.483 Chirality : 0.064 1.265 1985 Planarity : 0.016 0.367 2280 Dihedral : 13.992 116.205 5067 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 25.32 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.16 % Favored : 94.65 % Rotamer: Outliers : 2.57 % Allowed : 5.06 % Favored : 92.37 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.19 % 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: -0.40 (0.22), residues: 1591 helix: 0.09 (0.46), residues: 144 sheet: 0.42 (0.23), residues: 534 loop : -0.72 (0.22), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 948 TYR 0.011 0.001 TYR B 695 PHE 0.012 0.001 PHE B 396 TRP 0.009 0.001 TRP A 266 HIS 0.002 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.39 (12819) covalent geometry : angle 0.74252 / 0.47 (17415) SS BOND : bond 0.00306 / 0.20 ( 37) SS BOND : angle 1.02207 / 0.66 ( 74) hydrogen bonds : bond 0.24346 / 16.73 ( 397) hydrogen bonds : angle 10.02427 / 6.96 ( 1004) link_BETA1-4 : bond 0.03900 / 2.25 ( 10) link_BETA1-4 : angle 5.79219 / 3.53 ( 30) link_BETA1-6 : bond 0.03580 / 1.88 ( 1) link_BETA1-6 : angle 4.65135 / 2.43 ( 3) link_NAG-ASN : bond 0.00767 / 0.36 ( 8) link_NAG-ASN : angle 4.04535 / 2.34 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 THR cc_start: 0.9392 (p) cc_final: 0.9147 (p) REVERT: A 433 ARG cc_start: 0.8819 (mmm-85) cc_final: 0.8471 (tpp80) REVERT: A 532 LYS cc_start: 0.9181 (tptt) cc_final: 0.8871 (tppt) REVERT: A 547 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8191 (tmm160) REVERT: A 659 ASP cc_start: 0.8702 (p0) cc_final: 0.8353 (p0) REVERT: A 706 ASN cc_start: 0.8550 (m-40) cc_final: 0.8331 (m-40) REVERT: A 719 GLU cc_start: 0.8074 (mp0) cc_final: 0.7591 (mp0) REVERT: A 760 GLN cc_start: 0.8755 (mp10) cc_final: 0.8352 (mp10) REVERT: A 786 PHE cc_start: 0.8491 (m-80) cc_final: 0.8280 (m-10) REVERT: A 815 TYR cc_start: 0.8188 (m-80) cc_final: 0.7448 (m-10) REVERT: A 948 ARG cc_start: 0.7505 (ttm110) cc_final: 0.7024 (ttp-110) REVERT: A 950 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7242 (mm) REVERT: A 961 PHE cc_start: 0.8207 (t80) cc_final: 0.7863 (t80) REVERT: A 981 GLN cc_start: 0.8712 (mt0) cc_final: 0.8007 (mm110) REVERT: A 983 TRP cc_start: 0.7457 (p90) cc_final: 0.7161 (p90) REVERT: B 41 GLN cc_start: 0.8421 (tt0) cc_final: 0.7943 (tt0) REVERT: B 158 GLN cc_start: 0.8564 (tp40) cc_final: 0.8342 (tp40) REVERT: B 267 ASP cc_start: 0.8531 (p0) cc_final: 0.8216 (p0) REVERT: B 382 GLU cc_start: 0.8568 (tt0) cc_final: 0.8325 (tt0) REVERT: B 542 ILE cc_start: 0.9126 (mt) cc_final: 0.8888 (mp) REVERT: B 582 TYR cc_start: 0.7553 (t80) cc_final: 0.7316 (t80) REVERT: B 645 LYS cc_start: 0.8078 (tmtt) cc_final: 0.7622 (tmmm) outliers start: 35 outliers final: 13 residues processed: 173 average time/residue: 0.6584 time to fit residues: 123.1725 Evaluate side-chains 123 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 461 CYS Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 630 CYS Chi-restraints excluded: chain B residue 673 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN A 78 GLN A 95 GLN A 482 GLN A 490 GLN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 ASN A 622 HIS A 642 GLN A 644 GLN A 819 ASN ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 HIS A 837 GLN ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 930 GLN ** A 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 GLN A 981 GLN B 69 ASN B 105 GLN B 167 GLN B 300 HIS B 339 ASN ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 GLN ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.112704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.067874 restraints weight = 24520.318| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.85 r_work: 0.2802 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12875 Z= 0.145 Angle : 0.587 10.673 17546 Z= 0.290 Chirality : 0.044 0.291 1985 Planarity : 0.004 0.066 2280 Dihedral : 13.544 109.487 2205 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 30.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.78 % Favored : 95.16 % Rotamer: Outliers : 1.98 % Allowed : 9.90 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: -0.42 (0.22), residues: 1591 helix: -0.02 (0.44), residues: 154 sheet: 0.40 (0.23), residues: 531 loop : -0.71 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 931 TYR 0.011 0.001 TYR A 946 PHE 0.008 0.001 PHE A 516 TRP 0.009 0.001 TRP A 266 HIS 0.002 0.001 HIS B 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (12819) covalent geometry : angle 0.55949 / 0.28 (17415) SS BOND : bond 0.00450 / 0.20 ( 37) SS BOND : angle 1.37554 / 0.95 ( 74) hydrogen bonds : bond 0.04508 / 3.12 ( 397) hydrogen bonds : angle 7.43437 / 5.13 ( 1004) link_BETA1-4 : bond 0.00480 / 0.31 ( 10) link_BETA1-4 : angle 2.17778 / 1.48 ( 30) link_BETA1-6 : bond 0.00450 / 0.24 ( 1) link_BETA1-6 : angle 3.20174 / 1.57 ( 3) link_NAG-ASN : bond 0.00305 / 0.18 ( 8) link_NAG-ASN : angle 3.45644 / 1.95 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.496 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 156 THR cc_start: 0.9397 (p) cc_final: 0.9135 (p) REVERT: A 433 ARG cc_start: 0.9138 (mmm-85) cc_final: 0.8844 (tpp80) REVERT: A 532 LYS cc_start: 0.9279 (tptt) cc_final: 0.8900 (tppt) REVERT: A 547 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8272 (tmm160) REVERT: A 659 ASP cc_start: 0.8796 (p0) cc_final: 0.8445 (p0) REVERT: A 706 ASN cc_start: 0.8723 (m-40) cc_final: 0.8471 (m-40) REVERT: A 719 GLU cc_start: 0.8290 (mp0) cc_final: 0.7745 (mp0) REVERT: A 760 GLN cc_start: 0.8790 (mp10) cc_final: 0.8474 (mp10) REVERT: A 786 PHE cc_start: 0.8041 (m-80) cc_final: 0.7795 (m-10) REVERT: A 815 TYR cc_start: 0.7654 (m-80) cc_final: 0.6844 (m-10) REVERT: A 948 ARG cc_start: 0.7556 (ttm110) cc_final: 0.7045 (ttp80) REVERT: A 960 TRP cc_start: 0.7201 (t60) cc_final: 0.6953 (t60) REVERT: A 961 PHE cc_start: 0.8508 (t80) cc_final: 0.8095 (t80) REVERT: A 983 TRP cc_start: 0.7809 (p90) cc_final: 0.7588 (p90) REVERT: B 41 GLN cc_start: 0.8937 (tt0) cc_final: 0.8390 (tt0) REVERT: B 382 GLU cc_start: 0.8778 (tt0) cc_final: 0.8550 (tt0) REVERT: B 542 ILE cc_start: 0.9105 (mt) cc_final: 0.8886 (mp) REVERT: B 582 TYR cc_start: 0.7653 (t80) cc_final: 0.7362 (t80) REVERT: B 632 ASP cc_start: 0.8039 (t0) cc_final: 0.7749 (t0) REVERT: B 710 GLU cc_start: 0.8541 (pm20) cc_final: 0.7722 (tp30) REVERT: C 493 ARG cc_start: 0.6550 (OUTLIER) cc_final: 0.5709 (ttp-170) outliers start: 27 outliers final: 14 residues processed: 133 average time/residue: 0.5837 time to fit residues: 85.3556 Evaluate side-chains 116 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 461 CYS Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 630 CYS Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain C residue 493 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 37 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 151 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 48 optimal weight: 0.1980 chunk 51 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 490 GLN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 GLN ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 GLN ** 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 = 0.3635 r_free = 0.3635 target = 0.110752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.063936 restraints weight = 32381.246| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.23 r_work: 0.2689 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12875 Z= 0.227 Angle : 0.601 9.248 17546 Z= 0.293 Chirality : 0.046 0.337 1985 Planarity : 0.004 0.054 2280 Dihedral : 11.359 103.257 2199 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 31.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.04 % Favored : 93.90 % Rotamer: Outliers : 2.79 % Allowed : 9.83 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: -0.63 (0.21), residues: 1591 helix: -0.25 (0.42), residues: 156 sheet: 0.17 (0.22), residues: 536 loop : -0.79 (0.22), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 473 TYR 0.023 0.002 TYR A 690 PHE 0.014 0.002 PHE B 447 TRP 0.011 0.001 TRP B 264 HIS 0.004 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.23 (12819) covalent geometry : angle 0.57990 / 0.29 (17415) SS BOND : bond 0.00314 / 0.18 ( 37) SS BOND : angle 1.24746 / 0.85 ( 74) hydrogen bonds : bond 0.03743 / 2.61 ( 397) hydrogen bonds : angle 6.57896 / 4.50 ( 1004) link_BETA1-4 : bond 0.00386 / 0.28 ( 10) link_BETA1-4 : angle 1.95498 / 1.31 ( 30) link_BETA1-6 : bond 0.00399 / 0.21 ( 1) link_BETA1-6 : angle 3.45593 / 1.54 ( 3) link_NAG-ASN : bond 0.00419 / 0.21 ( 8) link_NAG-ASN : angle 3.05210 / 1.75 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 107 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ARG cc_start: 0.9200 (mmm-85) cc_final: 0.8928 (tpp80) REVERT: A 532 LYS cc_start: 0.9266 (tptt) cc_final: 0.8892 (tppt) REVERT: A 659 ASP cc_start: 0.8817 (p0) cc_final: 0.8463 (p0) REVERT: A 706 ASN cc_start: 0.8758 (m-40) cc_final: 0.8501 (m-40) REVERT: A 719 GLU cc_start: 0.8471 (mp0) cc_final: 0.7859 (mp0) REVERT: A 760 GLN cc_start: 0.8989 (mp10) cc_final: 0.8667 (mp10) REVERT: A 815 TYR cc_start: 0.7540 (m-80) cc_final: 0.6640 (m-10) REVERT: A 828 LEU cc_start: 0.8921 (tm) cc_final: 0.8664 (tm) REVERT: A 926 MET cc_start: 0.7347 (tpt) cc_final: 0.7011 (tpt) REVERT: A 939 PHE cc_start: 0.6089 (OUTLIER) cc_final: 0.5421 (m-80) REVERT: A 948 ARG cc_start: 0.7799 (ttm110) cc_final: 0.7228 (ttp-110) REVERT: A 961 PHE cc_start: 0.8506 (t80) cc_final: 0.8058 (t80) REVERT: B 41 GLN cc_start: 0.8981 (tt0) cc_final: 0.8398 (tt0) REVERT: B 632 ASP cc_start: 0.8258 (t0) cc_final: 0.7948 (t0) REVERT: B 664 GLU cc_start: 0.5468 (OUTLIER) cc_final: 0.4654 (mp0) outliers start: 38 outliers final: 18 residues processed: 131 average time/residue: 0.5993 time to fit residues: 85.9432 Evaluate side-chains 118 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 630 CYS Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 683 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 130 optimal weight: 0.4980 chunk 82 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 158 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN B 241 ASN ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 GLN ** 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 = 0.3648 r_free = 0.3648 target = 0.111149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.065940 restraints weight = 22158.599| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.66 r_work: 0.2740 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2615 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12875 Z= 0.195 Angle : 0.567 9.478 17546 Z= 0.275 Chirality : 0.044 0.332 1985 Planarity : 0.003 0.055 2280 Dihedral : 10.037 102.297 2198 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 32.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.28 % Favored : 94.59 % Rotamer: Outliers : 2.27 % Allowed : 10.71 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.21), residues: 1591 helix: -0.06 (0.43), residues: 149 sheet: 0.23 (0.23), residues: 519 loop : -0.81 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 473 TYR 0.012 0.001 TYR A 946 PHE 0.010 0.001 PHE B 447 TRP 0.011 0.001 TRP A 266 HIS 0.003 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (12819) covalent geometry : angle 0.54628 / 0.27 (17415) SS BOND : bond 0.00332 / 0.20 ( 37) SS BOND : angle 1.28258 / 0.92 ( 74) hydrogen bonds : bond 0.03258 / 2.25 ( 397) hydrogen bonds : angle 6.29673 / 4.30 ( 1004) link_BETA1-4 : bond 0.00406 / 0.31 ( 10) link_BETA1-4 : angle 1.87624 / 1.25 ( 30) link_BETA1-6 : bond 0.00489 / 0.26 ( 1) link_BETA1-6 : angle 3.20735 / 1.49 ( 3) link_NAG-ASN : bond 0.00301 / 0.15 ( 8) link_NAG-ASN : angle 2.83259 / 1.70 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ARG cc_start: 0.9145 (mmm-85) cc_final: 0.8859 (tpp80) REVERT: A 532 LYS cc_start: 0.9267 (tptt) cc_final: 0.8898 (tppt) REVERT: A 659 ASP cc_start: 0.8808 (p0) cc_final: 0.8456 (p0) REVERT: A 706 ASN cc_start: 0.8752 (m-40) cc_final: 0.8498 (m-40) REVERT: A 719 GLU cc_start: 0.8485 (mp0) cc_final: 0.7826 (mp0) REVERT: A 760 GLN cc_start: 0.9023 (mp10) cc_final: 0.8608 (mp10) REVERT: A 815 TYR cc_start: 0.7383 (m-80) cc_final: 0.6550 (m-10) REVERT: A 939 PHE cc_start: 0.6173 (OUTLIER) cc_final: 0.5466 (m-80) REVERT: A 961 PHE cc_start: 0.8508 (t80) cc_final: 0.8060 (t80) REVERT: B 41 GLN cc_start: 0.8948 (tt0) cc_final: 0.8366 (tt0) REVERT: B 57 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6502 (tm) REVERT: B 632 ASP cc_start: 0.8244 (t0) cc_final: 0.7928 (t0) REVERT: B 664 GLU cc_start: 0.5662 (OUTLIER) cc_final: 0.5058 (mp0) outliers start: 31 outliers final: 18 residues processed: 118 average time/residue: 0.5778 time to fit residues: 74.9807 Evaluate side-chains 117 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 630 CYS Chi-restraints excluded: chain B residue 646 PHE Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 683 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 106 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 155 optimal weight: 20.0000 chunk 97 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.111645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.066450 restraints weight = 22163.028| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.67 r_work: 0.2749 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12875 Z= 0.154 Angle : 0.541 9.225 17546 Z= 0.260 Chirality : 0.043 0.323 1985 Planarity : 0.003 0.050 2280 Dihedral : 9.138 104.081 2197 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 31.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.66 % Favored : 94.21 % Rotamer: Outliers : 2.05 % Allowed : 11.37 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: -0.58 (0.21), residues: 1591 helix: -0.03 (0.43), residues: 155 sheet: 0.22 (0.23), residues: 512 loop : -0.78 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 473 TYR 0.011 0.001 TYR A 946 PHE 0.008 0.001 PHE B 447 TRP 0.012 0.001 TRP A 983 HIS 0.002 0.000 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (12819) covalent geometry : angle 0.52012 / 0.25 (17415) SS BOND : bond 0.00243 / 0.14 ( 37) SS BOND : angle 1.24701 / 0.96 ( 74) hydrogen bonds : bond 0.02909 / 2.02 ( 397) hydrogen bonds : angle 6.06049 / 4.14 ( 1004) link_BETA1-4 : bond 0.00375 / 0.28 ( 10) link_BETA1-4 : angle 1.95724 / 1.23 ( 30) link_BETA1-6 : bond 0.00644 / 0.34 ( 1) link_BETA1-6 : angle 3.16629 / 1.56 ( 3) link_NAG-ASN : bond 0.00238 / 0.12 ( 8) link_NAG-ASN : angle 2.68224 / 1.61 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ARG cc_start: 0.9136 (mmm-85) cc_final: 0.8848 (tpp80) REVERT: A 532 LYS cc_start: 0.9280 (tptt) cc_final: 0.8915 (tppt) REVERT: A 547 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8342 (tmm160) REVERT: A 659 ASP cc_start: 0.8818 (p0) cc_final: 0.8469 (p0) REVERT: A 706 ASN cc_start: 0.8694 (m-40) cc_final: 0.8443 (m-40) REVERT: A 719 GLU cc_start: 0.8492 (mp0) cc_final: 0.7798 (mp0) REVERT: A 760 GLN cc_start: 0.9035 (mp10) cc_final: 0.8613 (mp10) REVERT: A 815 TYR cc_start: 0.7235 (m-80) cc_final: 0.6402 (m-80) REVERT: A 828 LEU cc_start: 0.8983 (tm) cc_final: 0.8721 (tm) REVERT: A 926 MET cc_start: 0.7261 (tpt) cc_final: 0.6948 (tpt) REVERT: A 939 PHE cc_start: 0.6263 (OUTLIER) cc_final: 0.5469 (m-80) REVERT: A 961 PHE cc_start: 0.8463 (t80) cc_final: 0.8007 (t80) REVERT: B 41 GLN cc_start: 0.8912 (tt0) cc_final: 0.8291 (tt0) REVERT: B 57 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6606 (tm) REVERT: B 253 MET cc_start: 0.9385 (OUTLIER) cc_final: 0.9033 (tpp) REVERT: B 632 ASP cc_start: 0.8279 (t0) cc_final: 0.7968 (t0) REVERT: B 664 GLU cc_start: 0.5677 (OUTLIER) cc_final: 0.5094 (mp0) outliers start: 28 outliers final: 15 residues processed: 116 average time/residue: 0.5877 time to fit residues: 75.0241 Evaluate side-chains 117 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 630 CYS Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 705 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN B 241 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 GLN ** 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 = 0.3633 r_free = 0.3633 target = 0.110682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.065629 restraints weight = 25609.083| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.92 r_work: 0.2747 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 12875 Z= 0.205 Angle : 0.565 9.199 17546 Z= 0.273 Chirality : 0.044 0.295 1985 Planarity : 0.003 0.052 2280 Dihedral : 8.567 102.941 2197 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 31.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.29 % Favored : 93.58 % Rotamer: Outliers : 2.27 % Allowed : 11.52 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: -0.64 (0.21), residues: 1591 helix: -0.10 (0.42), residues: 155 sheet: 0.18 (0.23), residues: 514 loop : -0.81 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 473 TYR 0.013 0.001 TYR B 683 PHE 0.010 0.001 PHE B 447 TRP 0.010 0.001 TRP B 264 HIS 0.003 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (12819) covalent geometry : angle 0.54117 / 0.27 (17415) SS BOND : bond 0.00374 / 0.25 ( 37) SS BOND : angle 1.43492 / 1.16 ( 74) hydrogen bonds : bond 0.03005 / 2.09 ( 397) hydrogen bonds : angle 6.04308 / 4.13 ( 1004) link_BETA1-4 : bond 0.00502 / 0.39 ( 10) link_BETA1-4 : angle 2.15839 / 1.23 ( 30) link_BETA1-6 : bond 0.00590 / 0.31 ( 1) link_BETA1-6 : angle 3.17014 / 1.53 ( 3) link_NAG-ASN : bond 0.00311 / 0.16 ( 8) link_NAG-ASN : angle 2.77100 / 1.66 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 0.491 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 433 ARG cc_start: 0.9117 (mmm-85) cc_final: 0.8804 (tpp80) REVERT: A 532 LYS cc_start: 0.9275 (tptt) cc_final: 0.8896 (tppt) REVERT: A 659 ASP cc_start: 0.8853 (p0) cc_final: 0.8495 (p0) REVERT: A 706 ASN cc_start: 0.8616 (m-40) cc_final: 0.8362 (m-40) REVERT: A 719 GLU cc_start: 0.8423 (mp0) cc_final: 0.7722 (mp0) REVERT: A 760 GLN cc_start: 0.8921 (mp10) cc_final: 0.8498 (mp10) REVERT: A 815 TYR cc_start: 0.7214 (m-80) cc_final: 0.6366 (m-10) REVERT: A 828 LEU cc_start: 0.8954 (tm) cc_final: 0.8684 (tm) REVERT: A 939 PHE cc_start: 0.6152 (OUTLIER) cc_final: 0.5448 (m-80) REVERT: A 960 TRP cc_start: 0.7384 (t60) cc_final: 0.7157 (t60) REVERT: A 961 PHE cc_start: 0.8496 (t80) cc_final: 0.8026 (t80) REVERT: B 41 GLN cc_start: 0.8834 (tt0) cc_final: 0.8183 (tt0) REVERT: B 57 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6508 (tm) REVERT: B 253 MET cc_start: 0.9275 (OUTLIER) cc_final: 0.8922 (tpp) REVERT: B 561 MET cc_start: 0.8487 (ttp) cc_final: 0.8089 (ttp) REVERT: B 632 ASP cc_start: 0.8243 (t0) cc_final: 0.7940 (t0) REVERT: B 664 GLU cc_start: 0.5730 (OUTLIER) cc_final: 0.5104 (mp0) outliers start: 31 outliers final: 22 residues processed: 115 average time/residue: 0.5418 time to fit residues: 68.2400 Evaluate side-chains 123 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 630 CYS Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain C residue 493 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.0980 chunk 93 optimal weight: 0.5980 chunk 139 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 104 optimal weight: 0.0470 chunk 91 optimal weight: 0.0050 chunk 7 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.3494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.113185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.068344 restraints weight = 25461.002| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.93 r_work: 0.2799 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12875 Z= 0.083 Angle : 0.494 8.368 17546 Z= 0.237 Chirality : 0.042 0.266 1985 Planarity : 0.003 0.053 2280 Dihedral : 8.295 107.052 2197 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 31.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.47 % Favored : 94.40 % Rotamer: Outliers : 1.76 % Allowed : 12.18 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: -0.44 (0.22), residues: 1591 helix: 0.28 (0.44), residues: 155 sheet: 0.32 (0.23), residues: 506 loop : -0.73 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 473 TYR 0.020 0.001 TYR A 690 PHE 0.007 0.001 PHE A 750 TRP 0.012 0.001 TRP A 266 HIS 0.002 0.000 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.08 (12819) covalent geometry : angle 0.47377 / 0.23 (17415) SS BOND : bond 0.00177 / 0.10 ( 37) SS BOND : angle 1.01656 / 0.82 ( 74) hydrogen bonds : bond 0.02414 / 1.66 ( 397) hydrogen bonds : angle 5.71873 / 3.90 ( 1004) link_BETA1-4 : bond 0.00407 / 0.29 ( 10) link_BETA1-4 : angle 1.92482 / 1.18 ( 30) link_BETA1-6 : bond 0.00668 / 0.35 ( 1) link_BETA1-6 : angle 3.28652 / 1.66 ( 3) link_NAG-ASN : bond 0.00217 / 0.11 ( 8) link_NAG-ASN : angle 2.57573 / 1.55 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ARG cc_start: 0.9129 (mmm-85) cc_final: 0.8811 (tpp80) REVERT: A 532 LYS cc_start: 0.9289 (tptt) cc_final: 0.8926 (tppt) REVERT: A 547 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8237 (tmm160) REVERT: A 659 ASP cc_start: 0.8846 (p0) cc_final: 0.8485 (p0) REVERT: A 677 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7913 (mt-10) REVERT: A 706 ASN cc_start: 0.8618 (m-40) cc_final: 0.8373 (m-40) REVERT: A 719 GLU cc_start: 0.8422 (mp0) cc_final: 0.7668 (mp0) REVERT: A 760 GLN cc_start: 0.8968 (mp10) cc_final: 0.8545 (mp10) REVERT: A 815 TYR cc_start: 0.7044 (m-80) cc_final: 0.6217 (m-10) REVERT: A 828 LEU cc_start: 0.8990 (tm) cc_final: 0.8716 (tm) REVERT: A 926 MET cc_start: 0.7150 (tpt) cc_final: 0.6744 (tpt) REVERT: A 939 PHE cc_start: 0.6292 (OUTLIER) cc_final: 0.5641 (m-80) REVERT: A 960 TRP cc_start: 0.7399 (t60) cc_final: 0.7156 (t60) REVERT: A 961 PHE cc_start: 0.8384 (t80) cc_final: 0.7890 (t80) REVERT: B 41 GLN cc_start: 0.8869 (tt0) cc_final: 0.8254 (tt0) REVERT: B 253 MET cc_start: 0.9245 (OUTLIER) cc_final: 0.8821 (tpp) REVERT: B 390 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8807 (tp30) REVERT: B 632 ASP cc_start: 0.8241 (t0) cc_final: 0.7942 (t0) REVERT: B 664 GLU cc_start: 0.6029 (OUTLIER) cc_final: 0.5470 (mp0) outliers start: 24 outliers final: 17 residues processed: 115 average time/residue: 0.5962 time to fit residues: 75.1893 Evaluate side-chains 117 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 630 CYS Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 705 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 6 optimal weight: 0.0670 chunk 155 optimal weight: 30.0000 chunk 29 optimal weight: 0.9980 chunk 7 optimal weight: 0.1980 chunk 3 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 47 optimal weight: 0.0470 chunk 65 optimal weight: 5.9990 chunk 151 optimal weight: 0.0470 chunk 63 optimal weight: 0.7980 overall best weight: 0.2314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 364 GLN ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 GLN ** 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 = 0.3699 r_free = 0.3699 target = 0.114316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.068380 restraints weight = 32188.550| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.26 r_work: 0.2794 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12875 Z= 0.072 Angle : 0.475 8.107 17546 Z= 0.227 Chirality : 0.042 0.261 1985 Planarity : 0.003 0.051 2280 Dihedral : 7.944 106.611 2197 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 31.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.84 % Favored : 95.03 % Rotamer: Outliers : 1.69 % Allowed : 12.25 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: -0.24 (0.22), residues: 1591 helix: 0.68 (0.46), residues: 155 sheet: 0.47 (0.23), residues: 509 loop : -0.65 (0.22), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 473 TYR 0.010 0.001 TYR B 683 PHE 0.011 0.001 PHE A 786 TRP 0.007 0.001 TRP A 144 HIS 0.001 0.000 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00166 / 0.07 (12819) covalent geometry : angle 0.45506 / 0.22 (17415) SS BOND : bond 0.00166 / 0.10 ( 37) SS BOND : angle 0.88271 / 0.69 ( 74) hydrogen bonds : bond 0.02142 / 1.47 ( 397) hydrogen bonds : angle 5.40691 / 3.68 ( 1004) link_BETA1-4 : bond 0.00439 / 0.30 ( 10) link_BETA1-4 : angle 1.75516 / 1.10 ( 30) link_BETA1-6 : bond 0.00704 / 0.37 ( 1) link_BETA1-6 : angle 3.23210 / 1.59 ( 3) link_NAG-ASN : bond 0.00204 / 0.11 ( 8) link_NAG-ASN : angle 2.60379 / 1.55 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ARG cc_start: 0.9064 (mmm-85) cc_final: 0.8755 (tpp80) REVERT: A 532 LYS cc_start: 0.9258 (tptt) cc_final: 0.8899 (tppt) REVERT: A 547 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8223 (tmm160) REVERT: A 659 ASP cc_start: 0.8733 (p0) cc_final: 0.8387 (p0) REVERT: A 677 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7817 (mt-10) REVERT: A 706 ASN cc_start: 0.8633 (m-40) cc_final: 0.8398 (m-40) REVERT: A 719 GLU cc_start: 0.8464 (mp0) cc_final: 0.7734 (mp0) REVERT: A 760 GLN cc_start: 0.8994 (mp10) cc_final: 0.8538 (mp10) REVERT: A 815 TYR cc_start: 0.6960 (m-80) cc_final: 0.6138 (m-80) REVERT: A 828 LEU cc_start: 0.9040 (tm) cc_final: 0.8749 (tm) REVERT: A 926 MET cc_start: 0.7174 (tpt) cc_final: 0.6809 (tpt) REVERT: A 960 TRP cc_start: 0.7357 (t60) cc_final: 0.7141 (t60) REVERT: A 961 PHE cc_start: 0.8311 (t80) cc_final: 0.7733 (t80) REVERT: B 41 GLN cc_start: 0.8860 (tt0) cc_final: 0.8316 (tt0) REVERT: B 204 TYR cc_start: 0.9124 (OUTLIER) cc_final: 0.8834 (p90) REVERT: B 253 MET cc_start: 0.9323 (OUTLIER) cc_final: 0.9054 (tpp) REVERT: B 390 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8614 (tp30) REVERT: B 632 ASP cc_start: 0.8205 (t0) cc_final: 0.7905 (t0) REVERT: B 664 GLU cc_start: 0.6206 (OUTLIER) cc_final: 0.5635 (mp0) outliers start: 23 outliers final: 12 residues processed: 117 average time/residue: 0.6240 time to fit residues: 79.6619 Evaluate side-chains 112 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 630 CYS Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 705 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 156 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.111027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.065216 restraints weight = 32416.808| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 3.14 r_work: 0.2706 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2578 r_free = 0.2578 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2578 r_free = 0.2578 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12875 Z= 0.208 Angle : 0.572 14.064 17546 Z= 0.275 Chirality : 0.044 0.262 1985 Planarity : 0.004 0.053 2280 Dihedral : 7.911 96.963 2197 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 32.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.85 % Favored : 94.03 % Rotamer: Outliers : 1.54 % Allowed : 12.84 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: -0.40 (0.22), residues: 1591 helix: 0.34 (0.44), residues: 155 sheet: 0.31 (0.23), residues: 519 loop : -0.69 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 473 TYR 0.024 0.001 TYR B 683 PHE 0.011 0.001 PHE B 447 TRP 0.010 0.001 TRP A 141 HIS 0.004 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 (12819) covalent geometry : angle 0.55354 / 0.27 (17415) SS BOND : bond 0.00309 / 0.19 ( 37) SS BOND : angle 1.15305 / 0.79 ( 74) hydrogen bonds : bond 0.02880 / 2.00 ( 397) hydrogen bonds : angle 5.62489 / 3.83 ( 1004) link_BETA1-4 : bond 0.00440 / 0.31 ( 10) link_BETA1-4 : angle 1.71673 / 1.07 ( 30) link_BETA1-6 : bond 0.00725 / 0.38 ( 1) link_BETA1-6 : angle 3.13684 / 1.48 ( 3) link_NAG-ASN : bond 0.00359 / 0.21 ( 8) link_NAG-ASN : angle 2.82634 / 1.69 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ARG cc_start: 0.9205 (mmm-85) cc_final: 0.8920 (tpp80) REVERT: A 532 LYS cc_start: 0.9274 (tptt) cc_final: 0.8914 (tppt) REVERT: A 547 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8304 (tmm160) REVERT: A 659 ASP cc_start: 0.8784 (p0) cc_final: 0.8458 (p0) REVERT: A 706 ASN cc_start: 0.8690 (m-40) cc_final: 0.8461 (m-40) REVERT: A 719 GLU cc_start: 0.8598 (mp0) cc_final: 0.7860 (mp0) REVERT: A 760 GLN cc_start: 0.9015 (mp10) cc_final: 0.8478 (mp10) REVERT: A 815 TYR cc_start: 0.7271 (m-80) cc_final: 0.6399 (m-10) REVERT: A 828 LEU cc_start: 0.9059 (tm) cc_final: 0.8742 (tm) REVERT: A 926 MET cc_start: 0.7157 (tpt) cc_final: 0.6826 (tpt) REVERT: A 960 TRP cc_start: 0.7421 (t60) cc_final: 0.7171 (t60) REVERT: A 961 PHE cc_start: 0.8439 (t80) cc_final: 0.7941 (t80) REVERT: B 41 GLN cc_start: 0.8943 (tt0) cc_final: 0.8314 (tt0) REVERT: B 253 MET cc_start: 0.9426 (OUTLIER) cc_final: 0.9027 (tpp) REVERT: B 561 MET cc_start: 0.8668 (ttp) cc_final: 0.8320 (ttp) REVERT: B 632 ASP cc_start: 0.8228 (t0) cc_final: 0.7941 (t0) REVERT: B 664 GLU cc_start: 0.6192 (OUTLIER) cc_final: 0.5588 (mp0) outliers start: 21 outliers final: 17 residues processed: 114 average time/residue: 0.6050 time to fit residues: 75.6045 Evaluate side-chains 114 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 630 CYS Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 705 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 155 optimal weight: 20.0000 chunk 73 optimal weight: 4.9990 chunk 151 optimal weight: 0.0370 chunk 152 optimal weight: 1.9990 chunk 82 optimal weight: 0.0370 chunk 141 optimal weight: 4.9990 chunk 34 optimal weight: 0.0270 chunk 75 optimal weight: 4.9990 chunk 144 optimal weight: 0.0770 chunk 131 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.4354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.112855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.067768 restraints weight = 25830.257| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.85 r_work: 0.2724 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12875 Z= 0.089 Angle : 0.507 9.766 17546 Z= 0.243 Chirality : 0.042 0.237 1985 Planarity : 0.003 0.053 2280 Dihedral : 7.692 95.365 2197 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 32.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.22 % Favored : 94.65 % Rotamer: Outliers : 1.25 % Allowed : 13.28 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: -0.32 (0.22), residues: 1591 helix: 0.45 (0.44), residues: 155 sheet: 0.37 (0.23), residues: 514 loop : -0.64 (0.22), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 473 TYR 0.010 0.001 TYR B 344 PHE 0.009 0.001 PHE A 786 TRP 0.009 0.001 TRP A 266 HIS 0.001 0.000 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 (12819) covalent geometry : angle 0.48943 / 0.24 (17415) SS BOND : bond 0.00162 / 0.09 ( 37) SS BOND : angle 0.92639 / 0.69 ( 74) hydrogen bonds : bond 0.02410 / 1.67 ( 397) hydrogen bonds : angle 5.49906 / 3.75 ( 1004) link_BETA1-4 : bond 0.00444 / 0.31 ( 10) link_BETA1-4 : angle 1.62026 / 1.03 ( 30) link_BETA1-6 : bond 0.00739 / 0.39 ( 1) link_BETA1-6 : angle 3.21698 / 1.57 ( 3) link_NAG-ASN : bond 0.00187 / 0.09 ( 8) link_NAG-ASN : angle 2.66511 / 1.60 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ARG cc_start: 0.9158 (mmm-85) cc_final: 0.8850 (tpp80) REVERT: A 532 LYS cc_start: 0.9274 (tptt) cc_final: 0.8908 (tppt) REVERT: A 547 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8265 (tmm160) REVERT: A 659 ASP cc_start: 0.8778 (p0) cc_final: 0.8455 (p0) REVERT: A 677 GLU cc_start: 0.8460 (mt-10) cc_final: 0.7943 (mt-10) REVERT: A 706 ASN cc_start: 0.8639 (m-40) cc_final: 0.8401 (m-40) REVERT: A 719 GLU cc_start: 0.8566 (mp0) cc_final: 0.7867 (mp0) REVERT: A 760 GLN cc_start: 0.9023 (mp10) cc_final: 0.8598 (mp10) REVERT: A 815 TYR cc_start: 0.7079 (m-80) cc_final: 0.6162 (m-80) REVERT: A 828 LEU cc_start: 0.9033 (tm) cc_final: 0.8725 (tm) REVERT: A 926 MET cc_start: 0.7135 (tpt) cc_final: 0.6801 (tpt) REVERT: A 960 TRP cc_start: 0.7378 (t60) cc_final: 0.7091 (t60) REVERT: A 961 PHE cc_start: 0.8433 (t80) cc_final: 0.7892 (t80) REVERT: B 41 GLN cc_start: 0.8886 (tt0) cc_final: 0.8272 (tt0) REVERT: B 204 TYR cc_start: 0.9157 (OUTLIER) cc_final: 0.8880 (p90) REVERT: B 253 MET cc_start: 0.9364 (OUTLIER) cc_final: 0.8920 (tpp) REVERT: B 632 ASP cc_start: 0.8188 (t0) cc_final: 0.7895 (t0) REVERT: B 664 GLU cc_start: 0.6201 (OUTLIER) cc_final: 0.5606 (mp0) outliers start: 17 outliers final: 12 residues processed: 107 average time/residue: 0.6507 time to fit residues: 75.9903 Evaluate side-chains 107 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 607 CYS Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 630 CYS Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 705 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 0.0270 chunk 147 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.9444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.112237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.067329 restraints weight = 24695.019| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.88 r_work: 0.2781 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12875 Z= 0.131 Angle : 0.513 10.944 17546 Z= 0.246 Chirality : 0.042 0.208 1985 Planarity : 0.003 0.052 2280 Dihedral : 7.316 83.192 2197 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 32.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.91 % Favored : 93.96 % Rotamer: Outliers : 1.69 % Allowed : 12.69 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: -0.27 (0.22), residues: 1591 helix: 0.60 (0.45), residues: 149 sheet: 0.37 (0.23), residues: 520 loop : -0.61 (0.22), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 473 TYR 0.010 0.001 TYR B 344 PHE 0.008 0.001 PHE A 222 TRP 0.008 0.001 TRP A 141 HIS 0.002 0.000 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (12819) covalent geometry : angle 0.49479 / 0.24 (17415) SS BOND : bond 0.00204 / 0.12 ( 37) SS BOND : angle 0.90115 / 0.62 ( 74) hydrogen bonds : bond 0.02509 / 1.74 ( 397) hydrogen bonds : angle 5.46904 / 3.72 ( 1004) link_BETA1-4 : bond 0.00425 / 0.30 ( 10) link_BETA1-4 : angle 1.62381 / 1.03 ( 30) link_BETA1-6 : bond 0.00795 / 0.42 ( 1) link_BETA1-6 : angle 3.13343 / 1.50 ( 3) link_NAG-ASN : bond 0.00247 / 0.15 ( 8) link_NAG-ASN : angle 2.77580 / 1.69 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6052.39 seconds wall clock time: 103 minutes 52.06 seconds (6232.06 seconds total)