Starting phenix.real_space_refine on Thu Mar 5 13:55:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a4n_11639/03_2026/7a4n_11639_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a4n_11639/03_2026/7a4n_11639.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7a4n_11639/03_2026/7a4n_11639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a4n_11639/03_2026/7a4n_11639.map" model { file = "/net/cci-nas-00/data/ceres_data/7a4n_11639/03_2026/7a4n_11639_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a4n_11639/03_2026/7a4n_11639_neut.cif" } 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= 0.002 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 14576 2.51 5 N 3741 2.21 5 O 4396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22809 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7511 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 963, 7493 Classifications: {'peptide': 963} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 49, 'TRANS': 913} Chain breaks: 10 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 963, 7493 Classifications: {'peptide': 963} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 49, 'TRANS': 913} Chain breaks: 10 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 7638 Chain: "B" Number of atoms: 7502 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 963, 7479 Classifications: {'peptide': 963} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 49, 'TRANS': 913} Chain breaks: 10 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASN:plan1': 4, 'ARG:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 963, 7479 Classifications: {'peptide': 963} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 49, 'TRANS': 913} Chain breaks: 10 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASN:plan1': 4, 'ARG:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 7616 Chain: "C" Number of atoms: 7502 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 963, 7478 Classifications: {'peptide': 963} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 49, 'TRANS': 913} Chain breaks: 10 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 963, 7478 Classifications: {'peptide': 963} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 49, 'TRANS': 913} Chain breaks: 10 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 7614 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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 8.72, per 1000 atoms: 0.38 Number of scatterers: 22809 At special positions: 0 Unit cell: (165.528, 129.58, 126.236, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 4396 8.00 N 3741 7.00 C 14576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=1.88 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=1.89 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=1.87 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-ASN " NAG A1301 " - " ASN A 709 " " NAG A1302 " - " ASN A 801 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A1098 " " NAG A1305 " - " ASN A1134 " " NAG B1301 " - " ASN B 709 " " NAG B1302 " - " ASN B 801 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B1098 " " NAG B1305 " - " ASN B1134 " " NAG C1301 " - " ASN C 709 " " NAG C1302 " - " ASN C 801 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C1098 " " NAG C1305 " - " ASN C1134 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN B 717 " " NAG F 1 " - " ASN C 717 " Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 1.6 seconds 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5440 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 54 sheets defined 25.8% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 344 removed outlier: 4.030A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.624A pdb=" N GLU A 619 " --> pdb=" O ASN A 616 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 616 through 620' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.614A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.083A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.740A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.604A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.662A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.624A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.554A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.225A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.762A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 344 removed outlier: 3.827A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.726A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.293A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.860A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.700A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.551A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.816A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.597A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.994A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 92 removed outlier: 3.772A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 106 through 107 removed outlier: 4.314A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 118 through 121 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.028A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.566A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AB4, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.374A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.755A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.523A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.523A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.418A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC3, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.626A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 50 through 55 removed outlier: 4.111A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 89 through 92 removed outlier: 3.796A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 118 through 121 Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.060A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.573A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 538 through 539 Processing sheet with id=AD4, first strand: chain 'B' and resid 542 through 543 Processing sheet with id=AD5, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.663A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.380A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.768A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.595A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.595A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.455A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE3, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.613A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 50 through 55 removed outlier: 4.108A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 89 through 92 removed outlier: 3.668A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 118 through 121 Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.005A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.493A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF3, first strand: chain 'C' and resid 538 through 539 Processing sheet with id=AF4, first strand: chain 'C' and resid 542 through 543 Processing sheet with id=AF5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.279A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.512A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.512A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.403A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1120 through 1122 957 hydrogen bonds defined for protein. 2595 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.87 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7280 1.34 - 1.46: 5803 1.46 - 1.58: 10123 1.58 - 1.70: 0 1.70 - 1.83: 120 Bond restraints: 23326 Sorted by residual: bond pdb=" N HIS C1101 " pdb=" CA HIS C1101 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.15e-02 7.56e+03 7.82e+00 bond pdb=" N THR C1100 " pdb=" CA THR C1100 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.06e-02 8.90e+03 6.31e+00 bond pdb=" N TRP C1102 " pdb=" CA TRP C1102 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.22e-02 6.72e+03 6.03e+00 bond pdb=" N PHE C1103 " pdb=" CA PHE C1103 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.29e-02 6.01e+03 5.55e+00 bond pdb=" N ASN C1098 " pdb=" CA ASN C1098 " ideal model delta sigma weight residual 1.457 1.485 -0.029 1.32e-02 5.74e+03 4.67e+00 ... (remaining 23321 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.71: 31734 5.71 - 11.41: 33 11.41 - 17.12: 3 17.12 - 22.82: 0 22.82 - 28.53: 4 Bond angle restraints: 31774 Sorted by residual: angle pdb=" CD LYS A 776 " pdb=" CE LYS A 776 " pdb=" NZ LYS A 776 " ideal model delta sigma weight residual 111.90 140.43 -28.53 3.20e+00 9.77e-02 7.95e+01 angle pdb=" CD LYS B 206 " pdb=" CE LYS B 206 " pdb=" NZ LYS B 206 " ideal model delta sigma weight residual 111.90 140.35 -28.45 3.20e+00 9.77e-02 7.90e+01 angle pdb=" CD LYS C 424 " pdb=" CE LYS C 424 " pdb=" NZ LYS C 424 " ideal model delta sigma weight residual 111.90 139.97 -28.07 3.20e+00 9.77e-02 7.69e+01 angle pdb=" CD LYS B 378 " pdb=" CE LYS B 378 " pdb=" NZ LYS B 378 " ideal model delta sigma weight residual 111.90 86.87 25.03 3.20e+00 9.77e-02 6.12e+01 angle pdb=" CG ARG A 357 " pdb=" CD ARG A 357 " pdb=" NE ARG A 357 " ideal model delta sigma weight residual 112.00 124.99 -12.99 2.20e+00 2.07e-01 3.49e+01 ... (remaining 31769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 13126 17.78 - 35.56: 843 35.56 - 53.34: 172 53.34 - 71.11: 37 71.11 - 88.89: 23 Dihedral angle restraints: 14201 sinusoidal: 5746 harmonic: 8455 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -11.72 -74.28 1 1.00e+01 1.00e-02 7.00e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -12.51 -73.49 1 1.00e+01 1.00e-02 6.87e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -14.47 -71.53 1 1.00e+01 1.00e-02 6.56e+01 ... (remaining 14198 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.358: 3700 0.358 - 0.716: 2 0.716 - 1.075: 0 1.075 - 1.433: 4 1.433 - 1.791: 7 Chirality restraints: 3713 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-02 2.50e+03 3.41e+02 chirality pdb=" CG LEU C1141 " pdb=" CB LEU C1141 " pdb=" CD1 LEU C1141 " pdb=" CD2 LEU C1141 " both_signs ideal model delta sigma weight residual False -2.59 -0.80 -1.79 2.00e-01 2.50e+01 8.02e+01 chirality pdb=" CG LEU A 189 " pdb=" CB LEU A 189 " pdb=" CD1 LEU A 189 " pdb=" CD2 LEU A 189 " both_signs ideal model delta sigma weight residual False -2.59 -0.80 -1.79 2.00e-01 2.50e+01 8.00e+01 ... (remaining 3710 not shown) Planarity restraints: 4096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 189 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.90e+00 pdb=" C LEU A 189 " -0.034 2.00e-02 2.50e+03 pdb=" O LEU A 189 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG A 190 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 189 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C LEU B 189 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU B 189 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG B 190 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 189 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C LEU C 189 " 0.031 2.00e-02 2.50e+03 pdb=" O LEU C 189 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG C 190 " -0.010 2.00e-02 2.50e+03 ... (remaining 4093 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 227 2.58 - 3.16: 19427 3.16 - 3.74: 33034 3.74 - 4.32: 50745 4.32 - 4.90: 84265 Nonbonded interactions: 187698 Sorted by model distance: nonbonded pdb=" OH TYR B 37 " pdb=" OD2 ASP B 53 " model vdw 2.003 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" OD2 ASP A 53 " model vdw 2.098 3.040 nonbonded pdb=" OG1 THR A 618 " pdb=" OE1 GLU A 619 " model vdw 2.099 3.040 nonbonded pdb=" O LYS C 386 " pdb=" OD1 ASP C 389 " model vdw 2.111 3.040 nonbonded pdb=" OD1 ASP C 568 " pdb=" N ILE C 569 " model vdw 2.116 3.120 ... (remaining 187693 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 124 or (resid 125 and (name N or name CA or nam \ e C or name O or name CB )) or resid 126 through 318 or (resid 319 and (name N o \ r name CA or name C or name O or name CB )) or resid 320 through 339 or resid 34 \ 1 through 344 or resid 346 through 381 or resid 383 through 402 or (resid 403 an \ d (name N or name CA or name C or name O or name CB )) or resid 404 through 429 \ or resid 431 through 442 or resid 444 through 468 or resid 470 through 494 or (r \ esid 495 and (name N or name CA or name C or name O or name CB )) or resid 496 t \ hrough 504 or (resid 505 through 506 and (name N or name CA or name C or name O \ or name CB )) or resid 507 through 1305)) selection = (chain 'B' and (resid 27 through 318 or (resid 319 and (name N or name CA or nam \ e C or name O or name CB )) or resid 320 through 339 or resid 341 through 344 or \ resid 346 through 381 or resid 383 through 402 or (resid 403 and (name N or nam \ e CA or name C or name O or name CB )) or resid 404 through 429 or resid 431 thr \ ough 442 or resid 444 through 468 or resid 470 through 1141 or (resid 1142 and ( \ name N or name CA or name C or name O or name CB )) or resid 1143 through 1305)) \ selection = (chain 'C' and (resid 27 through 124 or (resid 125 and (name N or name CA or nam \ e C or name O or name CB )) or resid 126 through 339 or resid 341 through 344 or \ resid 346 through 381 or resid 383 through 421 or (resid 422 and (name N or nam \ e CA or name C or name O or name CB )) or resid 423 through 429 or resid 431 thr \ ough 442 or resid 444 through 468 or resid 470 through 505 or (resid 506 and (na \ me N or name CA or name C or name O or name CB )) or resid 507 through 1141 or ( \ resid 1142 and (name N or name CA or name C or name O or name CB )) or resid 114 \ 3 through 1305)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.50 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: 6.060 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: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 25.920 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 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:5.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 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 : 0.008 0.162 23383 Z= 0.312 Angle : 0.836 28.531 31909 Z= 0.414 Chirality : 0.098 1.791 3713 Planarity : 0.004 0.045 4078 Dihedral : 12.788 88.893 8653 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.20 % Allowed : 5.16 % Favored : 94.64 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.14), residues: 2840 helix: 0.25 (0.19), residues: 653 sheet: -1.47 (0.19), residues: 534 loop : -2.01 (0.13), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 357 TYR 0.022 0.002 TYR C1067 PHE 0.015 0.002 PHE C 65 TRP 0.010 0.001 TRP B 436 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00743 (23326) covalent geometry : angle 0.80502 (31774) SS BOND : bond 0.04357 ( 36) SS BOND : angle 3.53611 ( 72) hydrogen bonds : bond 0.11413 ( 921) hydrogen bonds : angle 7.16076 ( 2595) link_BETA1-4 : bond 0.06582 ( 3) link_BETA1-4 : angle 4.64491 ( 9) link_NAG-ASN : bond 0.00515 ( 18) link_NAG-ASN : angle 3.39630 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 299 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.4778 (m-40) cc_final: 0.4097 (p0) REVERT: A 127 VAL cc_start: 0.6693 (t) cc_final: 0.6468 (p) REVERT: A 192 PHE cc_start: 0.6298 (m-80) cc_final: 0.6006 (m-80) REVERT: A 979 ASP cc_start: 0.6732 (m-30) cc_final: 0.6529 (m-30) REVERT: B 368 LEU cc_start: 0.7377 (mm) cc_final: 0.7081 (mt) REVERT: B 421 TYR cc_start: 0.5292 (m-10) cc_final: 0.4870 (m-80) REVERT: C 28 TYR cc_start: 0.6564 (m-80) cc_final: 0.6307 (m-80) REVERT: C 196 ASN cc_start: 0.5012 (m-40) cc_final: 0.4495 (t0) REVERT: C 353 TRP cc_start: 0.7325 (p-90) cc_final: 0.6919 (p-90) REVERT: C 354 ASN cc_start: 0.6552 (p0) cc_final: 0.6155 (t0) REVERT: C 392 PHE cc_start: 0.7219 (m-80) cc_final: 0.6951 (m-80) outliers start: 4 outliers final: 1 residues processed: 303 average time/residue: 0.5460 time to fit residues: 191.9215 Evaluate side-chains 173 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1127 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 764 ASN A1083 HIS A1088 HIS A1101 HIS A1113 GLN A1119 ASN B 121 ASN B 239 GLN B 314 GLN B 321 GLN B 954 GLN B1002 GLN B1071 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 439 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 ASN C1088 HIS C1119 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.163707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.110846 restraints weight = 81959.852| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.81 r_work: 0.3060 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 23383 Z= 0.147 Angle : 0.599 15.333 31909 Z= 0.308 Chirality : 0.046 0.168 3713 Planarity : 0.004 0.046 4078 Dihedral : 5.466 96.721 3546 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.19 % Allowed : 9.10 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.15), residues: 2840 helix: 1.44 (0.21), residues: 651 sheet: -1.06 (0.19), residues: 609 loop : -1.45 (0.14), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 403 TYR 0.024 0.002 TYR B 380 PHE 0.027 0.002 PHE B 168 TRP 0.019 0.001 TRP B 436 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00338 (23326) covalent geometry : angle 0.59225 (31774) SS BOND : bond 0.00252 ( 36) SS BOND : angle 0.87480 ( 72) hydrogen bonds : bond 0.04539 ( 921) hydrogen bonds : angle 5.86649 ( 2595) link_BETA1-4 : bond 0.00109 ( 3) link_BETA1-4 : angle 1.33975 ( 9) link_NAG-ASN : bond 0.00194 ( 18) link_NAG-ASN : angle 2.13295 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.884 Fit side-chains REVERT: A 61 ASN cc_start: 0.4932 (m-40) cc_final: 0.3994 (p0) REVERT: A 127 VAL cc_start: 0.6554 (t) cc_final: 0.6180 (p) REVERT: A 191 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7535 (mt-10) REVERT: A 192 PHE cc_start: 0.6507 (m-80) cc_final: 0.5956 (m-80) REVERT: A 347 PHE cc_start: 0.5636 (m-80) cc_final: 0.5419 (m-10) REVERT: A 396 TYR cc_start: 0.7411 (m-80) cc_final: 0.7039 (m-80) REVERT: A 452 LEU cc_start: 0.5084 (mt) cc_final: 0.4828 (mt) REVERT: A 900 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8714 (mtp) REVERT: A 1072 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: B 269 TYR cc_start: 0.6552 (m-10) cc_final: 0.6316 (m-80) REVERT: B 368 LEU cc_start: 0.7182 (mm) cc_final: 0.6820 (mt) REVERT: B 514 SER cc_start: 0.8380 (t) cc_final: 0.7923 (m) REVERT: B 553 THR cc_start: 0.7604 (m) cc_final: 0.7223 (p) REVERT: B 567 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6908 (tpt-90) REVERT: B 607 GLN cc_start: 0.8334 (pt0) cc_final: 0.8062 (pt0) REVERT: B 935 GLN cc_start: 0.7165 (tm130) cc_final: 0.6732 (tm-30) REVERT: B 988 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: B 1010 GLN cc_start: 0.8313 (mm110) cc_final: 0.7936 (pt0) REVERT: B 1029 MET cc_start: 0.9448 (tpp) cc_final: 0.9097 (tpp) REVERT: C 28 TYR cc_start: 0.6754 (m-80) cc_final: 0.6411 (m-80) REVERT: C 32 PHE cc_start: 0.7441 (m-80) cc_final: 0.7220 (m-80) REVERT: C 105 ILE cc_start: 0.6503 (mp) cc_final: 0.6299 (mp) REVERT: C 196 ASN cc_start: 0.4599 (m-40) cc_final: 0.4089 (t0) REVERT: C 353 TRP cc_start: 0.7199 (p-90) cc_final: 0.6553 (p-90) REVERT: C 380 TYR cc_start: 0.7713 (m-80) cc_final: 0.7507 (m-80) REVERT: C 392 PHE cc_start: 0.7505 (m-80) cc_final: 0.7157 (m-80) REVERT: C 408 ARG cc_start: 0.6958 (pmt170) cc_final: 0.6746 (ppt90) REVERT: C 546 LEU cc_start: 0.5834 (pp) cc_final: 0.5600 (pt) outliers start: 29 outliers final: 12 residues processed: 206 average time/residue: 0.5244 time to fit residues: 126.6997 Evaluate side-chains 167 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 827 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 104 optimal weight: 5.9990 chunk 131 optimal weight: 0.4980 chunk 281 optimal weight: 0.7980 chunk 152 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 276 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 239 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN A1119 ASN B 121 ASN B 314 GLN B1002 GLN B1101 HIS C 121 ASN C 439 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.162628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.109815 restraints weight = 81158.120| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.79 r_work: 0.3064 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23383 Z= 0.142 Angle : 0.553 11.689 31909 Z= 0.284 Chirality : 0.045 0.151 3713 Planarity : 0.004 0.046 4078 Dihedral : 4.727 50.329 3544 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.47 % Allowed : 10.37 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.15), residues: 2840 helix: 1.72 (0.20), residues: 653 sheet: -0.84 (0.19), residues: 645 loop : -1.28 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 237 TYR 0.032 0.002 TYR B 369 PHE 0.031 0.001 PHE B 168 TRP 0.019 0.001 TRP B 436 HIS 0.004 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00331 (23326) covalent geometry : angle 0.54622 (31774) SS BOND : bond 0.00222 ( 36) SS BOND : angle 0.82905 ( 72) hydrogen bonds : bond 0.04466 ( 921) hydrogen bonds : angle 5.64076 ( 2595) link_BETA1-4 : bond 0.00160 ( 3) link_BETA1-4 : angle 1.39647 ( 9) link_NAG-ASN : bond 0.00183 ( 18) link_NAG-ASN : angle 2.05611 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 0.726 Fit side-chains REVERT: A 61 ASN cc_start: 0.4947 (m-40) cc_final: 0.4093 (p0) REVERT: A 127 VAL cc_start: 0.6607 (t) cc_final: 0.6211 (p) REVERT: A 192 PHE cc_start: 0.6518 (m-80) cc_final: 0.5972 (m-80) REVERT: A 347 PHE cc_start: 0.5651 (m-80) cc_final: 0.5423 (m-10) REVERT: A 396 TYR cc_start: 0.7354 (m-80) cc_final: 0.6924 (m-80) REVERT: A 452 LEU cc_start: 0.5140 (mt) cc_final: 0.4887 (mt) REVERT: A 553 THR cc_start: 0.7718 (m) cc_final: 0.7397 (p) REVERT: A 654 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7646 (tp30) REVERT: A 748 GLU cc_start: 0.7495 (mp0) cc_final: 0.7250 (mp0) REVERT: A 900 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8684 (mtp) REVERT: A 1072 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: B 368 LEU cc_start: 0.7199 (mm) cc_final: 0.6813 (mt) REVERT: B 400 PHE cc_start: 0.7330 (p90) cc_final: 0.7083 (p90) REVERT: B 514 SER cc_start: 0.8341 (t) cc_final: 0.7922 (m) REVERT: B 553 THR cc_start: 0.7609 (m) cc_final: 0.7248 (p) REVERT: B 567 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6885 (tpt-90) REVERT: B 607 GLN cc_start: 0.8289 (pt0) cc_final: 0.8020 (pt0) REVERT: B 935 GLN cc_start: 0.7164 (tm130) cc_final: 0.6792 (tm-30) REVERT: B 988 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7615 (mp0) REVERT: B 1010 GLN cc_start: 0.8366 (mm110) cc_final: 0.7932 (pt0) REVERT: C 32 PHE cc_start: 0.7458 (m-80) cc_final: 0.7212 (m-80) REVERT: C 105 ILE cc_start: 0.6558 (mp) cc_final: 0.6338 (mp) REVERT: C 196 ASN cc_start: 0.4702 (m-40) cc_final: 0.4142 (t0) REVERT: C 266 TYR cc_start: 0.7266 (OUTLIER) cc_final: 0.6985 (m-80) REVERT: C 353 TRP cc_start: 0.7188 (p-90) cc_final: 0.6489 (p-90) REVERT: C 380 TYR cc_start: 0.7597 (m-80) cc_final: 0.7293 (m-80) REVERT: C 392 PHE cc_start: 0.7666 (m-80) cc_final: 0.7252 (m-80) REVERT: C 408 ARG cc_start: 0.6952 (pmt170) cc_final: 0.6744 (ppt90) REVERT: C 433 VAL cc_start: 0.7675 (t) cc_final: 0.7394 (m) REVERT: C 546 LEU cc_start: 0.5881 (pp) cc_final: 0.5656 (pt) outliers start: 36 outliers final: 20 residues processed: 199 average time/residue: 0.4836 time to fit residues: 114.5061 Evaluate side-chains 183 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 135 optimal weight: 0.9980 chunk 223 optimal weight: 8.9990 chunk 176 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 226 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 174 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 437 ASN A1119 ASN B 188 ASN B 207 HIS B 314 GLN C 439 ASN C1119 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.160130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.107263 restraints weight = 82975.222| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.78 r_work: 0.3020 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 23383 Z= 0.234 Angle : 0.651 12.395 31909 Z= 0.333 Chirality : 0.048 0.332 3713 Planarity : 0.004 0.046 4078 Dihedral : 5.124 37.797 3544 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.19 % Allowed : 10.69 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.15), residues: 2840 helix: 1.57 (0.20), residues: 653 sheet: -0.91 (0.19), residues: 642 loop : -1.26 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 190 TYR 0.023 0.002 TYR C1067 PHE 0.031 0.002 PHE A 377 TRP 0.018 0.002 TRP B 436 HIS 0.015 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00558 (23326) covalent geometry : angle 0.64106 (31774) SS BOND : bond 0.00434 ( 36) SS BOND : angle 1.36128 ( 72) hydrogen bonds : bond 0.05240 ( 921) hydrogen bonds : angle 5.80038 ( 2595) link_BETA1-4 : bond 0.00272 ( 3) link_BETA1-4 : angle 1.67371 ( 9) link_NAG-ASN : bond 0.00308 ( 18) link_NAG-ASN : angle 2.42792 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 161 time to evaluate : 0.743 Fit side-chains REVERT: A 61 ASN cc_start: 0.4985 (m-40) cc_final: 0.4125 (p0) REVERT: A 127 VAL cc_start: 0.6761 (t) cc_final: 0.6346 (p) REVERT: A 192 PHE cc_start: 0.6489 (m-80) cc_final: 0.5907 (m-80) REVERT: A 396 TYR cc_start: 0.7481 (m-80) cc_final: 0.6763 (m-80) REVERT: A 452 LEU cc_start: 0.5154 (mt) cc_final: 0.4875 (mt) REVERT: A 529 LYS cc_start: 0.7046 (mmtt) cc_final: 0.6837 (tptm) REVERT: A 553 THR cc_start: 0.7738 (m) cc_final: 0.7427 (p) REVERT: A 654 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7729 (tp30) REVERT: B 207 HIS cc_start: 0.6178 (OUTLIER) cc_final: 0.4624 (m90) REVERT: B 368 LEU cc_start: 0.7314 (mm) cc_final: 0.6917 (mt) REVERT: B 400 PHE cc_start: 0.7356 (p90) cc_final: 0.7127 (p90) REVERT: B 514 SER cc_start: 0.8398 (t) cc_final: 0.7982 (m) REVERT: B 553 THR cc_start: 0.7675 (m) cc_final: 0.7290 (p) REVERT: B 567 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.6846 (tpt-90) REVERT: B 616 ASN cc_start: 0.7938 (OUTLIER) cc_final: 0.7737 (m-40) REVERT: B 935 GLN cc_start: 0.7321 (tm130) cc_final: 0.6986 (tm-30) REVERT: B 988 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7745 (mp0) REVERT: B 1010 GLN cc_start: 0.8390 (mm110) cc_final: 0.7965 (pt0) REVERT: B 1119 ASN cc_start: 0.8599 (m110) cc_final: 0.8345 (m-40) REVERT: C 32 PHE cc_start: 0.7666 (m-80) cc_final: 0.7311 (m-80) REVERT: C 266 TYR cc_start: 0.7370 (OUTLIER) cc_final: 0.7100 (m-80) REVERT: C 353 TRP cc_start: 0.7388 (p-90) cc_final: 0.6851 (p-90) REVERT: C 380 TYR cc_start: 0.7749 (m-80) cc_final: 0.7505 (m-80) REVERT: C 433 VAL cc_start: 0.7617 (t) cc_final: 0.7270 (m) REVERT: C 619 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6395 (pt0) outliers start: 54 outliers final: 27 residues processed: 208 average time/residue: 0.4854 time to fit residues: 119.6791 Evaluate side-chains 186 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 827 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 190 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 146 optimal weight: 0.8980 chunk 213 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 127 optimal weight: 0.0870 chunk 244 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN B 188 ASN B 314 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN C 564 GLN C1119 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.162142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.108231 restraints weight = 75153.017| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.31 r_work: 0.3064 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 23383 Z= 0.127 Angle : 0.548 14.435 31909 Z= 0.283 Chirality : 0.044 0.327 3713 Planarity : 0.004 0.045 4078 Dihedral : 4.613 35.551 3544 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.47 % Allowed : 11.92 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.15), residues: 2840 helix: 1.83 (0.20), residues: 656 sheet: -0.67 (0.19), residues: 654 loop : -1.14 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 190 TYR 0.030 0.001 TYR B 369 PHE 0.028 0.001 PHE C 168 TRP 0.019 0.001 TRP B 436 HIS 0.023 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00293 (23326) covalent geometry : angle 0.53918 (31774) SS BOND : bond 0.00402 ( 36) SS BOND : angle 1.26437 ( 72) hydrogen bonds : bond 0.04368 ( 921) hydrogen bonds : angle 5.51181 ( 2595) link_BETA1-4 : bond 0.00064 ( 3) link_BETA1-4 : angle 1.31982 ( 9) link_NAG-ASN : bond 0.00160 ( 18) link_NAG-ASN : angle 2.00861 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 0.901 Fit side-chains REVERT: A 28 TYR cc_start: 0.7064 (m-80) cc_final: 0.6700 (m-80) REVERT: A 127 VAL cc_start: 0.6767 (t) cc_final: 0.6341 (p) REVERT: A 190 ARG cc_start: 0.5549 (mtp180) cc_final: 0.4450 (mmm-85) REVERT: A 192 PHE cc_start: 0.6632 (m-80) cc_final: 0.6091 (m-80) REVERT: A 396 TYR cc_start: 0.7436 (m-80) cc_final: 0.6865 (m-80) REVERT: A 452 LEU cc_start: 0.5287 (mt) cc_final: 0.4985 (mt) REVERT: A 553 THR cc_start: 0.7782 (m) cc_final: 0.7502 (p) REVERT: B 33 THR cc_start: 0.7405 (p) cc_final: 0.6969 (p) REVERT: B 190 ARG cc_start: 0.6142 (mmt180) cc_final: 0.4861 (mtt90) REVERT: B 206 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.7043 (tmtp) REVERT: B 368 LEU cc_start: 0.7312 (mm) cc_final: 0.6893 (mt) REVERT: B 400 PHE cc_start: 0.7419 (p90) cc_final: 0.7176 (p90) REVERT: B 514 SER cc_start: 0.8444 (t) cc_final: 0.8030 (m) REVERT: B 553 THR cc_start: 0.7623 (m) cc_final: 0.7310 (p) REVERT: B 567 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6894 (tpt-90) REVERT: B 616 ASN cc_start: 0.7954 (OUTLIER) cc_final: 0.7745 (t0) REVERT: B 654 GLU cc_start: 0.7733 (tp30) cc_final: 0.7316 (tt0) REVERT: B 916 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8425 (tp) REVERT: B 935 GLN cc_start: 0.7177 (tm130) cc_final: 0.6878 (tt0) REVERT: B 1010 GLN cc_start: 0.8386 (mm110) cc_final: 0.7987 (pt0) REVERT: C 32 PHE cc_start: 0.7627 (m-80) cc_final: 0.7320 (m-80) REVERT: C 196 ASN cc_start: 0.4908 (m-40) cc_final: 0.4212 (t0) REVERT: C 266 TYR cc_start: 0.7380 (OUTLIER) cc_final: 0.7146 (m-80) REVERT: C 353 TRP cc_start: 0.7331 (p-90) cc_final: 0.6876 (p-90) REVERT: C 380 TYR cc_start: 0.7776 (m-80) cc_final: 0.7514 (m-80) REVERT: C 433 VAL cc_start: 0.7689 (t) cc_final: 0.7371 (m) REVERT: C 619 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6319 (pt0) REVERT: C 1101 HIS cc_start: 0.8132 (m90) cc_final: 0.7465 (m90) outliers start: 36 outliers final: 18 residues processed: 197 average time/residue: 0.4913 time to fit residues: 114.4696 Evaluate side-chains 183 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 8 optimal weight: 0.0050 chunk 91 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 154 optimal weight: 0.2980 chunk 62 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 246 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 115 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A1119 ASN B 314 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.163224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.112993 restraints weight = 84554.098| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.99 r_work: 0.3067 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 23383 Z= 0.111 Angle : 0.524 12.623 31909 Z= 0.271 Chirality : 0.044 0.282 3713 Planarity : 0.004 0.045 4078 Dihedral : 4.302 28.859 3544 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.63 % Allowed : 12.40 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.15), residues: 2840 helix: 2.01 (0.20), residues: 656 sheet: -0.47 (0.19), residues: 654 loop : -1.05 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 357 TYR 0.019 0.001 TYR C 369 PHE 0.025 0.001 PHE C 168 TRP 0.020 0.001 TRP B 436 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00252 (23326) covalent geometry : angle 0.51533 (31774) SS BOND : bond 0.00312 ( 36) SS BOND : angle 1.27860 ( 72) hydrogen bonds : bond 0.04086 ( 921) hydrogen bonds : angle 5.32814 ( 2595) link_BETA1-4 : bond 0.00056 ( 3) link_BETA1-4 : angle 1.20799 ( 9) link_NAG-ASN : bond 0.00155 ( 18) link_NAG-ASN : angle 1.83999 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 0.846 Fit side-chains REVERT: A 101 ILE cc_start: 0.2771 (OUTLIER) cc_final: 0.1628 (tp) REVERT: A 127 VAL cc_start: 0.6790 (t) cc_final: 0.6349 (p) REVERT: A 190 ARG cc_start: 0.5541 (mtp180) cc_final: 0.4405 (mmm-85) REVERT: A 192 PHE cc_start: 0.6695 (m-80) cc_final: 0.6142 (m-80) REVERT: A 396 TYR cc_start: 0.7361 (m-80) cc_final: 0.6959 (m-10) REVERT: A 452 LEU cc_start: 0.5217 (mt) cc_final: 0.4922 (mt) REVERT: A 553 THR cc_start: 0.7774 (m) cc_final: 0.7502 (p) REVERT: A 614 ASN cc_start: 0.7490 (m110) cc_final: 0.6933 (p0) REVERT: A 654 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7638 (tp30) REVERT: A 748 GLU cc_start: 0.7557 (mp0) cc_final: 0.7255 (mp0) REVERT: B 33 THR cc_start: 0.7401 (p) cc_final: 0.6951 (p) REVERT: B 368 LEU cc_start: 0.7337 (mm) cc_final: 0.6940 (mt) REVERT: B 400 PHE cc_start: 0.7400 (p90) cc_final: 0.7120 (p90) REVERT: B 514 SER cc_start: 0.8430 (t) cc_final: 0.8023 (m) REVERT: B 553 THR cc_start: 0.7656 (OUTLIER) cc_final: 0.7337 (p) REVERT: B 567 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.6884 (tpt-90) REVERT: B 654 GLU cc_start: 0.7791 (tp30) cc_final: 0.7363 (tt0) REVERT: B 916 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8431 (tp) REVERT: B 935 GLN cc_start: 0.7180 (tm130) cc_final: 0.6900 (tt0) REVERT: C 32 PHE cc_start: 0.7708 (m-80) cc_final: 0.7408 (m-80) REVERT: C 196 ASN cc_start: 0.4847 (m-40) cc_final: 0.4190 (t0) REVERT: C 266 TYR cc_start: 0.7413 (OUTLIER) cc_final: 0.7160 (m-80) REVERT: C 321 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.6532 (mp10) REVERT: C 353 TRP cc_start: 0.7328 (p-90) cc_final: 0.6913 (p-90) REVERT: C 380 TYR cc_start: 0.7725 (m-80) cc_final: 0.7420 (m-80) REVERT: C 433 VAL cc_start: 0.7692 (t) cc_final: 0.7433 (m) outliers start: 40 outliers final: 25 residues processed: 198 average time/residue: 0.4738 time to fit residues: 111.9856 Evaluate side-chains 188 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 65 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 127 optimal weight: 0.0040 chunk 153 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 287 optimal weight: 0.5980 chunk 250 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 224 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A1119 ASN B 314 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN B1002 GLN C 207 HIS C1119 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.162693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109532 restraints weight = 73986.218| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.45 r_work: 0.3044 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23383 Z= 0.125 Angle : 0.532 12.152 31909 Z= 0.274 Chirality : 0.044 0.266 3713 Planarity : 0.004 0.045 4078 Dihedral : 4.253 25.404 3544 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.79 % Allowed : 12.44 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.15), residues: 2840 helix: 2.07 (0.20), residues: 656 sheet: -0.45 (0.19), residues: 648 loop : -0.99 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 357 TYR 0.028 0.001 TYR B 369 PHE 0.023 0.001 PHE C 168 TRP 0.020 0.001 TRP B 436 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00291 (23326) covalent geometry : angle 0.52452 (31774) SS BOND : bond 0.00307 ( 36) SS BOND : angle 1.20045 ( 72) hydrogen bonds : bond 0.04215 ( 921) hydrogen bonds : angle 5.29818 ( 2595) link_BETA1-4 : bond 0.00095 ( 3) link_BETA1-4 : angle 1.30172 ( 9) link_NAG-ASN : bond 0.00144 ( 18) link_NAG-ASN : angle 1.84688 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: A 101 ILE cc_start: 0.2753 (OUTLIER) cc_final: 0.1645 (tp) REVERT: A 127 VAL cc_start: 0.6799 (t) cc_final: 0.6365 (p) REVERT: A 190 ARG cc_start: 0.5524 (mtp180) cc_final: 0.4356 (mmm-85) REVERT: A 192 PHE cc_start: 0.6716 (m-80) cc_final: 0.6125 (m-80) REVERT: A 396 TYR cc_start: 0.7465 (m-80) cc_final: 0.6973 (m-80) REVERT: A 452 LEU cc_start: 0.5235 (mt) cc_final: 0.4948 (mt) REVERT: A 553 THR cc_start: 0.7718 (m) cc_final: 0.7470 (p) REVERT: A 614 ASN cc_start: 0.7509 (m110) cc_final: 0.6949 (p0) REVERT: A 654 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7643 (tp30) REVERT: A 748 GLU cc_start: 0.7631 (mp0) cc_final: 0.7260 (mp0) REVERT: B 33 THR cc_start: 0.7372 (p) cc_final: 0.6936 (p) REVERT: B 368 LEU cc_start: 0.7287 (mm) cc_final: 0.6867 (mt) REVERT: B 400 PHE cc_start: 0.7416 (p90) cc_final: 0.7180 (p90) REVERT: B 423 TYR cc_start: 0.5466 (t80) cc_final: 0.5159 (t80) REVERT: B 514 SER cc_start: 0.8470 (t) cc_final: 0.8065 (m) REVERT: B 553 THR cc_start: 0.7687 (OUTLIER) cc_final: 0.7358 (p) REVERT: B 567 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6899 (tpt-90) REVERT: B 916 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8484 (tp) REVERT: B 935 GLN cc_start: 0.7194 (tm130) cc_final: 0.6938 (tt0) REVERT: B 1002 GLN cc_start: 0.8758 (tt0) cc_final: 0.8511 (tt0) REVERT: C 32 PHE cc_start: 0.7685 (m-80) cc_final: 0.7345 (m-80) REVERT: C 196 ASN cc_start: 0.4866 (m-40) cc_final: 0.4179 (t0) REVERT: C 207 HIS cc_start: 0.5774 (OUTLIER) cc_final: 0.4200 (t70) REVERT: C 353 TRP cc_start: 0.7310 (p-90) cc_final: 0.6844 (p-90) REVERT: C 380 TYR cc_start: 0.7754 (m-80) cc_final: 0.7448 (m-80) REVERT: C 433 VAL cc_start: 0.7633 (t) cc_final: 0.7398 (m) REVERT: C 619 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6254 (pt0) outliers start: 44 outliers final: 32 residues processed: 201 average time/residue: 0.4495 time to fit residues: 108.7013 Evaluate side-chains 197 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 74 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 201 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A1119 ASN B 314 GLN ** B 388 ASN ** 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 = 0.4029 r_free = 0.4029 target = 0.161390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.108097 restraints weight = 77766.833| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 3.45 r_work: 0.3037 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 23383 Z= 0.192 Angle : 0.597 15.040 31909 Z= 0.307 Chirality : 0.046 0.271 3713 Planarity : 0.004 0.044 4078 Dihedral : 4.632 31.594 3544 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.67 % Allowed : 12.87 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.31 (0.15), residues: 2840 helix: 2.14 (0.20), residues: 635 sheet: -0.57 (0.20), residues: 633 loop : -1.06 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 408 TYR 0.023 0.002 TYR C1067 PHE 0.024 0.002 PHE C 168 TRP 0.019 0.002 TRP B 436 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00458 (23326) covalent geometry : angle 0.58448 (31774) SS BOND : bond 0.00432 ( 36) SS BOND : angle 1.91685 ( 72) hydrogen bonds : bond 0.04748 ( 921) hydrogen bonds : angle 5.47504 ( 2595) link_BETA1-4 : bond 0.00157 ( 3) link_BETA1-4 : angle 1.49001 ( 9) link_NAG-ASN : bond 0.00216 ( 18) link_NAG-ASN : angle 2.05459 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 154 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: A 101 ILE cc_start: 0.2812 (OUTLIER) cc_final: 0.1724 (tp) REVERT: A 127 VAL cc_start: 0.6813 (t) cc_final: 0.6386 (p) REVERT: A 190 ARG cc_start: 0.5546 (mtp180) cc_final: 0.4381 (mmm-85) REVERT: A 192 PHE cc_start: 0.6632 (m-80) cc_final: 0.6012 (m-80) REVERT: A 347 PHE cc_start: 0.5806 (m-10) cc_final: 0.5599 (m-10) REVERT: A 396 TYR cc_start: 0.7478 (m-80) cc_final: 0.6886 (m-80) REVERT: A 452 LEU cc_start: 0.5230 (mt) cc_final: 0.4981 (mt) REVERT: A 553 THR cc_start: 0.7764 (m) cc_final: 0.7503 (p) REVERT: A 614 ASN cc_start: 0.7459 (m110) cc_final: 0.6951 (p0) REVERT: A 654 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7667 (tp30) REVERT: A 748 GLU cc_start: 0.7579 (mp0) cc_final: 0.7279 (mp0) REVERT: B 33 THR cc_start: 0.7358 (p) cc_final: 0.6927 (p) REVERT: B 368 LEU cc_start: 0.7354 (mm) cc_final: 0.6961 (mt) REVERT: B 400 PHE cc_start: 0.7433 (p90) cc_final: 0.7213 (p90) REVERT: B 423 TYR cc_start: 0.5650 (t80) cc_final: 0.5348 (t80) REVERT: B 514 SER cc_start: 0.8451 (t) cc_final: 0.8039 (m) REVERT: B 553 THR cc_start: 0.7720 (OUTLIER) cc_final: 0.7352 (p) REVERT: B 564 GLN cc_start: 0.6511 (OUTLIER) cc_final: 0.5984 (mm-40) REVERT: B 567 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6861 (tpt-90) REVERT: B 916 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8518 (tp) REVERT: B 935 GLN cc_start: 0.7200 (tm130) cc_final: 0.6950 (tt0) REVERT: B 1010 GLN cc_start: 0.8406 (mm110) cc_final: 0.8053 (pt0) REVERT: C 32 PHE cc_start: 0.7766 (m-80) cc_final: 0.7436 (m-80) REVERT: C 353 TRP cc_start: 0.7323 (p-90) cc_final: 0.6964 (p-90) REVERT: C 380 TYR cc_start: 0.7762 (m-80) cc_final: 0.7405 (m-80) REVERT: C 433 VAL cc_start: 0.7622 (t) cc_final: 0.7354 (m) REVERT: C 619 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6251 (pt0) REVERT: C 1101 HIS cc_start: 0.8069 (m90) cc_final: 0.7600 (m90) outliers start: 41 outliers final: 31 residues processed: 187 average time/residue: 0.4604 time to fit residues: 102.6576 Evaluate side-chains 190 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 827 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 233 optimal weight: 2.9990 chunk 283 optimal weight: 0.3980 chunk 22 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 135 optimal weight: 0.0020 chunk 178 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 75 optimal weight: 0.5980 chunk 193 optimal weight: 0.2980 chunk 17 optimal weight: 0.9990 chunk 243 optimal weight: 4.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A1119 ASN B 314 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.163146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.114022 restraints weight = 89393.969| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 4.29 r_work: 0.3052 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 23383 Z= 0.110 Angle : 0.523 14.343 31909 Z= 0.270 Chirality : 0.043 0.253 3713 Planarity : 0.003 0.044 4078 Dihedral : 4.252 27.865 3544 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.63 % Allowed : 12.91 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.15), residues: 2840 helix: 2.10 (0.20), residues: 659 sheet: -0.36 (0.19), residues: 651 loop : -0.94 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 408 TYR 0.025 0.001 TYR B 170 PHE 0.025 0.001 PHE A 168 TRP 0.021 0.001 TRP B 436 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00253 (23326) covalent geometry : angle 0.51347 (31774) SS BOND : bond 0.00334 ( 36) SS BOND : angle 1.43318 ( 72) hydrogen bonds : bond 0.04046 ( 921) hydrogen bonds : angle 5.23553 ( 2595) link_BETA1-4 : bond 0.00096 ( 3) link_BETA1-4 : angle 1.18371 ( 9) link_NAG-ASN : bond 0.00150 ( 18) link_NAG-ASN : angle 1.80520 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 164 time to evaluate : 0.793 Fit side-chains revert: symmetry clash REVERT: A 101 ILE cc_start: 0.2827 (OUTLIER) cc_final: 0.1759 (tp) REVERT: A 127 VAL cc_start: 0.6796 (t) cc_final: 0.6360 (p) REVERT: A 190 ARG cc_start: 0.5493 (mtp180) cc_final: 0.4314 (mmm-85) REVERT: A 192 PHE cc_start: 0.6703 (m-80) cc_final: 0.6127 (m-80) REVERT: A 396 TYR cc_start: 0.7453 (m-80) cc_final: 0.6965 (m-80) REVERT: A 452 LEU cc_start: 0.5263 (mt) cc_final: 0.4966 (mt) REVERT: A 553 THR cc_start: 0.7781 (m) cc_final: 0.7515 (p) REVERT: A 654 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7655 (tp30) REVERT: A 748 GLU cc_start: 0.7594 (mp0) cc_final: 0.7207 (mp0) REVERT: B 33 THR cc_start: 0.7307 (p) cc_final: 0.6877 (p) REVERT: B 368 LEU cc_start: 0.7310 (mm) cc_final: 0.6906 (mt) REVERT: B 400 PHE cc_start: 0.7428 (p90) cc_final: 0.7190 (p90) REVERT: B 423 TYR cc_start: 0.5474 (t80) cc_final: 0.5093 (t80) REVERT: B 514 SER cc_start: 0.8475 (t) cc_final: 0.8070 (m) REVERT: B 553 THR cc_start: 0.7713 (OUTLIER) cc_final: 0.7357 (p) REVERT: B 564 GLN cc_start: 0.6371 (OUTLIER) cc_final: 0.5821 (mm-40) REVERT: B 567 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.6832 (tpt-90) REVERT: B 916 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8428 (tp) REVERT: B 935 GLN cc_start: 0.7251 (tm130) cc_final: 0.7000 (tt0) REVERT: C 32 PHE cc_start: 0.7716 (m-80) cc_final: 0.7378 (m-80) REVERT: C 196 ASN cc_start: 0.4877 (m-40) cc_final: 0.4183 (t0) REVERT: C 207 HIS cc_start: 0.5552 (OUTLIER) cc_final: 0.4136 (t70) REVERT: C 353 TRP cc_start: 0.7238 (p-90) cc_final: 0.6854 (p-90) REVERT: C 380 TYR cc_start: 0.7752 (m-80) cc_final: 0.7434 (m-80) REVERT: C 1101 HIS cc_start: 0.8034 (m90) cc_final: 0.7590 (m90) outliers start: 40 outliers final: 25 residues processed: 195 average time/residue: 0.4551 time to fit residues: 106.2613 Evaluate side-chains 187 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 827 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 19 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 72 optimal weight: 0.0470 chunk 264 optimal weight: 0.4980 chunk 87 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 268 optimal weight: 0.6980 chunk 236 optimal weight: 1.9990 chunk 249 optimal weight: 1.9990 chunk 278 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN B 314 GLN ** B 388 ASN ** 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 = 0.4046 r_free = 0.4046 target = 0.162934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.111583 restraints weight = 92931.046| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 4.25 r_work: 0.3044 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 23383 Z= 0.124 Angle : 0.538 14.128 31909 Z= 0.277 Chirality : 0.044 0.301 3713 Planarity : 0.003 0.044 4078 Dihedral : 4.236 27.057 3544 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.43 % Allowed : 13.19 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.15), residues: 2840 helix: 2.33 (0.20), residues: 638 sheet: -0.43 (0.19), residues: 648 loop : -0.96 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.031 0.001 TYR B 369 PHE 0.022 0.001 PHE C 168 TRP 0.020 0.001 TRP B 436 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00293 (23326) covalent geometry : angle 0.52713 (31774) SS BOND : bond 0.00482 ( 36) SS BOND : angle 1.66119 ( 72) hydrogen bonds : bond 0.04148 ( 921) hydrogen bonds : angle 5.24535 ( 2595) link_BETA1-4 : bond 0.00103 ( 3) link_BETA1-4 : angle 1.26933 ( 9) link_NAG-ASN : bond 0.00137 ( 18) link_NAG-ASN : angle 1.80995 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 101 ILE cc_start: 0.2813 (OUTLIER) cc_final: 0.1768 (tp) REVERT: A 127 VAL cc_start: 0.6693 (t) cc_final: 0.6256 (p) REVERT: A 190 ARG cc_start: 0.5450 (mtp180) cc_final: 0.4247 (mmm-85) REVERT: A 192 PHE cc_start: 0.6619 (m-80) cc_final: 0.6007 (m-80) REVERT: A 396 TYR cc_start: 0.7389 (m-80) cc_final: 0.6877 (m-80) REVERT: A 452 LEU cc_start: 0.5152 (mt) cc_final: 0.4855 (mt) REVERT: A 553 THR cc_start: 0.7675 (m) cc_final: 0.7397 (p) REVERT: A 654 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7603 (tp30) REVERT: A 748 GLU cc_start: 0.7568 (mp0) cc_final: 0.7174 (mp0) REVERT: B 33 THR cc_start: 0.7315 (p) cc_final: 0.6879 (p) REVERT: B 368 LEU cc_start: 0.7267 (mm) cc_final: 0.6863 (mt) REVERT: B 400 PHE cc_start: 0.7370 (p90) cc_final: 0.7133 (p90) REVERT: B 423 TYR cc_start: 0.5474 (t80) cc_final: 0.5088 (t80) REVERT: B 514 SER cc_start: 0.8324 (t) cc_final: 0.7905 (m) REVERT: B 553 THR cc_start: 0.7670 (m) cc_final: 0.7292 (p) REVERT: B 564 GLN cc_start: 0.6370 (OUTLIER) cc_final: 0.5836 (mm-40) REVERT: B 567 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.6804 (tpt-90) REVERT: B 916 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8459 (tp) REVERT: B 935 GLN cc_start: 0.7271 (tm130) cc_final: 0.6974 (tt0) REVERT: C 32 PHE cc_start: 0.7685 (m-80) cc_final: 0.7310 (m-80) REVERT: C 55 PHE cc_start: 0.6867 (m-80) cc_final: 0.6078 (m-80) REVERT: C 196 ASN cc_start: 0.4857 (m-40) cc_final: 0.4154 (t0) REVERT: C 353 TRP cc_start: 0.7202 (p-90) cc_final: 0.6826 (p-90) REVERT: C 378 LYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6796 (ttmt) REVERT: C 380 TYR cc_start: 0.7804 (m-80) cc_final: 0.7511 (m-80) REVERT: C 1101 HIS cc_start: 0.7996 (m90) cc_final: 0.7514 (m90) outliers start: 35 outliers final: 29 residues processed: 186 average time/residue: 0.4370 time to fit residues: 98.1199 Evaluate side-chains 190 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 827 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 188 optimal weight: 0.9990 chunk 252 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 233 optimal weight: 1.9990 chunk 208 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 62 optimal weight: 0.0010 chunk 189 optimal weight: 0.9980 overall best weight: 0.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN B 314 GLN C 207 HIS C 354 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.161754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.108115 restraints weight = 78068.401| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 3.44 r_work: 0.3045 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 23383 Z= 0.160 Angle : 0.574 14.676 31909 Z= 0.295 Chirality : 0.045 0.246 3713 Planarity : 0.004 0.044 4078 Dihedral : 4.504 28.487 3544 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.67 % Allowed : 12.91 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.15), residues: 2840 helix: 2.24 (0.20), residues: 638 sheet: -0.39 (0.20), residues: 612 loop : -1.02 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.029 0.002 TYR B 170 PHE 0.023 0.002 PHE C 168 TRP 0.018 0.001 TRP B 436 HIS 0.003 0.001 HIS A1101 Details of bonding type rmsd covalent geometry : bond 0.00382 (23326) covalent geometry : angle 0.56367 (31774) SS BOND : bond 0.00483 ( 36) SS BOND : angle 1.51335 ( 72) hydrogen bonds : bond 0.04562 ( 921) hydrogen bonds : angle 5.40899 ( 2595) link_BETA1-4 : bond 0.00083 ( 3) link_BETA1-4 : angle 1.44903 ( 9) link_NAG-ASN : bond 0.00185 ( 18) link_NAG-ASN : angle 2.00836 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7879.79 seconds wall clock time: 134 minutes 45.01 seconds (8085.01 seconds total)