Starting phenix.real_space_refine on Sun May 18 22:01:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dmg_27536/05_2025/8dmg_27536.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dmg_27536/05_2025/8dmg_27536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dmg_27536/05_2025/8dmg_27536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dmg_27536/05_2025/8dmg_27536.map" model { file = "/net/cci-nas-00/data/ceres_data/8dmg_27536/05_2025/8dmg_27536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dmg_27536/05_2025/8dmg_27536.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 sd= 0.128 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 2 7.16 5 P 6 5.49 5 S 78 5.16 5 C 10544 2.51 5 N 2812 2.21 5 O 3200 1.98 5 H 202 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16844 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8236 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1034, 8200 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 54, 'TRANS': 979} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 13, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 59 Conformer: "B" Number of residues, atoms: 1034, 8200 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 54, 'TRANS': 979} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 13, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 59 bond proxies already assigned to first conformer: 8341 Chain: "B" Number of atoms: 8238 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1034, 8202 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 54, 'TRANS': 979} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 13, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 59 Conformer: "B" Number of residues, atoms: 1034, 8202 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 54, 'TRANS': 979} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 13, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 59 bond proxies already assigned to first conformer: 8342 Chain: "A" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 185 Unusual residues: {'1C6': 1, 'FAD': 1, 'FMN': 1, 'HEM': 1, 'PG4': 2, 'SO4': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "B" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 185 Unusual residues: {'1C6': 1, 'FAD': 1, 'FMN': 1, 'HEM': 1, 'PG4': 2, 'SO4': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3247 SG CYS A 400 53.201 45.582 102.548 1.00 11.59 S ATOM 11483 SG CYS B 400 38.400 45.550 47.133 1.00 11.59 S Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N APHE A 87 " occ=0.20 ... (20 atoms not shown) pdb=" CZ BPHE A 87 " occ=0.20 residue: pdb=" N AASP A 168 " occ=0.20 ... (14 atoms not shown) pdb=" OD2BASP A 168 " occ=0.20 residue: pdb=" N AASP A 182 " occ=0.20 ... (14 atoms not shown) pdb=" OD2BASP A 182 " occ=0.20 residue: pdb=" N AGLN A 310 " occ=0.20 ... (16 atoms not shown) pdb=" NE2BGLN A 310 " occ=0.20 residue: pdb=" N APHE B 87 " occ=0.20 ... (20 atoms not shown) pdb=" CZ BPHE B 87 " occ=0.20 residue: pdb=" N AASP B 168 " occ=0.20 ... (14 atoms not shown) pdb=" OD2BASP B 168 " occ=0.20 residue: pdb=" N AASP B 182 " occ=0.20 ... (14 atoms not shown) pdb=" OD2BASP B 182 " occ=0.20 residue: pdb=" N AGLN B 310 " occ=0.20 ... (16 atoms not shown) pdb=" NE2BGLN B 310 " occ=0.20 Time building chain proxies: 17.00, per 1000 atoms: 1.01 Number of scatterers: 16844 At special positions: 0 Unit cell: (96.96, 133.32, 153.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 2 26.01 S 78 16.00 P 6 15.00 O 3200 8.00 N 2812 7.00 C 10544 6.00 H 202 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.43 Conformation dependent library (CDL) restraints added in 4.0 seconds 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3908 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 18 sheets defined 51.0% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 Processing helix chain 'A' and resid 16 through 21 Processing helix chain 'A' and resid 24 through 37 Processing helix chain 'A' and resid 54 through 62 removed outlier: 4.256A pdb=" N GLU A 60 " --> pdb=" O ARG A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 83 removed outlier: 3.899A pdb=" N ASP A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N PHE A 81 " --> pdb=" O PHE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 4.065A pdb=" N LYS A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 107 No H-bonds generated for 'chain 'A' and resid 105 through 107' Processing helix chain 'A' and resid 108 through 132 removed outlier: 4.760A pdb=" N ALA A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N MET A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 159 Processing helix chain 'A' and resid 163 through 167 Processing helix chain 'A' and resid 171 through 188 removed outlier: 3.650A pdb=" N LEU A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 198 through 226 Processing helix chain 'A' and resid 232 through 240 Processing helix chain 'A' and resid 250 through 265 Processing helix chain 'A' and resid 266 through 283 Processing helix chain 'A' and resid 283 through 298 Processing helix chain 'A' and resid 304 through 311 Processing helix chain 'A' and resid 311 through 325 Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 375 through 380 Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 402 through 420 Processing helix chain 'A' and resid 491 through 506 removed outlier: 3.553A pdb=" N SER A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 519 No H-bonds generated for 'chain 'A' and resid 517 through 519' Processing helix chain 'A' and resid 544 through 553 Processing helix chain 'A' and resid 574 through 578 removed outlier: 3.783A pdb=" N TYR A 578 " --> pdb=" O ALA A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 591 Processing helix chain 'A' and resid 608 through 628 Processing helix chain 'A' and resid 653 through 659 Processing helix chain 'A' and resid 707 through 719 Processing helix chain 'A' and resid 746 through 750 Processing helix chain 'A' and resid 751 through 753 No H-bonds generated for 'chain 'A' and resid 751 through 753' Processing helix chain 'A' and resid 760 through 770 Processing helix chain 'A' and resid 773 through 783 Processing helix chain 'A' and resid 785 through 793 Processing helix chain 'A' and resid 799 through 807 Processing helix chain 'A' and resid 813 through 820 removed outlier: 3.611A pdb=" N ALA A 819 " --> pdb=" O SER A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 871 Processing helix chain 'A' and resid 903 through 905 No H-bonds generated for 'chain 'A' and resid 903 through 905' Processing helix chain 'A' and resid 906 through 923 removed outlier: 4.702A pdb=" N PHE A 910 " --> pdb=" O GLY A 906 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 912 " --> pdb=" O ALA A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 955 Processing helix chain 'A' and resid 974 through 982 Processing helix chain 'A' and resid 982 through 992 Processing helix chain 'A' and resid 1004 through 1021 Processing helix chain 'A' and resid 1024 through 1036 Processing helix chain 'B' and resid 11 through 15 Processing helix chain 'B' and resid 16 through 21 Processing helix chain 'B' and resid 24 through 37 Processing helix chain 'B' and resid 54 through 62 removed outlier: 4.256A pdb=" N GLU B 60 " --> pdb=" O ARG B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 83 removed outlier: 3.899A pdb=" N ASP B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N PHE B 81 " --> pdb=" O PHE B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 4.065A pdb=" N LYS B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 107 No H-bonds generated for 'chain 'B' and resid 105 through 107' Processing helix chain 'B' and resid 108 through 132 removed outlier: 4.760A pdb=" N ALA B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N MET B 118 " --> pdb=" O GLY B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 171 through 188 removed outlier: 3.650A pdb=" N LEU B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 198 through 226 Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'B' and resid 250 through 265 Processing helix chain 'B' and resid 266 through 283 Processing helix chain 'B' and resid 283 through 298 Processing helix chain 'B' and resid 304 through 311 Processing helix chain 'B' and resid 311 through 325 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 363 through 368 Processing helix chain 'B' and resid 375 through 380 Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 395 through 399 Processing helix chain 'B' and resid 402 through 420 Processing helix chain 'B' and resid 491 through 506 removed outlier: 3.554A pdb=" N SER B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 519 No H-bonds generated for 'chain 'B' and resid 517 through 519' Processing helix chain 'B' and resid 544 through 553 Processing helix chain 'B' and resid 574 through 578 removed outlier: 3.784A pdb=" N TYR B 578 " --> pdb=" O ALA B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 591 Processing helix chain 'B' and resid 608 through 628 Processing helix chain 'B' and resid 634 through 638 removed outlier: 3.526A pdb=" N ASP B 637 " --> pdb=" O ASN B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 659 Processing helix chain 'B' and resid 707 through 719 Processing helix chain 'B' and resid 746 through 750 Processing helix chain 'B' and resid 751 through 753 No H-bonds generated for 'chain 'B' and resid 751 through 753' Processing helix chain 'B' and resid 760 through 770 Processing helix chain 'B' and resid 773 through 783 Processing helix chain 'B' and resid 785 through 793 Processing helix chain 'B' and resid 799 through 807 Processing helix chain 'B' and resid 813 through 820 removed outlier: 3.611A pdb=" N ALA B 819 " --> pdb=" O SER B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 871 Processing helix chain 'B' and resid 903 through 905 No H-bonds generated for 'chain 'B' and resid 903 through 905' Processing helix chain 'B' and resid 906 through 923 removed outlier: 4.703A pdb=" N PHE B 910 " --> pdb=" O GLY B 906 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY B 912 " --> pdb=" O ALA B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 955 Processing helix chain 'B' and resid 974 through 982 Processing helix chain 'B' and resid 982 through 992 Processing helix chain 'B' and resid 1004 through 1021 Processing helix chain 'B' and resid 1024 through 1036 Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 44 removed outlier: 4.840A pdb=" N GLU A 352 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N SER A 332 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 139 through 140 Processing sheet with id=AA3, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AA4, first strand: chain 'A' and resid 433 through 435 Processing sheet with id=AA5, first strand: chain 'A' and resid 512 through 515 removed outlier: 6.476A pdb=" N LEU A 483 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL A 532 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU A 485 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL A 529 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N PHE A 567 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE A 531 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N CYS A 569 " --> pdb=" O ILE A 531 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR A 533 " --> pdb=" O CYS A 569 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP A 599 " --> pdb=" O TYR A 564 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N VAL A 566 " --> pdb=" O ASP A 599 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 827 through 830 removed outlier: 4.840A pdb=" N THR A 878 " --> pdb=" O ILE A 703 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN A 665 " --> pdb=" O GLU A 687 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU A 685 " --> pdb=" O VAL A 667 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER A 669 " --> pdb=" O HIS A 683 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N HIS A 683 " --> pdb=" O SER A 669 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLU A 671 " --> pdb=" O THR A 681 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR A 681 " --> pdb=" O GLU A 671 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 743 through 745 removed outlier: 3.586A pdb=" N LEU A 728 " --> pdb=" O GLN B 645 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN B 645 " --> pdb=" O LEU A 728 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 850 through 852 Processing sheet with id=AA9, first strand: chain 'A' and resid 959 through 964 removed outlier: 6.368A pdb=" N ALA A 930 " --> pdb=" O THR A 959 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N HIS A 961 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU A 932 " --> pdb=" O HIS A 961 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ALA A 963 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE A 934 " --> pdb=" O ALA A 963 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU A 898 " --> pdb=" O HIS A 931 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N TYR A 933 " --> pdb=" O LEU A 898 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N MET A 900 " --> pdb=" O TYR A 933 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N GLY A 935 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 39 through 44 removed outlier: 4.840A pdb=" N GLU B 352 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N SER B 332 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 139 through 140 Processing sheet with id=AB3, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AB4, first strand: chain 'B' and resid 433 through 435 Processing sheet with id=AB5, first strand: chain 'B' and resid 512 through 515 removed outlier: 6.475A pdb=" N LEU B 483 " --> pdb=" O LEU B 530 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL B 532 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU B 485 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL B 529 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N PHE B 567 " --> pdb=" O VAL B 529 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE B 531 " --> pdb=" O PHE B 567 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N CYS B 569 " --> pdb=" O ILE B 531 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR B 533 " --> pdb=" O CYS B 569 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP B 599 " --> pdb=" O TYR B 564 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N VAL B 566 " --> pdb=" O ASP B 599 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 827 through 830 removed outlier: 4.841A pdb=" N THR B 878 " --> pdb=" O ILE B 703 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASN B 665 " --> pdb=" O GLU B 687 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLU B 685 " --> pdb=" O VAL B 667 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER B 669 " --> pdb=" O HIS B 683 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N HIS B 683 " --> pdb=" O SER B 669 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLU B 671 " --> pdb=" O THR B 681 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR B 681 " --> pdb=" O GLU B 671 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 725 through 727 Processing sheet with id=AB8, first strand: chain 'B' and resid 850 through 852 Processing sheet with id=AB9, first strand: chain 'B' and resid 959 through 964 removed outlier: 6.367A pdb=" N ALA B 930 " --> pdb=" O THR B 959 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N HIS B 961 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU B 932 " --> pdb=" O HIS B 961 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ALA B 963 " --> pdb=" O LEU B 932 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE B 934 " --> pdb=" O ALA B 963 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU B 898 " --> pdb=" O HIS B 931 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N TYR B 933 " --> pdb=" O LEU B 898 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET B 900 " --> pdb=" O TYR B 933 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N GLY B 935 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE B 899 " --> pdb=" O TYR B 997 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N CYS B 999 " --> pdb=" O ILE B 899 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL B 901 " --> pdb=" O CYS B 999 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ASP B1001 " --> pdb=" O VAL B 901 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N PHE B 996 " --> pdb=" O ALA B1042 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ASP B1044 " --> pdb=" O PHE B 996 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE B 998 " --> pdb=" O ASP B1044 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N TRP B1046 " --> pdb=" O ILE B 998 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLY B1000 " --> pdb=" O TRP B1046 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 800 hydrogen bonds defined for protein. 2263 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: 6.40 Time building geometry restraints manager: 6.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.23: 1569 1.23 - 1.65: 15523 1.65 - 2.06: 143 2.06 - 2.48: 2 2.48 - 2.89: 2 Bond restraints: 17239 Sorted by residual: bond pdb=" C HIS A 478 " pdb=" N ASN A 479 " ideal model delta sigma weight residual 1.332 2.890 -1.558 1.40e-02 5.10e+03 1.24e+04 bond pdb=" C LEU B 630 " pdb=" N ASP B 631 " ideal model delta sigma weight residual 1.333 2.502 -1.169 1.50e-02 4.44e+03 6.08e+03 bond pdb=" C ALA A 661 " pdb=" N PHE A 662 " ideal model delta sigma weight residual 1.330 0.856 0.473 1.37e-02 5.33e+03 1.19e+03 bond pdb=" C ALA B 661 " pdb=" N PHE B 662 " ideal model delta sigma weight residual 1.330 0.856 0.473 1.37e-02 5.33e+03 1.19e+03 bond pdb=" N PRO A 774 " pdb=" CD PRO A 774 " ideal model delta sigma weight residual 1.473 1.682 -0.209 1.40e-02 5.10e+03 2.23e+02 ... (remaining 17234 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.64: 23554 11.64 - 23.28: 49 23.28 - 34.93: 8 34.93 - 46.57: 7 46.57 - 58.21: 3 Bond angle restraints: 23621 Sorted by residual: angle pdb=" CA HIS A 478 " pdb=" C HIS A 478 " pdb=" N ASN A 479 " ideal model delta sigma weight residual 116.25 65.98 50.27 1.53e+00 4.27e-01 1.08e+03 angle pdb=" O LEU B 630 " pdb=" C LEU B 630 " pdb=" N ASP B 631 " ideal model delta sigma weight residual 123.28 85.84 37.44 1.16e+00 7.43e-01 1.04e+03 angle pdb=" N ALA B 736 " pdb=" CA ALA B 736 " pdb=" CB ALA B 736 " ideal model delta sigma weight residual 109.51 151.10 -41.59 1.58e+00 4.01e-01 6.93e+02 angle pdb=" N ALA A 736 " pdb=" CA ALA A 736 " pdb=" CB ALA A 736 " ideal model delta sigma weight residual 109.51 151.10 -41.59 1.58e+00 4.01e-01 6.93e+02 angle pdb=" N LYS B 734 " pdb=" CA LYS B 734 " pdb=" CB LYS B 734 " ideal model delta sigma weight residual 111.74 71.30 40.44 1.69e+00 3.50e-01 5.73e+02 ... (remaining 23616 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 9090 17.54 - 35.08: 805 35.08 - 52.61: 293 52.61 - 70.15: 97 70.15 - 87.69: 26 Dihedral angle restraints: 10311 sinusoidal: 4246 harmonic: 6065 Sorted by residual: dihedral pdb=" N LYS B 734 " pdb=" C LYS B 734 " pdb=" CA LYS B 734 " pdb=" CB LYS B 734 " ideal model delta harmonic sigma weight residual 122.80 78.24 44.56 0 2.50e+00 1.60e-01 3.18e+02 dihedral pdb=" N LYS A 734 " pdb=" C LYS A 734 " pdb=" CA LYS A 734 " pdb=" CB LYS A 734 " ideal model delta harmonic sigma weight residual 122.80 78.25 44.55 0 2.50e+00 1.60e-01 3.18e+02 dihedral pdb=" N ALA A 736 " pdb=" C ALA A 736 " pdb=" CA ALA A 736 " pdb=" CB ALA A 736 " ideal model delta harmonic sigma weight residual 122.90 156.51 -33.61 0 2.50e+00 1.60e-01 1.81e+02 ... (remaining 10308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.228: 2370 0.228 - 0.456: 97 0.456 - 0.683: 12 0.683 - 0.911: 0 0.911 - 1.139: 5 Chirality restraints: 2484 Sorted by residual: chirality pdb=" CA ALA A 736 " pdb=" N ALA A 736 " pdb=" C ALA A 736 " pdb=" CB ALA A 736 " both_signs ideal model delta sigma weight residual False 2.48 1.35 1.14 2.00e-01 2.50e+01 3.24e+01 chirality pdb=" CA ALA B 736 " pdb=" N ALA B 736 " pdb=" C ALA B 736 " pdb=" CB ALA B 736 " both_signs ideal model delta sigma weight residual False 2.48 1.35 1.13 2.00e-01 2.50e+01 3.22e+01 chirality pdb=" CA HIS B 478 " pdb=" N HIS B 478 " pdb=" C HIS B 478 " pdb=" CB HIS B 478 " both_signs ideal model delta sigma weight residual False 2.51 1.50 1.01 2.00e-01 2.50e+01 2.54e+01 ... (remaining 2481 not shown) Planarity restraints: 3025 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 630 " 0.188 2.00e-02 2.50e+03 2.74e-01 7.49e+02 pdb=" C LEU B 630 " -0.452 2.00e-02 2.50e+03 pdb=" O LEU B 630 " 0.245 2.00e-02 2.50e+03 pdb=" N ASP B 631 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 478 " -0.179 2.00e-02 2.50e+03 2.28e-01 5.19e+02 pdb=" C HIS A 478 " 0.349 2.00e-02 2.50e+03 pdb=" O HIS A 478 " -0.225 2.00e-02 2.50e+03 pdb=" N ASN A 479 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN B1103 " 0.034 2.00e-02 2.50e+03 6.13e-02 1.69e+02 pdb=" C10 FMN B1103 " 0.101 2.00e-02 2.50e+03 pdb=" C2 FMN B1103 " -0.013 2.00e-02 2.50e+03 pdb=" C4 FMN B1103 " -0.091 2.00e-02 2.50e+03 pdb=" C4A FMN B1103 " 0.085 2.00e-02 2.50e+03 pdb=" C5A FMN B1103 " -0.009 2.00e-02 2.50e+03 pdb=" C6 FMN B1103 " 0.032 2.00e-02 2.50e+03 pdb=" C7 FMN B1103 " 0.010 2.00e-02 2.50e+03 pdb=" C7M FMN B1103 " 0.037 2.00e-02 2.50e+03 pdb=" C8 FMN B1103 " -0.044 2.00e-02 2.50e+03 pdb=" C8M FMN B1103 " -0.079 2.00e-02 2.50e+03 pdb=" C9 FMN B1103 " -0.039 2.00e-02 2.50e+03 pdb=" C9A FMN B1103 " -0.026 2.00e-02 2.50e+03 pdb=" N1 FMN B1103 " 0.097 2.00e-02 2.50e+03 pdb=" N10 FMN B1103 " 0.000 2.00e-02 2.50e+03 pdb=" N3 FMN B1103 " -0.116 2.00e-02 2.50e+03 pdb=" N5 FMN B1103 " 0.058 2.00e-02 2.50e+03 pdb=" O2 FMN B1103 " -0.038 2.00e-02 2.50e+03 ... (remaining 3022 not shown) Histogram of nonbonded interaction distances: 0.31 - 1.17: 5 1.17 - 2.03: 77 2.03 - 2.88: 7673 2.88 - 3.74: 36575 3.74 - 4.60: 69867 Warning: very small nonbonded interaction distances. Nonbonded interactions: 114197 Sorted by model distance: nonbonded pdb=" OE1 GLU A 732 " pdb=" O THR B 641 " model vdw 0.312 2.800 nonbonded pdb=" CG ASN A 381 " pdb=" OE1 GLN B 546 " model vdw 0.380 3.100 nonbonded pdb=" O THR A 641 " pdb=" OE1 GLU B 732 " model vdw 0.707 2.800 nonbonded pdb=" NE2 GLN A 546 " pdb=" ND2 ASN B 381 " model vdw 0.898 3.100 nonbonded pdb=" OE1 GLU A 732 " pdb=" C THR B 641 " model vdw 1.055 3.100 ... (remaining 114192 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 3 through 86 or resid 88 through 167 or resid 169 through \ 181 or resid 183 through 309 or resid 311 through 1048 or resid 1101 through 110 \ 9)) selection = (chain 'B' and (resid 3 through 86 or resid 88 through 167 or resid 169 through \ 181 or resid 183 through 309 or resid 311 through 1040 or (resid 1041 and (name \ N or name CA or name C or name CB or name CG or name CD1 or name CD2 or name CE1 \ or name CE2 or name CZ or name OH )) or resid 1042 through 1043 or (resid 1044 \ and (name N or name CA or name C or name CB or name CG or name OD1 or name OD2)) \ or resid 1045 through 1048 or resid 1101 through 1109)) } 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=0.20 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 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: 0.430 Extract box with map and model: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 50.970 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 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 : 0.030 1.558 17044 Z= 2.021 Angle : 2.341 58.209 23153 Z= 1.420 Chirality : 0.122 1.139 2484 Planarity : 0.014 0.274 2997 Dihedral : 16.930 87.687 6337 Min Nonbonded Distance : 0.312 Molprobity Statistics. All-atom Clashscore : 28.72 Ramachandran Plot: Outliers : 1.65 % Allowed : 6.03 % Favored : 92.32 % Rotamer: Outliers : 6.80 % Allowed : 6.68 % Favored : 86.52 % Cbeta Deviations : 1.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.16), residues: 2082 helix: -1.76 (0.13), residues: 944 sheet: -0.76 (0.30), residues: 277 loop : -1.54 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.087 0.012 TRP B 96 HIS 0.030 0.007 HIS A 92 PHE 0.054 0.010 PHE A 107 TYR 0.047 0.010 TYR B 694 ARG 0.038 0.003 ARG B 398 Details of bonding type rmsd hydrogen bonds : bond 0.18694 ( 800) hydrogen bonds : angle 8.05440 ( 2263) covalent geometry : bond 0.02871 (17037) covalent geometry : angle 2.34074 (23153) Misc. bond : bond 0.46388 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 246 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP A1044 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 LEU cc_start: 0.7743 (tp) cc_final: 0.7529 (tp) REVERT: A 177 MET cc_start: 0.7413 (ttp) cc_final: 0.6763 (tmm) REVERT: A 272 LEU cc_start: 0.7757 (tp) cc_final: 0.7486 (tt) REVERT: A 314 VAL cc_start: 0.8500 (t) cc_final: 0.7883 (t) REVERT: A 357 ILE cc_start: 0.7172 (mt) cc_final: 0.6781 (mm) REVERT: A 411 THR cc_start: 0.8551 (m) cc_final: 0.7866 (t) REVERT: A 644 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6438 (pt) REVERT: A 913 PHE cc_start: 0.6518 (m-10) cc_final: 0.5984 (m-10) REVERT: A 1016 SER cc_start: 0.7616 (m) cc_final: 0.6909 (t) REVERT: B 62 CYS cc_start: 0.2999 (m) cc_final: 0.2569 (m) REVERT: B 216 VAL cc_start: 0.8727 (t) cc_final: 0.8400 (t) REVERT: B 471 ARG cc_start: 0.6184 (OUTLIER) cc_final: 0.5465 (ptt180) REVERT: B 629 ASN cc_start: 0.7530 (OUTLIER) cc_final: 0.6982 (p0) REVERT: B 659 HIS cc_start: 0.6522 (m-70) cc_final: 0.6051 (m-70) REVERT: B 793 VAL cc_start: 0.5659 (t) cc_final: 0.5043 (t) REVERT: B 847 SER cc_start: 0.6713 (OUTLIER) cc_final: 0.6101 (p) outliers start: 116 outliers final: 33 residues processed: 343 average time/residue: 0.3118 time to fit residues: 156.6699 Evaluate side-chains 180 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 161 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 27 GLN ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 ASN A 134 ASN A 201 ASN A 236 HIS ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 ASN ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN A 645 GLN A 923 GLN ** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN B 16 ASN B 73 GLN B 134 ASN B 201 ASN B 236 HIS B 253 ASN B 283 ASN B 388 HIS B 403 GLN ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN B 699 HIS B 923 GLN B 992 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.047047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.031911 restraints weight = 343641.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.034258 restraints weight = 160627.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.035933 restraints weight = 99506.362| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2898 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17044 Z= 0.161 Angle : 0.743 24.351 23153 Z= 0.370 Chirality : 0.041 0.208 2484 Planarity : 0.007 0.191 2997 Dihedral : 8.781 89.195 2405 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 37.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.66 % Favored : 95.10 % Rotamer: Outliers : 0.23 % Allowed : 0.94 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.18), residues: 2086 helix: 0.61 (0.16), residues: 965 sheet: -0.25 (0.29), residues: 293 loop : -0.93 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 96 HIS 0.007 0.001 HIS A 478 PHE 0.013 0.002 PHE B 82 TYR 0.023 0.001 TYR A 613 ARG 0.009 0.001 ARG A 296 Details of bonding type rmsd hydrogen bonds : bond 0.04500 ( 800) hydrogen bonds : angle 5.78381 ( 2263) covalent geometry : bond 0.00350 (17037) covalent geometry : angle 0.74303 (23153) Misc. bond : bond 0.01080 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 170 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP A1044 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.9495 (mpp) cc_final: 0.9151 (mpp) REVERT: A 177 MET cc_start: 0.9527 (ttp) cc_final: 0.9154 (ppp) REVERT: A 218 LYS cc_start: 0.9470 (mttt) cc_final: 0.9239 (mttt) REVERT: A 261 PHE cc_start: 0.9178 (m-80) cc_final: 0.8549 (m-80) REVERT: A 356 LEU cc_start: 0.8384 (mt) cc_final: 0.7673 (mp) REVERT: A 357 ILE cc_start: 0.9066 (mt) cc_final: 0.8762 (mm) REVERT: A 485 LEU cc_start: 0.9567 (mt) cc_final: 0.9365 (mt) REVERT: A 1005 MET cc_start: 0.9247 (mmp) cc_final: 0.8946 (mmm) REVERT: A 1034 GLN cc_start: 0.9478 (tp-100) cc_final: 0.8979 (tp-100) REVERT: B 20 LEU cc_start: 0.8875 (mt) cc_final: 0.8290 (tt) REVERT: B 86 LEU cc_start: 0.9450 (mt) cc_final: 0.8715 (tp) REVERT: B 118 MET cc_start: 0.9353 (mpp) cc_final: 0.8818 (mpp) REVERT: B 185 MET cc_start: 0.9093 (ttt) cc_final: 0.8823 (ttt) REVERT: B 237 MET cc_start: 0.9681 (mtm) cc_final: 0.9352 (mtp) REVERT: B 417 MET cc_start: 0.9517 (mtm) cc_final: 0.8933 (mtp) REVERT: B 960 LEU cc_start: 0.8611 (tp) cc_final: 0.8264 (mt) REVERT: B 992 GLN cc_start: 0.9327 (mt0) cc_final: 0.9004 (tp40) REVERT: B 1034 GLN cc_start: 0.9034 (mt0) cc_final: 0.8825 (mm-40) outliers start: 4 outliers final: 4 residues processed: 173 average time/residue: 0.3043 time to fit residues: 81.9042 Evaluate side-chains 129 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 125 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 48 optimal weight: 7.9990 chunk 181 optimal weight: 6.9990 chunk 180 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 200 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 GLN A 239 ASN ** A 310 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN A 665 ASN ** A 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 HIS B 27 GLN ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 841 GLN B1021 HIS B1034 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.038830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.025665 restraints weight = 452911.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.027600 restraints weight = 193624.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.029017 restraints weight = 116687.396| |-----------------------------------------------------------------------------| r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| r_final: 0.2680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.130 17044 Z= 0.393 Angle : 1.138 35.987 23153 Z= 0.521 Chirality : 0.045 0.206 2484 Planarity : 0.008 0.172 2997 Dihedral : 8.568 79.469 2405 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 76.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.13 % Favored : 92.73 % Rotamer: Outliers : 0.18 % Allowed : 1.35 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.18), residues: 2086 helix: -0.13 (0.15), residues: 965 sheet: -0.26 (0.31), residues: 265 loop : -1.19 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.004 TRP A 550 HIS 0.015 0.003 HIS A 931 PHE 0.032 0.004 PHE B 107 TYR 0.047 0.004 TYR B 829 ARG 0.009 0.001 ARG B1029 Details of bonding type rmsd hydrogen bonds : bond 0.04570 ( 800) hydrogen bonds : angle 6.14492 ( 2263) covalent geometry : bond 0.00783 (17037) covalent geometry : angle 1.13839 (23153) Misc. bond : bond 0.05429 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 107 time to evaluate : 1.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP A1044 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 MET cc_start: 0.9492 (mmp) cc_final: 0.9245 (mmp) REVERT: A 118 MET cc_start: 0.9464 (mpp) cc_final: 0.9160 (mpp) REVERT: A 218 LYS cc_start: 0.9574 (mttt) cc_final: 0.9352 (mttt) REVERT: A 261 PHE cc_start: 0.9025 (m-80) cc_final: 0.8390 (m-80) REVERT: A 356 LEU cc_start: 0.8364 (mt) cc_final: 0.7910 (mt) REVERT: A 482 LEU cc_start: 0.9623 (tp) cc_final: 0.9413 (tt) REVERT: A 569 CYS cc_start: 0.9443 (m) cc_final: 0.9010 (t) REVERT: A 812 MET cc_start: 0.8776 (mmp) cc_final: 0.8218 (tpp) REVERT: A 1005 MET cc_start: 0.9179 (mmp) cc_final: 0.8891 (mmm) REVERT: B 20 LEU cc_start: 0.8960 (mt) cc_final: 0.8219 (tt) REVERT: B 112 MET cc_start: 0.9180 (mmp) cc_final: 0.8879 (mmm) REVERT: B 118 MET cc_start: 0.9501 (mpp) cc_final: 0.9045 (mpp) REVERT: B 185 MET cc_start: 0.8866 (ttt) cc_final: 0.8664 (ttt) REVERT: B 237 MET cc_start: 0.9570 (mtm) cc_final: 0.9170 (mtp) REVERT: B 354 MET cc_start: 0.9100 (tpt) cc_final: 0.8899 (tpt) REVERT: B 1034 GLN cc_start: 0.9083 (mt0) cc_final: 0.8784 (mm-40) outliers start: 3 outliers final: 2 residues processed: 110 average time/residue: 0.2942 time to fit residues: 50.6034 Evaluate side-chains 80 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 43 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 37 optimal weight: 0.2980 chunk 131 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 841 GLN A 951 ASN A 992 GLN B 109 GLN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.040383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.026829 restraints weight = 402584.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.028909 restraints weight = 171869.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.030415 restraints weight = 102968.989| |-----------------------------------------------------------------------------| r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| r_final: 0.2745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 17044 Z= 0.119 Angle : 0.609 20.028 23153 Z= 0.290 Chirality : 0.037 0.202 2484 Planarity : 0.006 0.167 2997 Dihedral : 7.494 77.192 2405 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 53.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.46 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.18), residues: 2086 helix: 1.03 (0.16), residues: 967 sheet: -0.17 (0.31), residues: 270 loop : -0.86 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 96 HIS 0.006 0.001 HIS A 961 PHE 0.015 0.001 PHE A 158 TYR 0.016 0.001 TYR A 613 ARG 0.003 0.000 ARG A 617 Details of bonding type rmsd hydrogen bonds : bond 0.03415 ( 800) hydrogen bonds : angle 5.28551 ( 2263) covalent geometry : bond 0.00255 (17037) covalent geometry : angle 0.60893 (23153) Misc. bond : bond 0.01662 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP A1044 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.9459 (mpp) cc_final: 0.9200 (mpp) REVERT: A 218 LYS cc_start: 0.9552 (mttt) cc_final: 0.9303 (mttt) REVERT: A 262 LEU cc_start: 0.9654 (mm) cc_final: 0.9432 (mm) REVERT: A 356 LEU cc_start: 0.8337 (mt) cc_final: 0.7846 (mp) REVERT: A 357 ILE cc_start: 0.9152 (mt) cc_final: 0.8767 (mp) REVERT: A 416 MET cc_start: 0.9610 (mmp) cc_final: 0.9121 (mmm) REVERT: A 812 MET cc_start: 0.8140 (mmp) cc_final: 0.7664 (tpp) REVERT: A 900 MET cc_start: 0.8378 (mmp) cc_final: 0.7384 (mpp) REVERT: A 996 PHE cc_start: 0.8984 (t80) cc_final: 0.8727 (t80) REVERT: A 1005 MET cc_start: 0.9030 (mmp) cc_final: 0.8816 (mmm) REVERT: B 20 LEU cc_start: 0.8935 (mt) cc_final: 0.8217 (tt) REVERT: B 118 MET cc_start: 0.9488 (mpp) cc_final: 0.8874 (mpp) REVERT: B 185 MET cc_start: 0.8812 (ttt) cc_final: 0.8410 (ttt) REVERT: B 212 MET cc_start: 0.9703 (mmp) cc_final: 0.9340 (mmm) REVERT: B 237 MET cc_start: 0.9670 (mtm) cc_final: 0.9397 (mtp) REVERT: B 261 PHE cc_start: 0.9551 (m-80) cc_final: 0.8530 (m-80) REVERT: B 417 MET cc_start: 0.9573 (mtm) cc_final: 0.9296 (mtp) REVERT: B 712 ASN cc_start: 0.9217 (m-40) cc_final: 0.8865 (p0) REVERT: B 811 GLU cc_start: 0.9327 (mt-10) cc_final: 0.9041 (mp0) REVERT: B 821 LEU cc_start: 0.8895 (mt) cc_final: 0.8636 (mt) REVERT: B 890 LEU cc_start: 0.8663 (mt) cc_final: 0.8307 (tp) REVERT: B 1034 GLN cc_start: 0.9005 (mt0) cc_final: 0.8753 (mm-40) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.3065 time to fit residues: 54.2577 Evaluate side-chains 95 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 182 optimal weight: 0.2980 chunk 173 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 171 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 134 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 GLN A ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN B 125 GLN B 204 GLN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.039509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.026174 restraints weight = 429356.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.028208 restraints weight = 182591.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.029683 restraints weight = 109426.732| |-----------------------------------------------------------------------------| r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| r_final: 0.2715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.5572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 17044 Z= 0.152 Angle : 0.620 20.990 23153 Z= 0.288 Chirality : 0.037 0.188 2484 Planarity : 0.005 0.139 2997 Dihedral : 7.180 78.395 2405 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 59.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.67 % Favored : 94.18 % Rotamer: Outliers : 0.12 % Allowed : 0.59 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.19), residues: 2086 helix: 1.33 (0.17), residues: 964 sheet: -0.13 (0.33), residues: 256 loop : -0.76 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 96 HIS 0.006 0.001 HIS B 931 PHE 0.013 0.001 PHE B 405 TYR 0.017 0.001 TYR B 829 ARG 0.003 0.001 ARG B 398 Details of bonding type rmsd hydrogen bonds : bond 0.03150 ( 800) hydrogen bonds : angle 5.12297 ( 2263) covalent geometry : bond 0.00312 (17037) covalent geometry : angle 0.61963 (23153) Misc. bond : bond 0.02507 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP A1044 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.8745 (mmp) cc_final: 0.8211 (mmp) REVERT: A 118 MET cc_start: 0.9415 (mpp) cc_final: 0.9022 (mpp) REVERT: A 218 LYS cc_start: 0.9535 (mttt) cc_final: 0.9307 (mttt) REVERT: A 261 PHE cc_start: 0.9105 (m-80) cc_final: 0.8734 (m-80) REVERT: A 357 ILE cc_start: 0.9103 (mt) cc_final: 0.8896 (mt) REVERT: A 416 MET cc_start: 0.9624 (mmp) cc_final: 0.9122 (mmm) REVERT: A 812 MET cc_start: 0.8409 (mmp) cc_final: 0.7778 (tpp) REVERT: A 900 MET cc_start: 0.8560 (mmp) cc_final: 0.8285 (mmp) REVERT: A 996 PHE cc_start: 0.8858 (t80) cc_final: 0.8633 (t80) REVERT: A 1005 MET cc_start: 0.9022 (mmp) cc_final: 0.8770 (mmm) REVERT: B 20 LEU cc_start: 0.8998 (mt) cc_final: 0.8338 (tp) REVERT: B 112 MET cc_start: 0.9522 (mmp) cc_final: 0.9149 (mmm) REVERT: B 118 MET cc_start: 0.9489 (mpp) cc_final: 0.8902 (mpp) REVERT: B 185 MET cc_start: 0.9026 (ttt) cc_final: 0.8660 (ttt) REVERT: B 212 MET cc_start: 0.9692 (mmp) cc_final: 0.9304 (mmm) REVERT: B 237 MET cc_start: 0.9652 (mtm) cc_final: 0.9399 (mtp) REVERT: B 261 PHE cc_start: 0.9576 (m-80) cc_final: 0.8653 (m-80) REVERT: B 354 MET cc_start: 0.8647 (tpt) cc_final: 0.8392 (tpt) REVERT: B 417 MET cc_start: 0.9567 (mtm) cc_final: 0.9344 (mtp) REVERT: B 712 ASN cc_start: 0.9247 (m-40) cc_final: 0.8900 (p0) REVERT: B 811 GLU cc_start: 0.9396 (mt-10) cc_final: 0.9053 (mp0) REVERT: B 821 LEU cc_start: 0.8861 (mt) cc_final: 0.8658 (mt) REVERT: B 1034 GLN cc_start: 0.9037 (mt0) cc_final: 0.8781 (mm-40) outliers start: 2 outliers final: 2 residues processed: 110 average time/residue: 0.2680 time to fit residues: 47.5202 Evaluate side-chains 86 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 84 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 200 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 81 optimal weight: 0.0570 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 146 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 96 optimal weight: 0.0980 chunk 36 optimal weight: 9.9990 overall best weight: 2.0304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.038633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.025415 restraints weight = 492826.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.027453 restraints weight = 195376.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.028938 restraints weight = 114427.984| |-----------------------------------------------------------------------------| r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.6063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 17044 Z= 0.168 Angle : 0.625 19.977 23153 Z= 0.295 Chirality : 0.037 0.171 2484 Planarity : 0.004 0.050 2997 Dihedral : 7.180 82.249 2405 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 64.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.92 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.19), residues: 2086 helix: 1.24 (0.16), residues: 965 sheet: -0.32 (0.32), residues: 257 loop : -0.80 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 96 HIS 0.005 0.001 HIS A 266 PHE 0.015 0.001 PHE B 82 TYR 0.018 0.001 TYR B 829 ARG 0.003 0.001 ARG B 375 Details of bonding type rmsd hydrogen bonds : bond 0.03157 ( 800) hydrogen bonds : angle 5.12850 ( 2263) covalent geometry : bond 0.00349 (17037) covalent geometry : angle 0.62470 (23153) Misc. bond : bond 0.02646 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP A1044 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.9412 (mpp) cc_final: 0.9085 (mpp) REVERT: A 185 MET cc_start: 0.9425 (ttm) cc_final: 0.8922 (tmm) REVERT: A 218 LYS cc_start: 0.9544 (mttt) cc_final: 0.9307 (mttt) REVERT: A 261 PHE cc_start: 0.9102 (m-80) cc_final: 0.8727 (m-80) REVERT: A 316 MET cc_start: 0.9268 (mmp) cc_final: 0.9053 (mmt) REVERT: A 357 ILE cc_start: 0.9027 (mt) cc_final: 0.8658 (mp) REVERT: A 416 MET cc_start: 0.9621 (mmp) cc_final: 0.9228 (mmm) REVERT: A 781 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8739 (mt-10) REVERT: A 900 MET cc_start: 0.8800 (mmp) cc_final: 0.8512 (mmp) REVERT: A 967 MET cc_start: 0.7575 (mmm) cc_final: 0.6671 (mmm) REVERT: A 979 MET cc_start: 0.9491 (mmp) cc_final: 0.9182 (mmm) REVERT: B 20 LEU cc_start: 0.9098 (mt) cc_final: 0.8426 (tp) REVERT: B 112 MET cc_start: 0.9536 (mmp) cc_final: 0.9141 (mmm) REVERT: B 118 MET cc_start: 0.9517 (mpp) cc_final: 0.8939 (mpp) REVERT: B 185 MET cc_start: 0.9000 (ttt) cc_final: 0.8599 (ttt) REVERT: B 212 MET cc_start: 0.9663 (mmp) cc_final: 0.9421 (mmm) REVERT: B 237 MET cc_start: 0.9621 (mtm) cc_final: 0.9389 (mtp) REVERT: B 354 MET cc_start: 0.8486 (tpt) cc_final: 0.8244 (tpt) REVERT: B 417 MET cc_start: 0.9587 (mtm) cc_final: 0.9371 (mtp) REVERT: B 712 ASN cc_start: 0.9226 (m-40) cc_final: 0.8795 (p0) REVERT: B 811 GLU cc_start: 0.9398 (mt-10) cc_final: 0.9043 (mp0) REVERT: B 1034 GLN cc_start: 0.9099 (mt0) cc_final: 0.8722 (mm-40) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.2818 time to fit residues: 46.1229 Evaluate side-chains 80 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 74 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 182 optimal weight: 0.7980 chunk 162 optimal weight: 0.0010 chunk 199 optimal weight: 8.9990 chunk 46 optimal weight: 0.0970 chunk 87 optimal weight: 0.0570 chunk 102 optimal weight: 0.7980 chunk 142 optimal weight: 0.7980 overall best weight: 0.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.039903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.026289 restraints weight = 459370.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.028395 restraints weight = 184616.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.029949 restraints weight = 108817.652| |-----------------------------------------------------------------------------| r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.6025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 17044 Z= 0.078 Angle : 0.465 7.696 23153 Z= 0.236 Chirality : 0.036 0.154 2484 Planarity : 0.004 0.062 2997 Dihedral : 6.702 76.372 2405 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 53.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.17 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.19), residues: 2086 helix: 1.94 (0.17), residues: 964 sheet: -0.21 (0.32), residues: 257 loop : -0.59 (0.23), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 96 HIS 0.003 0.000 HIS B 285 PHE 0.014 0.001 PHE B 82 TYR 0.013 0.001 TYR A 613 ARG 0.002 0.000 ARG A 563 Details of bonding type rmsd hydrogen bonds : bond 0.02784 ( 800) hydrogen bonds : angle 4.74480 ( 2263) covalent geometry : bond 0.00187 (17037) covalent geometry : angle 0.46475 (23153) Misc. bond : bond 0.00510 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP A1044 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.9463 (mpp) cc_final: 0.9184 (mpp) REVERT: A 185 MET cc_start: 0.9393 (ttm) cc_final: 0.8880 (tmm) REVERT: A 218 LYS cc_start: 0.9537 (mttt) cc_final: 0.9291 (mttt) REVERT: A 261 PHE cc_start: 0.9069 (m-80) cc_final: 0.8724 (m-80) REVERT: A 316 MET cc_start: 0.9196 (mmp) cc_final: 0.8960 (mmt) REVERT: A 357 ILE cc_start: 0.9006 (mt) cc_final: 0.8625 (mp) REVERT: A 416 MET cc_start: 0.9557 (mmp) cc_final: 0.9282 (mmm) REVERT: A 767 MET cc_start: 0.9042 (ptp) cc_final: 0.8763 (ptp) REVERT: A 781 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8338 (mp0) REVERT: A 812 MET cc_start: 0.7593 (mmp) cc_final: 0.7319 (tpp) REVERT: A 900 MET cc_start: 0.8832 (mmp) cc_final: 0.8492 (mmp) REVERT: A 951 ASN cc_start: 0.9474 (m110) cc_final: 0.9249 (p0) REVERT: A 967 MET cc_start: 0.7794 (mmm) cc_final: 0.6688 (mmm) REVERT: A 979 MET cc_start: 0.9376 (mmp) cc_final: 0.8935 (mmm) REVERT: B 20 LEU cc_start: 0.9050 (mt) cc_final: 0.8390 (tp) REVERT: B 112 MET cc_start: 0.9514 (mmp) cc_final: 0.9112 (mmm) REVERT: B 118 MET cc_start: 0.9454 (mpp) cc_final: 0.8671 (mpp) REVERT: B 212 MET cc_start: 0.9706 (mmp) cc_final: 0.9460 (mmm) REVERT: B 237 MET cc_start: 0.9658 (mtm) cc_final: 0.9391 (mtp) REVERT: B 354 MET cc_start: 0.8601 (tpt) cc_final: 0.8203 (tpt) REVERT: B 417 MET cc_start: 0.9598 (mtm) cc_final: 0.9289 (ptp) REVERT: B 712 ASN cc_start: 0.9243 (m-40) cc_final: 0.8910 (p0) REVERT: B 811 GLU cc_start: 0.9308 (mt-10) cc_final: 0.8960 (mp0) REVERT: B 1034 GLN cc_start: 0.8983 (mt0) cc_final: 0.8650 (mm-40) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2757 time to fit residues: 45.1226 Evaluate side-chains 90 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 65 optimal weight: 10.0000 chunk 118 optimal weight: 0.9980 chunk 185 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 8 optimal weight: 0.3980 chunk 14 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.038442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.025259 restraints weight = 505539.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.027274 restraints weight = 197361.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.028759 restraints weight = 115799.773| |-----------------------------------------------------------------------------| r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.2685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.6384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 17044 Z= 0.161 Angle : 0.621 23.652 23153 Z= 0.285 Chirality : 0.036 0.161 2484 Planarity : 0.004 0.050 2997 Dihedral : 6.787 79.668 2405 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 64.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.97 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.19), residues: 2086 helix: 1.66 (0.17), residues: 961 sheet: -0.33 (0.32), residues: 256 loop : -0.70 (0.22), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 96 HIS 0.006 0.001 HIS A 266 PHE 0.014 0.001 PHE A 405 TYR 0.020 0.001 TYR B 829 ARG 0.003 0.001 ARG B 375 Details of bonding type rmsd hydrogen bonds : bond 0.02912 ( 800) hydrogen bonds : angle 4.94353 ( 2263) covalent geometry : bond 0.00330 (17037) covalent geometry : angle 0.62057 (23153) Misc. bond : bond 0.02870 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP A1044 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.9422 (mpp) cc_final: 0.9078 (mpp) REVERT: A 185 MET cc_start: 0.9401 (ttm) cc_final: 0.8921 (tmm) REVERT: A 218 LYS cc_start: 0.9547 (mttt) cc_final: 0.9309 (ptpt) REVERT: A 261 PHE cc_start: 0.9082 (m-80) cc_final: 0.8716 (m-80) REVERT: A 316 MET cc_start: 0.9289 (mmp) cc_final: 0.9070 (mmt) REVERT: A 357 ILE cc_start: 0.9045 (mt) cc_final: 0.8800 (mm) REVERT: A 416 MET cc_start: 0.9602 (mmp) cc_final: 0.9324 (mmm) REVERT: A 767 MET cc_start: 0.9006 (ptp) cc_final: 0.8671 (ptp) REVERT: A 781 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8742 (mt-10) REVERT: A 812 MET cc_start: 0.8130 (mmp) cc_final: 0.7458 (tpp) REVERT: A 900 MET cc_start: 0.8933 (mmp) cc_final: 0.8678 (mmp) REVERT: A 967 MET cc_start: 0.7643 (mmm) cc_final: 0.6716 (mmm) REVERT: A 979 MET cc_start: 0.9402 (mmp) cc_final: 0.9139 (mmm) REVERT: B 20 LEU cc_start: 0.9127 (mt) cc_final: 0.8477 (tp) REVERT: B 112 MET cc_start: 0.9519 (mmp) cc_final: 0.9118 (mmm) REVERT: B 118 MET cc_start: 0.9513 (mpp) cc_final: 0.8781 (mpp) REVERT: B 185 MET cc_start: 0.9157 (ttm) cc_final: 0.8790 (ttp) REVERT: B 212 MET cc_start: 0.9667 (mmp) cc_final: 0.9431 (mmm) REVERT: B 237 MET cc_start: 0.9618 (mtm) cc_final: 0.9370 (mtp) REVERT: B 354 MET cc_start: 0.8507 (tpt) cc_final: 0.8257 (tpt) REVERT: B 417 MET cc_start: 0.9609 (mtm) cc_final: 0.9382 (mtp) REVERT: B 712 ASN cc_start: 0.9230 (m-40) cc_final: 0.8809 (p0) REVERT: B 811 GLU cc_start: 0.9412 (mt-10) cc_final: 0.9050 (mp0) REVERT: B 821 LEU cc_start: 0.9042 (mt) cc_final: 0.8801 (mt) REVERT: B 1034 GLN cc_start: 0.9077 (mt0) cc_final: 0.8715 (mm-40) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.2839 time to fit residues: 45.0575 Evaluate side-chains 85 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 107 optimal weight: 3.9990 chunk 176 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 52 optimal weight: 0.4980 chunk 136 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.039024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.025646 restraints weight = 474818.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.027692 restraints weight = 185887.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.029230 restraints weight = 108410.590| |-----------------------------------------------------------------------------| r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.2702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.6425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 17044 Z= 0.089 Angle : 0.475 8.213 23153 Z= 0.240 Chirality : 0.036 0.159 2484 Planarity : 0.004 0.053 2997 Dihedral : 6.568 77.722 2405 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 56.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.22 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.19), residues: 2086 helix: 2.01 (0.17), residues: 961 sheet: -0.29 (0.32), residues: 257 loop : -0.57 (0.23), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 96 HIS 0.002 0.000 HIS A 266 PHE 0.014 0.001 PHE B 82 TYR 0.012 0.001 TYR A 613 ARG 0.004 0.000 ARG B 966 Details of bonding type rmsd hydrogen bonds : bond 0.02682 ( 800) hydrogen bonds : angle 4.67660 ( 2263) covalent geometry : bond 0.00211 (17037) covalent geometry : angle 0.47508 (23153) Misc. bond : bond 0.01006 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP A1044 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 MET cc_start: 0.9760 (mtm) cc_final: 0.9406 (mmp) REVERT: A 118 MET cc_start: 0.9464 (mpp) cc_final: 0.8971 (mtm) REVERT: A 185 MET cc_start: 0.9387 (ttm) cc_final: 0.8914 (tmm) REVERT: A 261 PHE cc_start: 0.9074 (m-80) cc_final: 0.8732 (m-80) REVERT: A 357 ILE cc_start: 0.8901 (mt) cc_final: 0.8535 (mm) REVERT: A 416 MET cc_start: 0.9599 (mmp) cc_final: 0.9318 (mmm) REVERT: A 767 MET cc_start: 0.9068 (ptp) cc_final: 0.8759 (ptp) REVERT: A 781 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8641 (mp0) REVERT: A 812 MET cc_start: 0.7946 (mmp) cc_final: 0.7348 (tpp) REVERT: A 900 MET cc_start: 0.8863 (mmp) cc_final: 0.8557 (mmp) REVERT: A 967 MET cc_start: 0.7608 (mmm) cc_final: 0.6625 (mmm) REVERT: A 979 MET cc_start: 0.9319 (mmp) cc_final: 0.8941 (mmm) REVERT: B 20 LEU cc_start: 0.9119 (mt) cc_final: 0.8499 (tp) REVERT: B 112 MET cc_start: 0.9515 (mmp) cc_final: 0.9107 (mmm) REVERT: B 118 MET cc_start: 0.9525 (mpp) cc_final: 0.8768 (mpp) REVERT: B 212 MET cc_start: 0.9663 (mmp) cc_final: 0.9450 (mmm) REVERT: B 237 MET cc_start: 0.9637 (mtm) cc_final: 0.9383 (mtp) REVERT: B 354 MET cc_start: 0.8452 (tpt) cc_final: 0.8229 (tpt) REVERT: B 417 MET cc_start: 0.9623 (mtm) cc_final: 0.9284 (ptp) REVERT: B 712 ASN cc_start: 0.9264 (m-40) cc_final: 0.8945 (p0) REVERT: B 811 GLU cc_start: 0.9361 (mt-10) cc_final: 0.9021 (mp0) REVERT: B 1034 GLN cc_start: 0.9031 (mt0) cc_final: 0.8648 (mm-40) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2905 time to fit residues: 46.3802 Evaluate side-chains 87 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 154 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 102 optimal weight: 0.0040 chunk 45 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.038943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.025929 restraints weight = 420128.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.027920 restraints weight = 176883.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.029394 restraints weight = 106011.749| |-----------------------------------------------------------------------------| r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.2705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.6541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 17044 Z= 0.097 Angle : 0.488 12.300 23153 Z= 0.238 Chirality : 0.036 0.157 2484 Planarity : 0.004 0.048 2997 Dihedral : 6.446 76.227 2405 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 58.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.90 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.19), residues: 2086 helix: 2.08 (0.17), residues: 962 sheet: -0.26 (0.32), residues: 257 loop : -0.56 (0.23), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 96 HIS 0.003 0.001 HIS A 266 PHE 0.013 0.001 PHE B 405 TYR 0.011 0.001 TYR A 613 ARG 0.003 0.000 ARG B1029 Details of bonding type rmsd hydrogen bonds : bond 0.02601 ( 800) hydrogen bonds : angle 4.65207 ( 2263) covalent geometry : bond 0.00224 (17037) covalent geometry : angle 0.48751 (23153) Misc. bond : bond 0.01416 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 2.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP A1044 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 MET cc_start: 0.9741 (mtm) cc_final: 0.9389 (mmp) REVERT: A 118 MET cc_start: 0.9445 (mpp) cc_final: 0.8941 (mtm) REVERT: A 185 MET cc_start: 0.9374 (ttm) cc_final: 0.8915 (tmm) REVERT: A 261 PHE cc_start: 0.9050 (m-80) cc_final: 0.8779 (m-80) REVERT: A 316 MET cc_start: 0.8904 (mpp) cc_final: 0.8332 (mpp) REVERT: A 357 ILE cc_start: 0.8951 (mt) cc_final: 0.8614 (mp) REVERT: A 416 MET cc_start: 0.9590 (mmp) cc_final: 0.9300 (mmm) REVERT: A 767 MET cc_start: 0.9072 (ptp) cc_final: 0.8755 (ptp) REVERT: A 781 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8631 (mp0) REVERT: A 812 MET cc_start: 0.7995 (mmp) cc_final: 0.7600 (tpp) REVERT: A 900 MET cc_start: 0.8851 (mmp) cc_final: 0.8579 (mmp) REVERT: A 967 MET cc_start: 0.7608 (mmm) cc_final: 0.6628 (mmm) REVERT: A 979 MET cc_start: 0.9312 (mmp) cc_final: 0.8933 (mmm) REVERT: B 20 LEU cc_start: 0.9001 (mt) cc_final: 0.8368 (tp) REVERT: B 112 MET cc_start: 0.9499 (mmp) cc_final: 0.9104 (mmm) REVERT: B 118 MET cc_start: 0.9561 (mpp) cc_final: 0.8849 (mpp) REVERT: B 212 MET cc_start: 0.9651 (mmp) cc_final: 0.9446 (mmm) REVERT: B 237 MET cc_start: 0.9666 (mtm) cc_final: 0.9363 (mtp) REVERT: B 354 MET cc_start: 0.8480 (tpt) cc_final: 0.8238 (tpt) REVERT: B 417 MET cc_start: 0.9620 (mtm) cc_final: 0.9283 (ptp) REVERT: B 712 ASN cc_start: 0.9202 (m-40) cc_final: 0.8767 (p0) REVERT: B 811 GLU cc_start: 0.9372 (mt-10) cc_final: 0.9044 (mp0) REVERT: B 967 MET cc_start: 0.7353 (mmp) cc_final: 0.7134 (mmt) REVERT: B 1034 GLN cc_start: 0.9097 (mt0) cc_final: 0.8750 (mm-40) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.2908 time to fit residues: 48.0261 Evaluate side-chains 88 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 101 optimal weight: 0.4980 chunk 157 optimal weight: 0.0170 chunk 184 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 151 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 overall best weight: 1.4822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.038346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.025109 restraints weight = 532982.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.027183 restraints weight = 200068.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.028680 restraints weight = 115462.375| |-----------------------------------------------------------------------------| r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.2685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.6753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 17044 Z= 0.130 Angle : 0.548 16.973 23153 Z= 0.260 Chirality : 0.036 0.160 2484 Planarity : 0.004 0.049 2997 Dihedral : 6.506 77.711 2405 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 62.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.24 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.19), residues: 2086 helix: 1.90 (0.17), residues: 971 sheet: -0.20 (0.33), residues: 257 loop : -0.55 (0.23), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 96 HIS 0.004 0.001 HIS A 266 PHE 0.013 0.001 PHE B 405 TYR 0.015 0.001 TYR B 829 ARG 0.003 0.000 ARG B 223 Details of bonding type rmsd hydrogen bonds : bond 0.02660 ( 800) hydrogen bonds : angle 4.76321 ( 2263) covalent geometry : bond 0.00284 (17037) covalent geometry : angle 0.54812 (23153) Misc. bond : bond 0.02108 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5332.20 seconds wall clock time: 95 minutes 2.97 seconds (5702.97 seconds total)