Starting phenix.real_space_refine on Thu Sep 18 14:41:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dmg_27536/09_2025/8dmg_27536.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dmg_27536/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8dmg_27536/09_2025/8dmg_27536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dmg_27536/09_2025/8dmg_27536.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dmg_27536/09_2025/8dmg_27536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dmg_27536/09_2025/8dmg_27536.map" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 13, 'GLN:plan1': 3, '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: {'GLU:plan': 13, 'GLN:plan1': 3, '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: {'GLU:plan': 13, 'GLN:plan1': 3, '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: {'GLU:plan': 13, 'GLN:plan1': 3, '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: 6.61, per 1000 atoms: 0.39 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: 1.65 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.52 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: 3.36 Time building geometry restraints manager: 2.10 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 1109)) 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 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: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.160 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.230 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.730 ------------------------------------------------------------------------------- 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 : 28.62 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.038 0.003 ARG B 398 TYR 0.047 0.010 TYR B 694 PHE 0.054 0.010 PHE A 107 TRP 0.087 0.012 TRP B 96 HIS 0.030 0.007 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.02871 (17037) covalent geometry : angle 2.34074 (23153) hydrogen bonds : bond 0.18694 ( 800) hydrogen bonds : angle 8.05440 ( 2263) 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 : 0.478 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: 0.7528 (tp) REVERT: A 177 MET cc_start: 0.7413 (ttp) cc_final: 0.6764 (tmm) REVERT: A 272 LEU cc_start: 0.7757 (tp) cc_final: 0.7484 (tt) REVERT: A 314 VAL cc_start: 0.8500 (t) cc_final: 0.7885 (t) REVERT: A 357 ILE cc_start: 0.7172 (mt) cc_final: 0.6783 (mm) REVERT: A 411 THR cc_start: 0.8551 (m) cc_final: 0.7868 (t) REVERT: A 644 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6441 (pt) REVERT: A 913 PHE cc_start: 0.6518 (m-10) cc_final: 0.5980 (m-10) REVERT: A 1016 SER cc_start: 0.7616 (m) cc_final: 0.6906 (t) REVERT: B 62 CYS cc_start: 0.2999 (m) cc_final: 0.2573 (m) REVERT: B 216 VAL cc_start: 0.8727 (t) cc_final: 0.8396 (t) REVERT: B 471 ARG cc_start: 0.6184 (OUTLIER) cc_final: 0.5463 (ptt180) REVERT: B 629 ASN cc_start: 0.7530 (OUTLIER) cc_final: 0.6984 (p0) REVERT: B 659 HIS cc_start: 0.6522 (m-70) cc_final: 0.6020 (m-70) REVERT: B 793 VAL cc_start: 0.5659 (t) cc_final: 0.5063 (t) REVERT: B 847 SER cc_start: 0.6713 (OUTLIER) cc_final: 0.6097 (p) outliers start: 116 outliers final: 33 residues processed: 343 average time/residue: 0.1372 time to fit residues: 69.3537 Evaluate side-chains 179 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 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 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 645 GLN B 699 HIS B 923 GLN B 992 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.046492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.031104 restraints weight = 387266.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.033485 restraints weight = 168606.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.035219 restraints weight = 101877.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.036470 restraints weight = 71204.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.037433 restraints weight = 54523.129| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17044 Z= 0.176 Angle : 0.762 24.268 23153 Z= 0.376 Chirality : 0.041 0.184 2484 Planarity : 0.007 0.193 2997 Dihedral : 8.728 88.077 2405 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 38.24 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.66 % Favored : 95.10 % Rotamer: Outliers : 0.23 % Allowed : 1.17 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.18), residues: 2086 helix: 0.56 (0.16), residues: 966 sheet: -0.16 (0.30), residues: 283 loop : -0.93 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 296 TYR 0.024 0.001 TYR A 613 PHE 0.016 0.002 PHE B 82 TRP 0.035 0.002 TRP B 96 HIS 0.010 0.001 HIS A 478 Details of bonding type rmsd covalent geometry : bond 0.00374 (17037) covalent geometry : angle 0.76183 (23153) hydrogen bonds : bond 0.04438 ( 800) hydrogen bonds : angle 5.80765 ( 2263) Misc. bond : bond 0.01462 ( 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 169 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 165 time to evaluate : 0.674 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 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: A 118 MET cc_start: 0.9475 (mpp) cc_final: 0.9119 (mpp) REVERT: A 218 LYS cc_start: 0.9443 (mttt) cc_final: 0.9213 (mttt) REVERT: A 261 PHE cc_start: 0.9087 (m-80) cc_final: 0.8375 (m-80) REVERT: A 262 LEU cc_start: 0.9680 (mm) cc_final: 0.9473 (mm) REVERT: A 356 LEU cc_start: 0.8438 (mt) cc_final: 0.7813 (mp) REVERT: A 357 ILE cc_start: 0.9055 (mt) cc_final: 0.8724 (mm) REVERT: A 967 MET cc_start: 0.8179 (mmm) cc_final: 0.7921 (mmm) REVERT: A 1005 MET cc_start: 0.9196 (mmp) cc_final: 0.8893 (mmm) REVERT: A 1034 GLN cc_start: 0.9420 (tp-100) cc_final: 0.8889 (tp-100) REVERT: B 20 LEU cc_start: 0.8840 (mt) cc_final: 0.8236 (tt) REVERT: B 86 LEU cc_start: 0.9582 (mt) cc_final: 0.8762 (tp) REVERT: B 118 MET cc_start: 0.9349 (mpp) cc_final: 0.8807 (mpp) REVERT: B 185 MET cc_start: 0.9064 (ttt) cc_final: 0.8804 (ttt) REVERT: B 237 MET cc_start: 0.9648 (mtm) cc_final: 0.9302 (mtp) REVERT: B 417 MET cc_start: 0.9510 (mtm) cc_final: 0.8923 (mtp) REVERT: B 960 LEU cc_start: 0.8688 (tp) cc_final: 0.8313 (mt) REVERT: B 969 ASN cc_start: 0.8722 (t0) cc_final: 0.8513 (t0) REVERT: B 992 GLN cc_start: 0.9303 (mt0) cc_final: 0.8968 (tp40) REVERT: B 1034 GLN cc_start: 0.9003 (mt0) cc_final: 0.8793 (mm-40) outliers start: 4 outliers final: 4 residues processed: 169 average time/residue: 0.1260 time to fit residues: 33.2362 Evaluate side-chains 124 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 61 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 180 optimal weight: 9.9990 chunk 155 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 148 optimal weight: 0.0470 chunk 153 optimal weight: 7.9990 chunk 178 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 overall best weight: 1.4882 ------------------------------------------------------------------------------- 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 109 GLN ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN B 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.043488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.028795 restraints weight = 408829.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.031005 restraints weight = 174754.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.032615 restraints weight = 105407.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.033814 restraints weight = 74038.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.034698 restraints weight = 56481.769| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17044 Z= 0.150 Angle : 0.652 20.234 23153 Z= 0.310 Chirality : 0.038 0.181 2484 Planarity : 0.006 0.170 2997 Dihedral : 7.519 87.959 2405 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 43.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.80 % Favored : 95.05 % Rotamer: Outliers : 0.12 % Allowed : 0.70 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.19), residues: 2086 helix: 1.36 (0.17), residues: 971 sheet: 0.02 (0.29), residues: 281 loop : -0.64 (0.23), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 296 TYR 0.026 0.001 TYR B 305 PHE 0.016 0.001 PHE B 158 TRP 0.040 0.003 TRP A 550 HIS 0.012 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00313 (17037) covalent geometry : angle 0.65201 (23153) hydrogen bonds : bond 0.03571 ( 800) hydrogen bonds : angle 5.24005 ( 2263) Misc. bond : bond 0.02224 ( 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 137 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 135 time to evaluate : 0.816 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: symmetry clash REVERT: A 112 MET cc_start: 0.9629 (mmp) cc_final: 0.9384 (mtp) REVERT: A 118 MET cc_start: 0.9486 (mpp) cc_final: 0.9190 (mpp) REVERT: A 218 LYS cc_start: 0.9448 (mttt) cc_final: 0.9221 (mttt) REVERT: A 261 PHE cc_start: 0.9024 (m-80) cc_final: 0.8269 (m-80) REVERT: A 356 LEU cc_start: 0.8293 (mt) cc_final: 0.7711 (mp) REVERT: A 357 ILE cc_start: 0.8877 (mt) cc_final: 0.8601 (mt) REVERT: A 416 MET cc_start: 0.9513 (mmp) cc_final: 0.9135 (mmm) REVERT: A 485 LEU cc_start: 0.9361 (mt) cc_final: 0.9146 (mt) REVERT: A 812 MET cc_start: 0.7791 (mmp) cc_final: 0.7423 (tpp) REVERT: A 898 LEU cc_start: 0.8328 (mt) cc_final: 0.7977 (mt) REVERT: A 967 MET cc_start: 0.8172 (mmm) cc_final: 0.7853 (mmm) REVERT: A 992 GLN cc_start: 0.9019 (mp10) cc_final: 0.8762 (mp10) REVERT: A 1005 MET cc_start: 0.9151 (mmp) cc_final: 0.8876 (mmm) REVERT: A 1034 GLN cc_start: 0.9181 (tp-100) cc_final: 0.8922 (tp-100) REVERT: B 20 LEU cc_start: 0.8940 (mt) cc_final: 0.8295 (tt) REVERT: B 86 LEU cc_start: 0.9364 (mt) cc_final: 0.8760 (tp) REVERT: B 112 MET cc_start: 0.9116 (mmp) cc_final: 0.8760 (mmm) REVERT: B 118 MET cc_start: 0.9409 (mpp) cc_final: 0.8929 (mpp) REVERT: B 185 MET cc_start: 0.8847 (ttt) cc_final: 0.8592 (ttt) REVERT: B 237 MET cc_start: 0.9702 (mtm) cc_final: 0.9338 (mtp) REVERT: B 416 MET cc_start: 0.9666 (mmm) cc_final: 0.9201 (mmm) REVERT: B 417 MET cc_start: 0.9516 (mtm) cc_final: 0.9002 (mtp) REVERT: B 712 ASN cc_start: 0.9419 (m-40) cc_final: 0.9079 (p0) REVERT: B 890 LEU cc_start: 0.9097 (mt) cc_final: 0.8706 (tp) REVERT: B 960 LEU cc_start: 0.8681 (tp) cc_final: 0.8265 (mt) REVERT: B 969 ASN cc_start: 0.8825 (t0) cc_final: 0.8594 (t0) REVERT: B 1034 GLN cc_start: 0.8964 (mt0) cc_final: 0.8750 (mm-40) outliers start: 2 outliers final: 2 residues processed: 137 average time/residue: 0.1260 time to fit residues: 27.1693 Evaluate side-chains 111 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 114 optimal weight: 7.9990 chunk 153 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 175 optimal weight: 8.9990 chunk 138 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 199 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN ** 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 841 GLN A 872 GLN A1021 HIS ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** B 841 GLN B1021 HIS B1034 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.037636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.025145 restraints weight = 458176.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.027036 restraints weight = 197581.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.028375 restraints weight = 119458.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.029344 restraints weight = 84015.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.030054 restraints weight = 64585.219| |-----------------------------------------------------------------------------| r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| r_final: 0.2723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.5990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.131 17044 Z= 0.426 Angle : 1.188 33.950 23153 Z= 0.549 Chirality : 0.047 0.231 2484 Planarity : 0.008 0.163 2997 Dihedral : 8.515 87.986 2405 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 91.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.76 % Favored : 92.10 % Rotamer: Outliers : 0.06 % Allowed : 1.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.17), residues: 2086 helix: -0.60 (0.15), residues: 969 sheet: -0.42 (0.32), residues: 258 loop : -1.54 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1029 TYR 0.041 0.004 TYR B 829 PHE 0.036 0.004 PHE B 107 TRP 0.034 0.004 TRP A 550 HIS 0.021 0.004 HIS A 931 Details of bonding type rmsd covalent geometry : bond 0.00839 (17037) covalent geometry : angle 1.18829 (23153) hydrogen bonds : bond 0.04875 ( 800) hydrogen bonds : angle 6.39045 ( 2263) Misc. bond : bond 0.06358 ( 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 102 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.501 Fit side-chains 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: A 112 MET cc_start: 0.9491 (mmp) cc_final: 0.9222 (mmp) REVERT: A 118 MET cc_start: 0.9393 (mpp) cc_final: 0.9034 (mpp) REVERT: A 145 MET cc_start: 0.9568 (mmp) cc_final: 0.9276 (mmp) REVERT: A 261 PHE cc_start: 0.9075 (m-80) cc_final: 0.8485 (m-80) REVERT: A 356 LEU cc_start: 0.8398 (mt) cc_final: 0.7946 (mt) REVERT: A 357 ILE cc_start: 0.9063 (mt) cc_final: 0.8858 (mt) REVERT: A 416 MET cc_start: 0.9588 (mmp) cc_final: 0.9375 (mmm) REVERT: A 417 MET cc_start: 0.9814 (mtp) cc_final: 0.9557 (mtm) REVERT: A 781 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8634 (mt-10) REVERT: A 812 MET cc_start: 0.8515 (mmp) cc_final: 0.8153 (tpp) REVERT: A 1005 MET cc_start: 0.9004 (mmp) cc_final: 0.8736 (mmm) REVERT: B 20 LEU cc_start: 0.9059 (mt) cc_final: 0.8344 (tp) REVERT: B 112 MET cc_start: 0.9152 (mmp) cc_final: 0.8885 (mmm) REVERT: B 118 MET cc_start: 0.9545 (mpp) cc_final: 0.9100 (mpp) REVERT: B 237 MET cc_start: 0.9478 (mtm) cc_final: 0.9158 (mtp) REVERT: B 416 MET cc_start: 0.9639 (mmm) cc_final: 0.9169 (tpp) REVERT: B 437 LEU cc_start: 0.9207 (mp) cc_final: 0.8863 (mt) REVERT: B 811 GLU cc_start: 0.9654 (mt-10) cc_final: 0.9145 (mp0) REVERT: B 1014 MET cc_start: 0.9636 (mtm) cc_final: 0.9050 (tmm) REVERT: B 1034 GLN cc_start: 0.9076 (mt0) cc_final: 0.8733 (mm-40) outliers start: 1 outliers final: 0 residues processed: 102 average time/residue: 0.1316 time to fit residues: 20.8586 Evaluate side-chains 76 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 30 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 206 GLN A 359 GLN ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.037919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.025275 restraints weight = 435850.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.027198 restraints weight = 187036.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.028558 restraints weight = 112202.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.029558 restraints weight = 78953.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.030298 restraints weight = 60360.924| |-----------------------------------------------------------------------------| r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.6202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 17044 Z= 0.225 Angle : 0.749 22.903 23153 Z= 0.349 Chirality : 0.039 0.200 2484 Planarity : 0.006 0.135 2997 Dihedral : 7.875 87.134 2405 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 72.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.16 % Favored : 93.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.18), residues: 2086 helix: 0.08 (0.16), residues: 961 sheet: -0.52 (0.32), residues: 262 loop : -1.25 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1029 TYR 0.022 0.002 TYR B 829 PHE 0.021 0.002 PHE B 82 TRP 0.025 0.002 TRP B 96 HIS 0.007 0.001 HIS A 931 Details of bonding type rmsd covalent geometry : bond 0.00460 (17037) covalent geometry : angle 0.74900 (23153) hydrogen bonds : bond 0.03811 ( 800) hydrogen bonds : angle 5.72019 ( 2263) Misc. bond : bond 0.03159 ( 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 98 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.564 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: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.9412 (mpp) cc_final: 0.9130 (mpp) REVERT: A 145 MET cc_start: 0.9583 (mmp) cc_final: 0.9244 (mmp) REVERT: A 261 PHE cc_start: 0.9147 (m-80) cc_final: 0.8640 (m-80) REVERT: A 356 LEU cc_start: 0.8082 (mt) cc_final: 0.7805 (mt) REVERT: A 416 MET cc_start: 0.9571 (mmp) cc_final: 0.9347 (mmm) REVERT: A 979 MET cc_start: 0.9445 (mmp) cc_final: 0.9038 (mmm) REVERT: A 996 PHE cc_start: 0.9128 (t80) cc_final: 0.8905 (t80) REVERT: B 20 LEU cc_start: 0.9096 (mt) cc_final: 0.8414 (tp) REVERT: B 118 MET cc_start: 0.9567 (mpp) cc_final: 0.8881 (mpp) REVERT: B 185 MET cc_start: 0.8174 (ptp) cc_final: 0.7754 (ptm) REVERT: B 212 MET cc_start: 0.9638 (mmp) cc_final: 0.9326 (mmm) REVERT: B 237 MET cc_start: 0.9571 (mtm) cc_final: 0.9252 (mtp) REVERT: B 416 MET cc_start: 0.9612 (mmm) cc_final: 0.9194 (mmm) REVERT: B 1014 MET cc_start: 0.9652 (mtm) cc_final: 0.9316 (ppp) outliers start: 2 outliers final: 2 residues processed: 98 average time/residue: 0.1279 time to fit residues: 19.8947 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 : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 51 optimal weight: 6.9990 chunk 204 optimal weight: 0.4980 chunk 36 optimal weight: 9.9990 chunk 156 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 192 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1022 GLN ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.038409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.025543 restraints weight = 453402.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.027523 restraints weight = 184142.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.028981 restraints weight = 108927.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.030012 restraints weight = 75167.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.030809 restraints weight = 57279.440| |-----------------------------------------------------------------------------| r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.6330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 17044 Z= 0.141 Angle : 0.580 15.754 23153 Z= 0.281 Chirality : 0.037 0.136 2484 Planarity : 0.004 0.050 2997 Dihedral : 7.508 84.945 2405 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 63.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.97 % Favored : 93.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.19), residues: 2086 helix: 0.85 (0.17), residues: 963 sheet: -0.39 (0.33), residues: 256 loop : -0.95 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 617 TYR 0.015 0.001 TYR A 613 PHE 0.013 0.001 PHE B 405 TRP 0.019 0.002 TRP B 96 HIS 0.004 0.001 HIS A 961 Details of bonding type rmsd covalent geometry : bond 0.00307 (17037) covalent geometry : angle 0.57963 (23153) hydrogen bonds : bond 0.03315 ( 800) hydrogen bonds : angle 5.25626 ( 2263) Misc. bond : bond 0.01822 ( 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 101 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.765 Fit side-chains 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: A 112 MET cc_start: 0.9754 (mtm) cc_final: 0.9077 (ptp) REVERT: A 118 MET cc_start: 0.9403 (mpp) cc_final: 0.9115 (mpp) REVERT: A 145 MET cc_start: 0.9546 (mmp) cc_final: 0.9257 (mmp) REVERT: A 261 PHE cc_start: 0.9178 (m-80) cc_final: 0.8918 (m-80) REVERT: A 316 MET cc_start: 0.8901 (mmm) cc_final: 0.8631 (mmm) REVERT: A 356 LEU cc_start: 0.8021 (mt) cc_final: 0.7503 (mt) REVERT: A 357 ILE cc_start: 0.9051 (mt) cc_final: 0.8650 (mp) REVERT: A 416 MET cc_start: 0.9568 (mmp) cc_final: 0.9293 (mmm) REVERT: A 417 MET cc_start: 0.9704 (mtm) cc_final: 0.9190 (mtp) REVERT: A 505 MET cc_start: 0.9676 (tpp) cc_final: 0.9266 (mmm) REVERT: A 781 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8671 (pp20) REVERT: A 900 MET cc_start: 0.8835 (mmp) cc_final: 0.8604 (mmp) REVERT: A 996 PHE cc_start: 0.9051 (t80) cc_final: 0.8765 (t80) REVERT: B 20 LEU cc_start: 0.9103 (mt) cc_final: 0.8446 (tp) REVERT: B 112 MET cc_start: 0.9524 (mmp) cc_final: 0.9181 (mmm) REVERT: B 118 MET cc_start: 0.9542 (mpp) cc_final: 0.8956 (mpp) REVERT: B 185 MET cc_start: 0.8020 (ptp) cc_final: 0.7616 (ptm) REVERT: B 212 MET cc_start: 0.9643 (mmp) cc_final: 0.9301 (mmm) REVERT: B 237 MET cc_start: 0.9567 (mtm) cc_final: 0.9342 (mtp) REVERT: B 354 MET cc_start: 0.8404 (tpt) cc_final: 0.8185 (tpt) REVERT: B 416 MET cc_start: 0.9594 (mmm) cc_final: 0.9142 (mmm) REVERT: B 417 MET cc_start: 0.9488 (mtm) cc_final: 0.9279 (mtp) REVERT: B 712 ASN cc_start: 0.9112 (m-40) cc_final: 0.8524 (p0) REVERT: B 811 GLU cc_start: 0.9348 (mt-10) cc_final: 0.9039 (mp0) REVERT: B 1014 MET cc_start: 0.9620 (mtm) cc_final: 0.9300 (ppp) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1281 time to fit residues: 20.6108 Evaluate side-chains 86 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 110 optimal weight: 0.3980 chunk 7 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.038694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.025736 restraints weight = 454302.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.027716 restraints weight = 181908.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.029177 restraints weight = 107409.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.030268 restraints weight = 74513.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.031067 restraints weight = 56177.615| |-----------------------------------------------------------------------------| r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.2770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.6462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 17044 Z= 0.107 Angle : 0.520 13.178 23153 Z= 0.256 Chirality : 0.036 0.160 2484 Planarity : 0.004 0.062 2997 Dihedral : 7.090 82.510 2405 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 59.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.75 % Favored : 95.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.19), residues: 2086 helix: 1.44 (0.17), residues: 967 sheet: -0.27 (0.33), residues: 256 loop : -0.78 (0.22), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1029 TYR 0.015 0.001 TYR A 613 PHE 0.014 0.001 PHE B 405 TRP 0.015 0.001 TRP B 96 HIS 0.004 0.001 HIS A 961 Details of bonding type rmsd covalent geometry : bond 0.00240 (17037) covalent geometry : angle 0.52021 (23153) hydrogen bonds : bond 0.02961 ( 800) hydrogen bonds : angle 4.96325 ( 2263) Misc. bond : bond 0.01568 ( 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 99 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.581 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 112 MET cc_start: 0.9681 (mtm) cc_final: 0.8996 (ptp) REVERT: A 118 MET cc_start: 0.9429 (mpp) cc_final: 0.9181 (mpp) REVERT: A 145 MET cc_start: 0.9466 (mmp) cc_final: 0.9182 (mmp) REVERT: A 261 PHE cc_start: 0.9068 (m-80) cc_final: 0.8784 (m-80) REVERT: A 354 MET cc_start: 0.8666 (tpp) cc_final: 0.8437 (tpp) REVERT: A 356 LEU cc_start: 0.8032 (mt) cc_final: 0.7464 (mt) REVERT: A 357 ILE cc_start: 0.9038 (mt) cc_final: 0.8609 (mp) REVERT: A 416 MET cc_start: 0.9553 (mmp) cc_final: 0.9270 (mmp) REVERT: A 417 MET cc_start: 0.9715 (mtm) cc_final: 0.9256 (mtp) REVERT: A 781 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8698 (mp0) REVERT: A 900 MET cc_start: 0.8974 (mmp) cc_final: 0.8670 (mmp) REVERT: A 951 ASN cc_start: 0.9457 (m110) cc_final: 0.9239 (p0) REVERT: A 979 MET cc_start: 0.9373 (mmp) cc_final: 0.8900 (mmm) REVERT: A 996 PHE cc_start: 0.8868 (t80) cc_final: 0.8613 (t80) REVERT: B 20 LEU cc_start: 0.9138 (mt) cc_final: 0.8476 (tp) REVERT: B 112 MET cc_start: 0.9511 (mmp) cc_final: 0.9111 (mmm) REVERT: B 118 MET cc_start: 0.9504 (mpp) cc_final: 0.8640 (mpp) REVERT: B 185 MET cc_start: 0.7953 (ptp) cc_final: 0.7543 (ptm) REVERT: B 212 MET cc_start: 0.9667 (mmp) cc_final: 0.9386 (mmm) REVERT: B 237 MET cc_start: 0.9594 (mtm) cc_final: 0.9334 (mtp) REVERT: B 416 MET cc_start: 0.9615 (mmm) cc_final: 0.9125 (mmm) REVERT: B 417 MET cc_start: 0.9496 (mtm) cc_final: 0.9181 (ptp) REVERT: B 712 ASN cc_start: 0.9025 (m-40) cc_final: 0.8519 (p0) REVERT: B 811 GLU cc_start: 0.9374 (mt-10) cc_final: 0.9032 (mp0) REVERT: B 821 LEU cc_start: 0.9155 (mt) cc_final: 0.8911 (mt) REVERT: B 1014 MET cc_start: 0.9617 (mtm) cc_final: 0.9286 (ppp) REVERT: B 1034 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8432 (tm-30) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1279 time to fit residues: 20.1030 Evaluate side-chains 86 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 107 optimal weight: 0.5980 chunk 184 optimal weight: 8.9990 chunk 185 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 123 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.038482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.025531 restraints weight = 472501.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.027572 restraints weight = 186376.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.029010 restraints weight = 108727.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.030087 restraints weight = 75414.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.030890 restraints weight = 56939.698| |-----------------------------------------------------------------------------| r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| r_final: 0.2763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.6673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 17044 Z= 0.122 Angle : 0.539 14.546 23153 Z= 0.259 Chirality : 0.036 0.165 2484 Planarity : 0.004 0.049 2997 Dihedral : 6.979 83.315 2405 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 62.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.58 % Favored : 94.37 % 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 : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.19), residues: 2086 helix: 1.59 (0.17), residues: 967 sheet: -0.31 (0.33), residues: 257 loop : -0.77 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 765 TYR 0.015 0.001 TYR B 829 PHE 0.026 0.001 PHE A 405 TRP 0.015 0.001 TRP B 96 HIS 0.004 0.001 HIS A 408 Details of bonding type rmsd covalent geometry : bond 0.00268 (17037) covalent geometry : angle 0.53859 (23153) hydrogen bonds : bond 0.02920 ( 800) hydrogen bonds : angle 4.89153 ( 2263) Misc. bond : bond 0.01868 ( 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 98 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.517 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: A 112 MET cc_start: 0.9642 (mtm) cc_final: 0.9132 (mtp) REVERT: A 118 MET cc_start: 0.9443 (mpp) cc_final: 0.8968 (mtm) REVERT: A 145 MET cc_start: 0.9492 (mmp) cc_final: 0.9206 (mmp) REVERT: A 261 PHE cc_start: 0.9137 (m-80) cc_final: 0.8826 (m-80) REVERT: A 354 MET cc_start: 0.8898 (tpp) cc_final: 0.8664 (tpp) REVERT: A 356 LEU cc_start: 0.8045 (mt) cc_final: 0.7453 (mt) REVERT: A 357 ILE cc_start: 0.9042 (mt) cc_final: 0.8615 (mp) REVERT: A 416 MET cc_start: 0.9577 (mmp) cc_final: 0.9267 (mmp) REVERT: A 417 MET cc_start: 0.9724 (mtm) cc_final: 0.9086 (ptp) REVERT: A 781 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8770 (pp20) REVERT: A 900 MET cc_start: 0.8976 (mmp) cc_final: 0.8710 (mmp) REVERT: A 979 MET cc_start: 0.9377 (mmp) cc_final: 0.9040 (mmm) REVERT: A 996 PHE cc_start: 0.8811 (t80) cc_final: 0.8554 (t80) REVERT: B 20 LEU cc_start: 0.9023 (mt) cc_final: 0.8340 (tp) REVERT: B 112 MET cc_start: 0.9512 (mmp) cc_final: 0.9109 (mmm) REVERT: B 118 MET cc_start: 0.9506 (mpp) cc_final: 0.8535 (mpp) REVERT: B 185 MET cc_start: 0.8045 (ptp) cc_final: 0.7607 (ptm) REVERT: B 212 MET cc_start: 0.9630 (mmp) cc_final: 0.9389 (mmm) REVERT: B 237 MET cc_start: 0.9565 (mtm) cc_final: 0.9314 (mtp) REVERT: B 416 MET cc_start: 0.9618 (mmm) cc_final: 0.9125 (mmm) REVERT: B 417 MET cc_start: 0.9518 (mtm) cc_final: 0.9204 (ptp) REVERT: B 712 ASN cc_start: 0.9253 (m-40) cc_final: 0.8759 (p0) REVERT: B 811 GLU cc_start: 0.9392 (mt-10) cc_final: 0.9043 (mp0) REVERT: B 821 LEU cc_start: 0.9204 (mt) cc_final: 0.8970 (mt) REVERT: B 1014 MET cc_start: 0.9606 (mtm) cc_final: 0.9270 (ppp) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1213 time to fit residues: 19.2251 Evaluate side-chains 83 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 21 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 310 GLN A ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.038456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.025475 restraints weight = 448252.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.027463 restraints weight = 182076.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.028865 restraints weight = 107759.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.029931 restraints weight = 75268.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.030734 restraints weight = 56883.854| |-----------------------------------------------------------------------------| r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.6789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 17044 Z= 0.110 Angle : 0.521 12.409 23153 Z= 0.255 Chirality : 0.036 0.164 2484 Planarity : 0.004 0.054 2997 Dihedral : 6.861 83.108 2405 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 60.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.75 % Favored : 95.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.19), residues: 2086 helix: 1.76 (0.17), residues: 966 sheet: -0.33 (0.32), residues: 255 loop : -0.67 (0.23), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 471 TYR 0.013 0.001 TYR A 613 PHE 0.014 0.001 PHE B 405 TRP 0.013 0.001 TRP B 96 HIS 0.003 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00249 (17037) covalent geometry : angle 0.52101 (23153) hydrogen bonds : bond 0.02834 ( 800) hydrogen bonds : angle 4.78255 ( 2263) Misc. bond : bond 0.01538 ( 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 98 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.592 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: A 112 MET cc_start: 0.9715 (mtm) cc_final: 0.9384 (mmp) REVERT: A 118 MET cc_start: 0.9425 (mpp) cc_final: 0.8951 (mtm) REVERT: A 145 MET cc_start: 0.9476 (mmp) cc_final: 0.9193 (mmp) REVERT: A 261 PHE cc_start: 0.9127 (m-80) cc_final: 0.8826 (m-80) REVERT: A 316 MET cc_start: 0.8864 (mmm) cc_final: 0.7827 (ttm) REVERT: A 354 MET cc_start: 0.8889 (tpp) cc_final: 0.8652 (tpp) REVERT: A 356 LEU cc_start: 0.8031 (mt) cc_final: 0.7438 (mt) REVERT: A 357 ILE cc_start: 0.9038 (mt) cc_final: 0.8607 (mp) REVERT: A 416 MET cc_start: 0.9559 (mmp) cc_final: 0.9290 (mmm) REVERT: A 417 MET cc_start: 0.9721 (mtm) cc_final: 0.9099 (ptp) REVERT: A 781 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8696 (mp0) REVERT: A 900 MET cc_start: 0.8951 (mmp) cc_final: 0.8698 (mmp) REVERT: A 951 ASN cc_start: 0.9455 (m110) cc_final: 0.9247 (p0) REVERT: A 979 MET cc_start: 0.9338 (mmp) cc_final: 0.8883 (mmm) REVERT: A 996 PHE cc_start: 0.8811 (t80) cc_final: 0.8561 (t80) REVERT: B 20 LEU cc_start: 0.9100 (mt) cc_final: 0.8314 (tp) REVERT: B 112 MET cc_start: 0.9526 (mmp) cc_final: 0.9095 (mmm) REVERT: B 118 MET cc_start: 0.9550 (mpp) cc_final: 0.8718 (mpp) REVERT: B 185 MET cc_start: 0.8005 (ptp) cc_final: 0.7542 (ptm) REVERT: B 212 MET cc_start: 0.9632 (mmp) cc_final: 0.9387 (mmm) REVERT: B 237 MET cc_start: 0.9648 (mtm) cc_final: 0.9325 (mtp) REVERT: B 416 MET cc_start: 0.9633 (mmm) cc_final: 0.9144 (mmm) REVERT: B 712 ASN cc_start: 0.9116 (m-40) cc_final: 0.8551 (p0) REVERT: B 811 GLU cc_start: 0.9375 (mt-10) cc_final: 0.9048 (mp0) REVERT: B 821 LEU cc_start: 0.9194 (mt) cc_final: 0.8978 (mt) REVERT: B 1014 MET cc_start: 0.9608 (mtm) cc_final: 0.9270 (ppp) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1155 time to fit residues: 18.1989 Evaluate side-chains 83 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 148 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 123 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 202 optimal weight: 0.0970 chunk 103 optimal weight: 10.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.038223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.025465 restraints weight = 416326.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.027392 restraints weight = 175763.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.028789 restraints weight = 105147.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.029815 restraints weight = 73535.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.030588 restraints weight = 56230.256| |-----------------------------------------------------------------------------| r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.6953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 17044 Z= 0.116 Angle : 0.524 13.325 23153 Z= 0.254 Chirality : 0.036 0.146 2484 Planarity : 0.004 0.048 2997 Dihedral : 6.745 83.327 2405 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 62.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.29 % Favored : 94.67 % 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 : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.19), residues: 2086 helix: 1.81 (0.17), residues: 964 sheet: -0.31 (0.32), residues: 255 loop : -0.70 (0.23), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1029 TYR 0.013 0.001 TYR B 829 PHE 0.013 0.001 PHE B 405 TRP 0.013 0.001 TRP B 96 HIS 0.003 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00260 (17037) covalent geometry : angle 0.52386 (23153) hydrogen bonds : bond 0.02832 ( 800) hydrogen bonds : angle 4.76625 ( 2263) Misc. bond : bond 0.01706 ( 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 99 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.645 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: symmetry clash REVERT: A 112 MET cc_start: 0.9731 (mtm) cc_final: 0.9193 (mtp) REVERT: A 118 MET cc_start: 0.9415 (mpp) cc_final: 0.8942 (mtm) REVERT: A 145 MET cc_start: 0.9474 (mmp) cc_final: 0.9196 (mmp) REVERT: A 261 PHE cc_start: 0.9125 (m-80) cc_final: 0.8797 (m-80) REVERT: A 316 MET cc_start: 0.8871 (mmm) cc_final: 0.7882 (ttm) REVERT: A 354 MET cc_start: 0.8876 (tpp) cc_final: 0.8650 (tpp) REVERT: A 356 LEU cc_start: 0.8039 (mt) cc_final: 0.7440 (mt) REVERT: A 357 ILE cc_start: 0.9055 (mt) cc_final: 0.8629 (mp) REVERT: A 416 MET cc_start: 0.9571 (mmp) cc_final: 0.9288 (mmm) REVERT: A 417 MET cc_start: 0.9743 (mtm) cc_final: 0.9133 (ptp) REVERT: A 767 MET cc_start: 0.9301 (pmm) cc_final: 0.8875 (pmm) REVERT: A 781 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8743 (mt-10) REVERT: A 900 MET cc_start: 0.8957 (mmp) cc_final: 0.8691 (mmp) REVERT: A 979 MET cc_start: 0.9314 (mmp) cc_final: 0.8878 (mmm) REVERT: A 996 PHE cc_start: 0.8773 (t80) cc_final: 0.8552 (t80) REVERT: B 112 MET cc_start: 0.9510 (mmp) cc_final: 0.9105 (mmm) REVERT: B 118 MET cc_start: 0.9534 (mpp) cc_final: 0.8745 (mpp) REVERT: B 185 MET cc_start: 0.8023 (ptp) cc_final: 0.7490 (ptm) REVERT: B 212 MET cc_start: 0.9610 (mmp) cc_final: 0.9389 (mmm) REVERT: B 416 MET cc_start: 0.9589 (mmm) cc_final: 0.9269 (mmm) REVERT: B 712 ASN cc_start: 0.9278 (m-40) cc_final: 0.9006 (p0) REVERT: B 811 GLU cc_start: 0.9597 (mt-10) cc_final: 0.9225 (pm20) REVERT: B 967 MET cc_start: 0.7453 (mmp) cc_final: 0.7128 (mmt) REVERT: B 1014 MET cc_start: 0.9596 (mtm) cc_final: 0.9254 (ppp) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1230 time to fit residues: 19.5288 Evaluate side-chains 83 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 40 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 34 optimal weight: 0.1980 chunk 192 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.038292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.025147 restraints weight = 530065.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.027195 restraints weight = 197361.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.028695 restraints weight = 113077.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.029779 restraints weight = 76865.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.030585 restraints weight = 57683.307| |-----------------------------------------------------------------------------| r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| r_final: 0.2754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.7037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 17044 Z= 0.107 Angle : 0.503 11.442 23153 Z= 0.246 Chirality : 0.036 0.158 2484 Planarity : 0.004 0.049 2997 Dihedral : 6.644 82.864 2405 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 62.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.00 % Favored : 94.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.19), residues: 2086 helix: 1.91 (0.17), residues: 970 sheet: -0.30 (0.32), residues: 255 loop : -0.64 (0.23), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1029 TYR 0.013 0.001 TYR A 613 PHE 0.014 0.001 PHE B 405 TRP 0.012 0.001 TRP B 96 HIS 0.003 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00247 (17037) covalent geometry : angle 0.50276 (23153) hydrogen bonds : bond 0.02704 ( 800) hydrogen bonds : angle 4.67957 ( 2263) Misc. bond : bond 0.01515 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2669.70 seconds wall clock time: 47 minutes 40.01 seconds (2860.01 seconds total)