Starting phenix.real_space_refine on Sun Jun 15 16:35:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dmg_27536/06_2025/8dmg_27536.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dmg_27536/06_2025/8dmg_27536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dmg_27536/06_2025/8dmg_27536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dmg_27536/06_2025/8dmg_27536.map" model { file = "/net/cci-nas-00/data/ceres_data/8dmg_27536/06_2025/8dmg_27536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dmg_27536/06_2025/8dmg_27536.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.128 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 2 7.16 5 P 6 5.49 5 S 78 5.16 5 C 10544 2.51 5 N 2812 2.21 5 O 3200 1.98 5 H 202 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16844 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8236 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1034, 8200 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 54, 'TRANS': 979} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 13, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 59 Conformer: "B" Number of residues, atoms: 1034, 8200 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 54, 'TRANS': 979} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 13, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 59 bond proxies already assigned to first conformer: 8341 Chain: "B" Number of atoms: 8238 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1034, 8202 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 54, 'TRANS': 979} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 13, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 59 Conformer: "B" Number of residues, atoms: 1034, 8202 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 54, 'TRANS': 979} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 13, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 59 bond proxies already assigned to first conformer: 8342 Chain: "A" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 185 Unusual residues: {'1C6': 1, 'FAD': 1, 'FMN': 1, 'HEM': 1, 'PG4': 2, 'SO4': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "B" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 185 Unusual residues: {'1C6': 1, 'FAD': 1, 'FMN': 1, 'HEM': 1, 'PG4': 2, 'SO4': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3247 SG CYS A 400 53.201 45.582 102.548 1.00 11.59 S ATOM 11483 SG CYS B 400 38.400 45.550 47.133 1.00 11.59 S Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N APHE A 87 " occ=0.20 ... (20 atoms not shown) pdb=" CZ BPHE A 87 " occ=0.20 residue: pdb=" N AASP A 168 " occ=0.20 ... (14 atoms not shown) pdb=" OD2BASP A 168 " occ=0.20 residue: pdb=" N AASP A 182 " occ=0.20 ... (14 atoms not shown) pdb=" OD2BASP A 182 " occ=0.20 residue: pdb=" N AGLN A 310 " occ=0.20 ... (16 atoms not shown) pdb=" NE2BGLN A 310 " occ=0.20 residue: pdb=" N APHE B 87 " occ=0.20 ... (20 atoms not shown) pdb=" CZ BPHE B 87 " occ=0.20 residue: pdb=" N AASP B 168 " occ=0.20 ... (14 atoms not shown) pdb=" OD2BASP B 168 " occ=0.20 residue: pdb=" N AASP B 182 " occ=0.20 ... (14 atoms not shown) pdb=" OD2BASP B 182 " occ=0.20 residue: pdb=" N AGLN B 310 " occ=0.20 ... (16 atoms not shown) pdb=" NE2BGLN B 310 " occ=0.20 Time building chain proxies: 18.29, per 1000 atoms: 1.09 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: 6.07 Conformation dependent library (CDL) restraints added in 3.9 seconds 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3908 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 18 sheets defined 51.0% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 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: 7.24 Time building geometry restraints manager: 5.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.23: 1569 1.23 - 1.65: 15523 1.65 - 2.06: 143 2.06 - 2.48: 2 2.48 - 2.89: 2 Bond restraints: 17239 Sorted by residual: bond pdb=" C HIS A 478 " pdb=" N ASN A 479 " ideal model delta sigma weight residual 1.332 2.890 -1.558 1.40e-02 5.10e+03 1.24e+04 bond pdb=" C LEU B 630 " pdb=" N ASP B 631 " ideal model delta sigma weight residual 1.333 2.502 -1.169 1.50e-02 4.44e+03 6.08e+03 bond pdb=" C ALA A 661 " pdb=" N PHE A 662 " ideal model delta sigma weight residual 1.330 0.856 0.473 1.37e-02 5.33e+03 1.19e+03 bond pdb=" C ALA B 661 " pdb=" N PHE B 662 " ideal model delta sigma weight residual 1.330 0.856 0.473 1.37e-02 5.33e+03 1.19e+03 bond pdb=" N PRO A 774 " pdb=" CD PRO A 774 " ideal model delta sigma weight residual 1.473 1.682 -0.209 1.40e-02 5.10e+03 2.23e+02 ... (remaining 17234 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.64: 23554 11.64 - 23.28: 49 23.28 - 34.93: 8 34.93 - 46.57: 7 46.57 - 58.21: 3 Bond angle restraints: 23621 Sorted by residual: angle pdb=" CA HIS A 478 " pdb=" C HIS A 478 " pdb=" N ASN A 479 " ideal model delta sigma weight residual 116.25 65.98 50.27 1.53e+00 4.27e-01 1.08e+03 angle pdb=" O LEU B 630 " pdb=" C LEU B 630 " pdb=" N ASP B 631 " ideal model delta sigma weight residual 123.28 85.84 37.44 1.16e+00 7.43e-01 1.04e+03 angle pdb=" N ALA B 736 " pdb=" CA ALA B 736 " pdb=" CB ALA B 736 " ideal model delta sigma weight residual 109.51 151.10 -41.59 1.58e+00 4.01e-01 6.93e+02 angle pdb=" N ALA A 736 " pdb=" CA ALA A 736 " pdb=" CB ALA A 736 " ideal model delta sigma weight residual 109.51 151.10 -41.59 1.58e+00 4.01e-01 6.93e+02 angle pdb=" N LYS B 734 " pdb=" CA LYS B 734 " pdb=" CB LYS B 734 " ideal model delta sigma weight residual 111.74 71.30 40.44 1.69e+00 3.50e-01 5.73e+02 ... (remaining 23616 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 9090 17.54 - 35.08: 805 35.08 - 52.61: 293 52.61 - 70.15: 97 70.15 - 87.69: 26 Dihedral angle restraints: 10311 sinusoidal: 4246 harmonic: 6065 Sorted by residual: dihedral pdb=" N LYS B 734 " pdb=" C LYS B 734 " pdb=" CA LYS B 734 " pdb=" CB LYS B 734 " ideal model delta harmonic sigma weight residual 122.80 78.24 44.56 0 2.50e+00 1.60e-01 3.18e+02 dihedral pdb=" N LYS A 734 " pdb=" C LYS A 734 " pdb=" CA LYS A 734 " pdb=" CB LYS A 734 " ideal model delta harmonic sigma weight residual 122.80 78.25 44.55 0 2.50e+00 1.60e-01 3.18e+02 dihedral pdb=" N ALA A 736 " pdb=" C ALA A 736 " pdb=" CA ALA A 736 " pdb=" CB ALA A 736 " ideal model delta harmonic sigma weight residual 122.90 156.51 -33.61 0 2.50e+00 1.60e-01 1.81e+02 ... (remaining 10308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.228: 2370 0.228 - 0.456: 97 0.456 - 0.683: 12 0.683 - 0.911: 0 0.911 - 1.139: 5 Chirality restraints: 2484 Sorted by residual: chirality pdb=" CA ALA A 736 " pdb=" N ALA A 736 " pdb=" C ALA A 736 " pdb=" CB ALA A 736 " both_signs ideal model delta sigma weight residual False 2.48 1.35 1.14 2.00e-01 2.50e+01 3.24e+01 chirality pdb=" CA ALA B 736 " pdb=" N ALA B 736 " pdb=" C ALA B 736 " pdb=" CB ALA B 736 " both_signs ideal model delta sigma weight residual False 2.48 1.35 1.13 2.00e-01 2.50e+01 3.22e+01 chirality pdb=" CA HIS B 478 " pdb=" N HIS B 478 " pdb=" C HIS B 478 " pdb=" CB HIS B 478 " both_signs ideal model delta sigma weight residual False 2.51 1.50 1.01 2.00e-01 2.50e+01 2.54e+01 ... (remaining 2481 not shown) Planarity restraints: 3025 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 630 " 0.188 2.00e-02 2.50e+03 2.74e-01 7.49e+02 pdb=" C LEU B 630 " -0.452 2.00e-02 2.50e+03 pdb=" O LEU B 630 " 0.245 2.00e-02 2.50e+03 pdb=" N ASP B 631 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 478 " -0.179 2.00e-02 2.50e+03 2.28e-01 5.19e+02 pdb=" C HIS A 478 " 0.349 2.00e-02 2.50e+03 pdb=" O HIS A 478 " -0.225 2.00e-02 2.50e+03 pdb=" N ASN A 479 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN B1103 " 0.034 2.00e-02 2.50e+03 6.13e-02 1.69e+02 pdb=" C10 FMN B1103 " 0.101 2.00e-02 2.50e+03 pdb=" C2 FMN B1103 " -0.013 2.00e-02 2.50e+03 pdb=" C4 FMN B1103 " -0.091 2.00e-02 2.50e+03 pdb=" C4A FMN B1103 " 0.085 2.00e-02 2.50e+03 pdb=" C5A FMN B1103 " -0.009 2.00e-02 2.50e+03 pdb=" C6 FMN B1103 " 0.032 2.00e-02 2.50e+03 pdb=" C7 FMN B1103 " 0.010 2.00e-02 2.50e+03 pdb=" C7M FMN B1103 " 0.037 2.00e-02 2.50e+03 pdb=" C8 FMN B1103 " -0.044 2.00e-02 2.50e+03 pdb=" C8M FMN B1103 " -0.079 2.00e-02 2.50e+03 pdb=" C9 FMN B1103 " -0.039 2.00e-02 2.50e+03 pdb=" C9A FMN B1103 " -0.026 2.00e-02 2.50e+03 pdb=" N1 FMN B1103 " 0.097 2.00e-02 2.50e+03 pdb=" N10 FMN B1103 " 0.000 2.00e-02 2.50e+03 pdb=" N3 FMN B1103 " -0.116 2.00e-02 2.50e+03 pdb=" N5 FMN B1103 " 0.058 2.00e-02 2.50e+03 pdb=" O2 FMN B1103 " -0.038 2.00e-02 2.50e+03 ... (remaining 3022 not shown) Histogram of nonbonded interaction distances: 0.31 - 1.17: 5 1.17 - 2.03: 77 2.03 - 2.88: 7673 2.88 - 3.74: 36575 3.74 - 4.60: 69867 Warning: very small nonbonded interaction distances. Nonbonded interactions: 114197 Sorted by model distance: nonbonded pdb=" OE1 GLU A 732 " pdb=" O THR B 641 " model vdw 0.312 2.800 nonbonded pdb=" CG ASN A 381 " pdb=" OE1 GLN B 546 " model vdw 0.380 3.100 nonbonded pdb=" O THR A 641 " pdb=" OE1 GLU B 732 " model vdw 0.707 2.800 nonbonded pdb=" NE2 GLN A 546 " pdb=" ND2 ASN B 381 " model vdw 0.898 3.100 nonbonded pdb=" OE1 GLU A 732 " pdb=" C THR B 641 " model vdw 1.055 3.100 ... (remaining 114192 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 86 or resid 88 through 167 or resid 169 through \ 181 or resid 183 through 309 or resid 311 through 1048 or resid 1101 through 110 \ 9)) selection = (chain 'B' and (resid 3 through 86 or resid 88 through 167 or resid 169 through \ 181 or resid 183 through 309 or resid 311 through 1040 or (resid 1041 and (name \ N or name CA or name C or name CB or name CG or name CD1 or name CD2 or name CE1 \ or name CE2 or name CZ or name OH )) or resid 1042 through 1043 or (resid 1044 \ and (name N or name CA or name C or name CB or name CG or name OD1 or name OD2)) \ or resid 1045 through 1048 or resid 1101 through 1109)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.20 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.490 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 53.530 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.030 1.558 17044 Z= 2.021 Angle : 2.341 58.209 23153 Z= 1.420 Chirality : 0.122 1.139 2484 Planarity : 0.014 0.274 2997 Dihedral : 16.930 87.687 6337 Min Nonbonded Distance : 0.312 Molprobity Statistics. All-atom Clashscore : 28.72 Ramachandran Plot: Outliers : 1.65 % Allowed : 6.03 % Favored : 92.32 % Rotamer: Outliers : 6.80 % Allowed : 6.68 % Favored : 86.52 % Cbeta Deviations : 1.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.16), residues: 2082 helix: -1.76 (0.13), residues: 944 sheet: -0.76 (0.30), residues: 277 loop : -1.54 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.087 0.012 TRP B 96 HIS 0.030 0.007 HIS A 92 PHE 0.054 0.010 PHE A 107 TYR 0.047 0.010 TYR B 694 ARG 0.038 0.003 ARG B 398 Details of bonding type rmsd hydrogen bonds : bond 0.18694 ( 800) hydrogen bonds : angle 8.05440 ( 2263) covalent geometry : bond 0.02871 (17037) covalent geometry : angle 2.34074 (23153) Misc. bond : bond 0.46388 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 246 time to evaluate : 1.753 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: 0.3215 time to fit residues: 163.3683 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 : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 161 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 27 GLN ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 ASN A 134 ASN A 201 ASN A 236 HIS ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 ASN ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN A 645 GLN A 923 GLN ** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN B 16 ASN B 73 GLN B 134 ASN B 201 ASN B 236 HIS B 253 ASN B 283 ASN B 388 HIS B 403 GLN ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN B 699 HIS B 923 GLN B 992 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.046975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.031649 restraints weight = 341501.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.034008 restraints weight = 157147.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.035712 restraints weight = 96779.682| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17044 Z= 0.162 Angle : 0.753 24.449 23153 Z= 0.373 Chirality : 0.041 0.177 2484 Planarity : 0.007 0.192 2997 Dihedral : 8.718 89.253 2405 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 37.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.70 % Favored : 95.05 % Rotamer: Outliers : 0.23 % Allowed : 1.23 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.18), residues: 2086 helix: 0.60 (0.16), residues: 966 sheet: -0.28 (0.29), residues: 293 loop : -0.90 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 96 HIS 0.010 0.001 HIS A 478 PHE 0.015 0.002 PHE B 646 TYR 0.025 0.001 TYR A 613 ARG 0.008 0.001 ARG A 79 Details of bonding type rmsd hydrogen bonds : bond 0.04367 ( 800) hydrogen bonds : angle 5.78330 ( 2263) covalent geometry : bond 0.00351 (17037) covalent geometry : angle 0.75324 (23153) Misc. bond : bond 0.00935 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 170 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP A1044 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.9496 (mpp) cc_final: 0.9148 (mpp) REVERT: A 218 LYS cc_start: 0.9475 (mttt) cc_final: 0.9244 (mttt) REVERT: A 261 PHE cc_start: 0.9098 (m-80) cc_final: 0.8430 (m-80) REVERT: A 262 LEU cc_start: 0.9699 (mm) cc_final: 0.9495 (mm) REVERT: A 356 LEU cc_start: 0.8368 (mt) cc_final: 0.7660 (mp) REVERT: A 357 ILE cc_start: 0.9033 (mt) cc_final: 0.8719 (mm) REVERT: A 1005 MET cc_start: 0.9242 (mmp) cc_final: 0.8931 (mmm) REVERT: A 1034 GLN cc_start: 0.9475 (tp-100) cc_final: 0.8965 (tp-100) REVERT: B 20 LEU cc_start: 0.8901 (mt) cc_final: 0.8317 (tt) REVERT: B 86 LEU cc_start: 0.9573 (mt) cc_final: 0.8747 (tp) REVERT: B 118 MET cc_start: 0.9358 (mpp) cc_final: 0.8818 (mpp) REVERT: B 185 MET cc_start: 0.9094 (ttt) cc_final: 0.8819 (ttt) REVERT: B 237 MET cc_start: 0.9675 (mtm) cc_final: 0.9343 (mtp) REVERT: B 417 MET cc_start: 0.9506 (mtm) cc_final: 0.8927 (mtp) REVERT: B 960 LEU cc_start: 0.8608 (tp) cc_final: 0.8264 (mt) REVERT: B 992 GLN cc_start: 0.9323 (mt0) cc_final: 0.9001 (tp40) REVERT: B 1034 GLN cc_start: 0.9032 (mt0) cc_final: 0.8824 (mm-40) outliers start: 4 outliers final: 4 residues processed: 173 average time/residue: 0.3750 time to fit residues: 101.5073 Evaluate side-chains 127 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 123 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 48 optimal weight: 7.9990 chunk 181 optimal weight: 7.9990 chunk 180 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 74 optimal weight: 0.4980 chunk 125 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 GLN A 239 ASN ** A 310 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN A 665 ASN ** A 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN A1021 HIS B 27 GLN ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** B1021 HIS B1034 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.039128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.025912 restraints weight = 452066.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.027865 restraints weight = 190792.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.029294 restraints weight = 114484.479| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.116 17044 Z= 0.380 Angle : 1.111 36.217 23153 Z= 0.509 Chirality : 0.045 0.223 2484 Planarity : 0.008 0.168 2997 Dihedral : 8.397 80.548 2405 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 73.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.89 % Favored : 92.92 % Rotamer: Outliers : 0.12 % Allowed : 1.23 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.18), residues: 2086 helix: -0.02 (0.16), residues: 968 sheet: -0.26 (0.31), residues: 262 loop : -1.14 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP A 550 HIS 0.016 0.003 HIS A 388 PHE 0.031 0.003 PHE B 107 TYR 0.047 0.004 TYR B 305 ARG 0.008 0.001 ARG B 797 Details of bonding type rmsd hydrogen bonds : bond 0.04523 ( 800) hydrogen bonds : angle 6.07785 ( 2263) covalent geometry : bond 0.00748 (17037) covalent geometry : angle 1.11063 (23153) Misc. bond : bond 0.05182 ( 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 113 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 2.478 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: symmetry clash REVERT: A 112 MET cc_start: 0.9491 (mmp) cc_final: 0.9255 (mmp) REVERT: A 218 LYS cc_start: 0.9572 (mttt) cc_final: 0.9346 (mttt) REVERT: A 261 PHE cc_start: 0.9040 (m-80) cc_final: 0.8408 (m-80) REVERT: A 316 MET cc_start: 0.9313 (mmp) cc_final: 0.8787 (mmm) REVERT: A 356 LEU cc_start: 0.8347 (mt) cc_final: 0.7837 (mt) REVERT: A 357 ILE cc_start: 0.9118 (mt) cc_final: 0.8901 (mt) REVERT: A 482 LEU cc_start: 0.9624 (tp) cc_final: 0.9394 (tt) REVERT: A 485 LEU cc_start: 0.8733 (mt) cc_final: 0.8465 (tp) REVERT: A 1005 MET cc_start: 0.9182 (mmp) cc_final: 0.8892 (mmm) REVERT: B 20 LEU cc_start: 0.9258 (mt) cc_final: 0.8610 (tt) REVERT: B 112 MET cc_start: 0.9186 (mmp) cc_final: 0.8873 (mmm) REVERT: B 118 MET cc_start: 0.9502 (mpp) cc_final: 0.9031 (mpp) REVERT: B 237 MET cc_start: 0.9574 (mtm) cc_final: 0.9163 (mtp) REVERT: B 296 ARG cc_start: 0.9317 (ttp-110) cc_final: 0.9030 (mtm110) REVERT: B 416 MET cc_start: 0.9729 (mmm) cc_final: 0.9369 (mmm) REVERT: B 417 MET cc_start: 0.9594 (mtm) cc_final: 0.9139 (mtp) REVERT: B 821 LEU cc_start: 0.8870 (mt) cc_final: 0.8655 (mt) REVERT: B 1034 GLN cc_start: 0.9072 (mt0) cc_final: 0.8772 (mm-40) outliers start: 2 outliers final: 2 residues processed: 113 average time/residue: 0.3791 time to fit residues: 66.8809 Evaluate side-chains 84 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 2.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 43 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 chunk 37 optimal weight: 0.0970 chunk 131 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 841 GLN B 109 GLN B 841 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.040738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.027137 restraints weight = 399154.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.029210 restraints weight = 172335.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.030692 restraints weight = 104129.463| |-----------------------------------------------------------------------------| r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 17044 Z= 0.108 Angle : 0.599 20.600 23153 Z= 0.286 Chirality : 0.038 0.196 2484 Planarity : 0.006 0.169 2997 Dihedral : 7.361 73.965 2405 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 51.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.36 % Favored : 95.49 % 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 : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.19), residues: 2086 helix: 1.14 (0.16), residues: 970 sheet: -0.11 (0.31), residues: 267 loop : -0.84 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 96 HIS 0.003 0.001 HIS A 961 PHE 0.014 0.001 PHE A 158 TYR 0.017 0.001 TYR A 613 ARG 0.003 0.000 ARG A 617 Details of bonding type rmsd hydrogen bonds : bond 0.03360 ( 800) hydrogen bonds : angle 5.19717 ( 2263) covalent geometry : bond 0.00240 (17037) covalent geometry : angle 0.59883 (23153) Misc. bond : bond 0.01479 ( 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 115 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.935 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: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.9455 (mpp) cc_final: 0.9255 (mpp) REVERT: A 218 LYS cc_start: 0.9570 (mttt) cc_final: 0.9347 (mttt) REVERT: A 261 PHE cc_start: 0.9110 (m-80) cc_final: 0.8680 (m-80) REVERT: A 262 LEU cc_start: 0.9668 (mm) cc_final: 0.9462 (mm) REVERT: A 356 LEU cc_start: 0.8289 (mt) cc_final: 0.7893 (mp) REVERT: A 416 MET cc_start: 0.9581 (mmp) cc_final: 0.9040 (mmm) REVERT: A 485 LEU cc_start: 0.9181 (mt) cc_final: 0.8922 (mt) REVERT: A 900 MET cc_start: 0.8384 (mmp) cc_final: 0.7675 (mpp) REVERT: A 996 PHE cc_start: 0.8981 (t80) cc_final: 0.8776 (t80) REVERT: A 1005 MET cc_start: 0.9043 (mmp) cc_final: 0.8782 (mmm) REVERT: B 20 LEU cc_start: 0.9214 (mt) cc_final: 0.8601 (tt) REVERT: B 118 MET cc_start: 0.9465 (mpp) cc_final: 0.8851 (mpp) REVERT: B 185 MET cc_start: 0.9070 (ttm) cc_final: 0.8608 (ttp) REVERT: B 212 MET cc_start: 0.9706 (mmp) cc_final: 0.9316 (mmm) REVERT: B 237 MET cc_start: 0.9674 (mtm) cc_final: 0.9384 (mtp) REVERT: B 261 PHE cc_start: 0.9545 (m-80) cc_final: 0.8510 (m-80) REVERT: B 354 MET cc_start: 0.8540 (tpt) cc_final: 0.8301 (tpt) REVERT: B 416 MET cc_start: 0.9557 (mmm) cc_final: 0.9088 (mmm) REVERT: B 417 MET cc_start: 0.9457 (mtm) cc_final: 0.9145 (ptp) REVERT: B 712 ASN cc_start: 0.9217 (m-40) cc_final: 0.8866 (p0) REVERT: B 890 LEU cc_start: 0.9158 (mt) cc_final: 0.8698 (tp) REVERT: B 1034 GLN cc_start: 0.8991 (mt0) cc_final: 0.8748 (mm-40) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.3639 time to fit residues: 67.1168 Evaluate side-chains 92 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 182 optimal weight: 0.0370 chunk 173 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 171 optimal weight: 0.3980 chunk 53 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 134 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 overall best weight: 1.4462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 GLN A ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.040000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.026503 restraints weight = 425249.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.028539 restraints weight = 180691.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.030024 restraints weight = 108665.659| |-----------------------------------------------------------------------------| r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| r_final: 0.2726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.5452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 17044 Z= 0.136 Angle : 0.596 19.711 23153 Z= 0.278 Chirality : 0.036 0.188 2484 Planarity : 0.005 0.141 2997 Dihedral : 7.063 73.442 2405 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 57.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.24 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.19), residues: 2086 helix: 1.46 (0.17), residues: 967 sheet: -0.13 (0.32), residues: 256 loop : -0.72 (0.22), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 96 HIS 0.006 0.001 HIS B 931 PHE 0.012 0.001 PHE B 158 TYR 0.015 0.001 TYR B 829 ARG 0.015 0.001 ARG A 471 Details of bonding type rmsd hydrogen bonds : bond 0.03074 ( 800) hydrogen bonds : angle 5.04936 ( 2263) covalent geometry : bond 0.00287 (17037) covalent geometry : angle 0.59646 (23153) Misc. bond : bond 0.02403 ( 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 103 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP A1044 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.8721 (mmp) cc_final: 0.8176 (mmp) REVERT: A 118 MET cc_start: 0.9473 (mpp) cc_final: 0.9187 (mpp) REVERT: A 218 LYS cc_start: 0.9546 (mttt) cc_final: 0.9321 (mttt) REVERT: A 261 PHE cc_start: 0.9135 (m-80) cc_final: 0.8767 (m-80) REVERT: A 357 ILE cc_start: 0.9095 (mt) cc_final: 0.8882 (mt) REVERT: A 416 MET cc_start: 0.9601 (mmp) cc_final: 0.9069 (mmm) REVERT: A 485 LEU cc_start: 0.8807 (mt) cc_final: 0.8514 (mt) REVERT: A 900 MET cc_start: 0.8586 (mmp) cc_final: 0.8324 (mmp) REVERT: A 1005 MET cc_start: 0.9033 (mmp) cc_final: 0.8783 (mmm) REVERT: B 20 LEU cc_start: 0.9272 (mt) cc_final: 0.8703 (tp) REVERT: B 112 MET cc_start: 0.9575 (mmp) cc_final: 0.9150 (mmm) REVERT: B 118 MET cc_start: 0.9454 (mpp) cc_final: 0.8884 (mpp) REVERT: B 185 MET cc_start: 0.9032 (ttm) cc_final: 0.8583 (ttp) REVERT: B 212 MET cc_start: 0.9690 (mmp) cc_final: 0.9244 (mmm) REVERT: B 237 MET cc_start: 0.9675 (mtm) cc_final: 0.9409 (mtp) REVERT: B 261 PHE cc_start: 0.9561 (m-80) cc_final: 0.8628 (m-80) REVERT: B 354 MET cc_start: 0.8595 (tpt) cc_final: 0.8365 (tpt) REVERT: B 416 MET cc_start: 0.9601 (mmm) cc_final: 0.9087 (mmm) REVERT: B 712 ASN cc_start: 0.9228 (m-40) cc_final: 0.8877 (p0) REVERT: B 811 GLU cc_start: 0.9394 (mt-10) cc_final: 0.9041 (mp0) REVERT: B 821 LEU cc_start: 0.8957 (mt) cc_final: 0.8725 (mt) REVERT: B 890 LEU cc_start: 0.8850 (mt) cc_final: 0.8515 (tp) REVERT: B 1034 GLN cc_start: 0.9027 (mt0) cc_final: 0.8779 (mm-40) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.2806 time to fit residues: 47.4718 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 : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 200 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 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 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN B 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.039611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.026025 restraints weight = 476863.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.028109 restraints weight = 187229.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.029626 restraints weight = 109396.493| |-----------------------------------------------------------------------------| r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| r_final: 0.2716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.5724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 17044 Z= 0.124 Angle : 0.541 14.574 23153 Z= 0.264 Chirality : 0.036 0.134 2484 Planarity : 0.004 0.049 2997 Dihedral : 6.971 72.900 2405 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 57.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.90 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.19), residues: 2086 helix: 1.67 (0.17), residues: 962 sheet: -0.21 (0.32), residues: 257 loop : -0.66 (0.23), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 96 HIS 0.003 0.001 HIS A 266 PHE 0.019 0.001 PHE B 82 TYR 0.013 0.001 TYR B 829 ARG 0.008 0.000 ARG A 471 Details of bonding type rmsd hydrogen bonds : bond 0.02978 ( 800) hydrogen bonds : angle 4.91374 ( 2263) covalent geometry : bond 0.00268 (17037) covalent geometry : angle 0.54056 (23153) Misc. bond : bond 0.01875 ( 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 98 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 2.244 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: symmetry clash REVERT: A 118 MET cc_start: 0.9486 (mpp) cc_final: 0.9192 (mpp) REVERT: A 218 LYS cc_start: 0.9536 (mttt) cc_final: 0.9298 (mttt) REVERT: A 261 PHE cc_start: 0.9108 (m-80) cc_final: 0.8717 (m-80) REVERT: A 316 MET cc_start: 0.8970 (mpp) cc_final: 0.8381 (mpp) REVERT: A 357 ILE cc_start: 0.8986 (mt) cc_final: 0.8641 (mm) REVERT: A 416 MET cc_start: 0.9609 (mmp) cc_final: 0.9196 (mmm) REVERT: A 485 LEU cc_start: 0.8898 (mt) cc_final: 0.8679 (mt) REVERT: A 900 MET cc_start: 0.8599 (mmp) cc_final: 0.8243 (mmp) REVERT: A 979 MET cc_start: 0.9443 (mmp) cc_final: 0.9190 (mmm) REVERT: A 996 PHE cc_start: 0.8866 (t80) cc_final: 0.8658 (t80) REVERT: A 1005 MET cc_start: 0.9054 (mmp) cc_final: 0.8817 (mmm) REVERT: B 20 LEU cc_start: 0.9012 (mt) cc_final: 0.8347 (tp) REVERT: B 112 MET cc_start: 0.9572 (mmp) cc_final: 0.9151 (mmm) REVERT: B 118 MET cc_start: 0.9454 (mpp) cc_final: 0.8771 (mpp) REVERT: B 185 MET cc_start: 0.9110 (ttm) cc_final: 0.8674 (ttp) REVERT: B 212 MET cc_start: 0.9706 (mmp) cc_final: 0.9371 (mmm) REVERT: B 237 MET cc_start: 0.9673 (mtm) cc_final: 0.9415 (mtp) REVERT: B 354 MET cc_start: 0.8602 (tpt) cc_final: 0.8388 (tpt) REVERT: B 416 MET cc_start: 0.9644 (mmm) cc_final: 0.9165 (mmm) REVERT: B 417 MET cc_start: 0.9495 (mtm) cc_final: 0.9196 (ptp) REVERT: B 712 ASN cc_start: 0.9244 (m-40) cc_final: 0.8908 (p0) REVERT: B 811 GLU cc_start: 0.9388 (mt-10) cc_final: 0.9026 (mp0) REVERT: B 821 LEU cc_start: 0.8956 (mt) cc_final: 0.8733 (mt) REVERT: B 890 LEU cc_start: 0.8866 (mt) cc_final: 0.8436 (tp) REVERT: B 1034 GLN cc_start: 0.9042 (mt0) cc_final: 0.8790 (mm-40) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.3335 time to fit residues: 55.1072 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 : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 74 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 182 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 199 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 102 optimal weight: 0.0770 chunk 142 optimal weight: 8.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.037760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.024903 restraints weight = 498477.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.026871 restraints weight = 200152.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.028263 restraints weight = 117638.469| |-----------------------------------------------------------------------------| r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.6380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 17044 Z= 0.255 Angle : 0.808 28.073 23153 Z= 0.367 Chirality : 0.039 0.159 2484 Planarity : 0.005 0.064 2997 Dihedral : 7.432 83.373 2405 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 74.80 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.60 % Favored : 93.26 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.18), residues: 2086 helix: 0.76 (0.16), residues: 968 sheet: -0.45 (0.32), residues: 255 loop : -1.00 (0.22), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 96 HIS 0.009 0.002 HIS A 931 PHE 0.021 0.002 PHE B 107 TYR 0.028 0.002 TYR B 829 ARG 0.005 0.001 ARG B 679 Details of bonding type rmsd hydrogen bonds : bond 0.03420 ( 800) hydrogen bonds : angle 5.39453 ( 2263) covalent geometry : bond 0.00516 (17037) covalent geometry : angle 0.80841 (23153) Misc. bond : bond 0.04128 ( 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 95 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 6.759 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: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.9439 (mpp) cc_final: 0.9090 (mpp) REVERT: A 261 PHE cc_start: 0.9103 (m-80) cc_final: 0.8753 (m-80) REVERT: A 357 ILE cc_start: 0.9092 (mt) cc_final: 0.8859 (mm) REVERT: A 416 MET cc_start: 0.9630 (mmp) cc_final: 0.9244 (mmm) REVERT: A 781 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8855 (mt-10) REVERT: A 967 MET cc_start: 0.7479 (mmm) cc_final: 0.6524 (mmm) REVERT: A 979 MET cc_start: 0.9492 (mmp) cc_final: 0.9162 (mmm) REVERT: A 996 PHE cc_start: 0.8746 (t80) cc_final: 0.8504 (t80) REVERT: B 112 MET cc_start: 0.9574 (mmp) cc_final: 0.9119 (mmm) REVERT: B 118 MET cc_start: 0.9467 (mpp) cc_final: 0.8782 (mpp) REVERT: B 185 MET cc_start: 0.9101 (ttm) cc_final: 0.8716 (ttp) REVERT: B 237 MET cc_start: 0.9572 (mtm) cc_final: 0.9254 (mtp) REVERT: B 416 MET cc_start: 0.9641 (mmm) cc_final: 0.9203 (mmm) REVERT: B 821 LEU cc_start: 0.9119 (mt) cc_final: 0.8885 (mt) REVERT: B 1034 GLN cc_start: 0.9121 (mt0) cc_final: 0.8757 (mm-40) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.4542 time to fit residues: 70.0616 Evaluate side-chains 75 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 65 optimal weight: 6.9990 chunk 118 optimal weight: 0.5980 chunk 185 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 8 optimal weight: 0.0870 chunk 14 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 160 optimal weight: 0.9990 overall best weight: 0.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1022 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.039213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.025886 restraints weight = 464400.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.027925 restraints weight = 186889.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.029421 restraints weight = 109806.905| |-----------------------------------------------------------------------------| r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.2714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.6304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 17044 Z= 0.091 Angle : 0.491 9.651 23153 Z= 0.247 Chirality : 0.036 0.160 2484 Planarity : 0.004 0.049 2997 Dihedral : 6.951 78.479 2405 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 57.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.32 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.19), residues: 2086 helix: 1.63 (0.17), residues: 962 sheet: -0.33 (0.32), residues: 259 loop : -0.72 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 96 HIS 0.003 0.001 HIS B 995 PHE 0.015 0.001 PHE B 82 TYR 0.013 0.001 TYR A 613 ARG 0.004 0.000 ARG A 471 Details of bonding type rmsd hydrogen bonds : bond 0.02886 ( 800) hydrogen bonds : angle 4.85413 ( 2263) covalent geometry : bond 0.00218 (17037) covalent geometry : angle 0.49137 (23153) Misc. bond : bond 0.00970 ( 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 95 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.966 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 118 MET cc_start: 0.9482 (mpp) cc_final: 0.9197 (mpp) REVERT: A 261 PHE cc_start: 0.9087 (m-80) cc_final: 0.8783 (m-80) REVERT: A 357 ILE cc_start: 0.9005 (mt) cc_final: 0.8662 (mm) REVERT: A 416 MET cc_start: 0.9594 (mmp) cc_final: 0.9290 (mmm) REVERT: A 781 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8685 (mp0) REVERT: A 900 MET cc_start: 0.8694 (mmp) cc_final: 0.8076 (mpp) REVERT: A 979 MET cc_start: 0.9393 (mmp) cc_final: 0.8984 (mmm) REVERT: A 996 PHE cc_start: 0.8537 (t80) cc_final: 0.8292 (t80) REVERT: B 112 MET cc_start: 0.9550 (mmp) cc_final: 0.9162 (mmm) REVERT: B 118 MET cc_start: 0.9508 (mpp) cc_final: 0.8836 (mpp) REVERT: B 185 MET cc_start: 0.8997 (ttm) cc_final: 0.8471 (ttp) REVERT: B 237 MET cc_start: 0.9611 (mtm) cc_final: 0.9373 (mtp) REVERT: B 416 MET cc_start: 0.9647 (mmm) cc_final: 0.9183 (mmm) REVERT: B 712 ASN cc_start: 0.9165 (m-40) cc_final: 0.8777 (p0) REVERT: B 811 GLU cc_start: 0.9332 (mt-10) cc_final: 0.9020 (mp0) REVERT: B 967 MET cc_start: 0.7613 (mmp) cc_final: 0.7251 (mmp) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2907 time to fit residues: 44.4186 Evaluate side-chains 82 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 107 optimal weight: 0.9980 chunk 176 optimal weight: 0.2980 chunk 128 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 166 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 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 = 0.3052 r_free = 0.3052 target = 0.039171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.025903 restraints weight = 466649.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.027922 restraints weight = 186205.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.029420 restraints weight = 110041.729| |-----------------------------------------------------------------------------| r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.2711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.6399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 17044 Z= 0.092 Angle : 0.489 11.499 23153 Z= 0.240 Chirality : 0.036 0.151 2484 Planarity : 0.004 0.050 2997 Dihedral : 6.777 75.820 2405 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 57.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.75 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.19), residues: 2086 helix: 1.95 (0.17), residues: 964 sheet: -0.29 (0.32), residues: 257 loop : -0.61 (0.23), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 96 HIS 0.002 0.001 HIS A 266 PHE 0.012 0.001 PHE B 82 TYR 0.011 0.001 TYR A 613 ARG 0.004 0.000 ARG A 471 Details of bonding type rmsd hydrogen bonds : bond 0.02709 ( 800) hydrogen bonds : angle 4.73692 ( 2263) covalent geometry : bond 0.00213 (17037) covalent geometry : angle 0.48944 (23153) Misc. bond : bond 0.01247 ( 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 95 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.821 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: symmetry clash REVERT: A 118 MET cc_start: 0.9466 (mpp) cc_final: 0.8957 (mtm) REVERT: A 261 PHE cc_start: 0.9022 (m-80) cc_final: 0.8703 (m-80) REVERT: A 357 ILE cc_start: 0.8958 (mt) cc_final: 0.8694 (mm) REVERT: A 416 MET cc_start: 0.9583 (mmp) cc_final: 0.9292 (mmm) REVERT: A 781 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8671 (mp0) REVERT: A 900 MET cc_start: 0.8805 (mmp) cc_final: 0.8212 (mpp) REVERT: A 979 MET cc_start: 0.9357 (mmp) cc_final: 0.8956 (mmm) REVERT: A 996 PHE cc_start: 0.8511 (t80) cc_final: 0.8254 (t80) REVERT: B 112 MET cc_start: 0.9533 (mmp) cc_final: 0.9146 (mmm) REVERT: B 118 MET cc_start: 0.9482 (mpp) cc_final: 0.8747 (mpp) REVERT: B 185 MET cc_start: 0.8954 (ttm) cc_final: 0.8503 (ttp) REVERT: B 237 MET cc_start: 0.9615 (mtm) cc_final: 0.9363 (mtp) REVERT: B 416 MET cc_start: 0.9628 (mmm) cc_final: 0.9203 (mmp) REVERT: B 437 LEU cc_start: 0.9079 (mp) cc_final: 0.8879 (mp) REVERT: B 712 ASN cc_start: 0.9255 (m-40) cc_final: 0.8923 (p0) REVERT: B 811 GLU cc_start: 0.9323 (mt-10) cc_final: 0.9014 (mp0) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.3037 time to fit residues: 46.6762 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 : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 154 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 110 optimal weight: 0.0970 chunk 48 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 194 optimal weight: 0.0010 chunk 20 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 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 = 0.3059 r_free = 0.3059 target = 0.039366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.026252 restraints weight = 402235.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.028241 restraints weight = 171781.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.029705 restraints weight = 103248.715| |-----------------------------------------------------------------------------| r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.6460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 17044 Z= 0.079 Angle : 0.458 7.061 23153 Z= 0.231 Chirality : 0.036 0.161 2484 Planarity : 0.004 0.047 2997 Dihedral : 6.609 72.691 2405 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 54.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.19), residues: 2086 helix: 2.16 (0.17), residues: 964 sheet: -0.17 (0.32), residues: 257 loop : -0.55 (0.23), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 96 HIS 0.002 0.000 HIS A 266 PHE 0.013 0.001 PHE B 82 TYR 0.011 0.001 TYR A 613 ARG 0.005 0.000 ARG A 471 Details of bonding type rmsd hydrogen bonds : bond 0.02625 ( 800) hydrogen bonds : angle 4.59705 ( 2263) covalent geometry : bond 0.00190 (17037) covalent geometry : angle 0.45835 (23153) Misc. bond : bond 0.00891 ( 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 101 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.811 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: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.9462 (mpp) cc_final: 0.8952 (mtm) REVERT: A 261 PHE cc_start: 0.9031 (m-80) cc_final: 0.8682 (m-80) REVERT: A 357 ILE cc_start: 0.8965 (mt) cc_final: 0.8698 (mm) REVERT: A 416 MET cc_start: 0.9575 (mmp) cc_final: 0.9282 (mmm) REVERT: A 781 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8636 (mp0) REVERT: A 979 MET cc_start: 0.9313 (mmp) cc_final: 0.8914 (mmm) REVERT: B 112 MET cc_start: 0.9541 (mmp) cc_final: 0.9154 (mmm) REVERT: B 118 MET cc_start: 0.9461 (mpp) cc_final: 0.8707 (mpp) REVERT: B 237 MET cc_start: 0.9670 (mtm) cc_final: 0.9327 (mtp) REVERT: B 416 MET cc_start: 0.9675 (mmm) cc_final: 0.9239 (mmm) REVERT: B 712 ASN cc_start: 0.9242 (m-40) cc_final: 0.8912 (p0) REVERT: B 811 GLU cc_start: 0.9351 (mt-10) cc_final: 0.9010 (mp0) REVERT: B 967 MET cc_start: 0.7886 (mmp) cc_final: 0.7677 (mmp) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2764 time to fit residues: 45.1667 Evaluate side-chains 85 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 101 optimal weight: 0.1980 chunk 157 optimal weight: 9.9990 chunk 184 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 137 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 62 optimal weight: 0.0010 chunk 77 optimal weight: 0.6980 chunk 151 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.039348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.025855 restraints weight = 497841.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.027934 restraints weight = 188636.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.029478 restraints weight = 109423.743| |-----------------------------------------------------------------------------| r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.2724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.6536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 17044 Z= 0.077 Angle : 0.453 7.850 23153 Z= 0.227 Chirality : 0.036 0.149 2484 Planarity : 0.004 0.047 2997 Dihedral : 6.427 69.526 2405 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 54.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.19), residues: 2086 helix: 2.29 (0.17), residues: 962 sheet: -0.12 (0.32), residues: 257 loop : -0.49 (0.23), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 96 HIS 0.002 0.000 HIS A 977 PHE 0.012 0.001 PHE B 82 TYR 0.017 0.001 TYR A 613 ARG 0.004 0.000 ARG A 471 Details of bonding type rmsd hydrogen bonds : bond 0.02536 ( 800) hydrogen bonds : angle 4.52129 ( 2263) covalent geometry : bond 0.00187 (17037) covalent geometry : angle 0.45347 (23153) Misc. bond : bond 0.00929 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6086.82 seconds wall clock time: 111 minutes 57.92 seconds (6717.92 seconds total)