Starting phenix.real_space_refine on Sat Sep 28 00:11:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmg_27536/09_2024/8dmg_27536.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmg_27536/09_2024/8dmg_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmg_27536/09_2024/8dmg_27536.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmg_27536/09_2024/8dmg_27536.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmg_27536/09_2024/8dmg_27536.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmg_27536/09_2024/8dmg_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-5461/modules/chem_data/mon_lib" Total number of atoms: 16844 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8236 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1034, 8200 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 54, 'TRANS': 979} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 13, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 59 Conformer: "B" Number of residues, atoms: 1034, 8200 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 54, 'TRANS': 979} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 13, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 59 bond proxies already assigned to first conformer: 8341 Chain: "B" Number of atoms: 8238 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1034, 8202 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 54, 'TRANS': 979} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 13, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 59 Conformer: "B" Number of residues, atoms: 1034, 8202 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 54, 'TRANS': 979} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 13, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 59 bond proxies already assigned to first conformer: 8342 Chain: "A" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 185 Unusual residues: {'1C6': 1, 'FAD': 1, 'FMN': 1, 'HEM': 1, 'PG4': 2, 'SO4': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "B" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 185 Unusual residues: {'1C6': 1, 'FAD': 1, 'FMN': 1, 'HEM': 1, 'PG4': 2, 'SO4': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3247 SG CYS A 400 53.201 45.582 102.548 1.00 11.59 S ATOM 11483 SG CYS B 400 38.400 45.550 47.133 1.00 11.59 S Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N APHE A 87 " occ=0.20 ... (20 atoms not shown) pdb=" CZ BPHE A 87 " occ=0.20 residue: pdb=" N AASP A 168 " occ=0.20 ... (14 atoms not shown) pdb=" OD2BASP A 168 " occ=0.20 residue: pdb=" N AASP A 182 " occ=0.20 ... (14 atoms not shown) pdb=" OD2BASP A 182 " occ=0.20 residue: pdb=" N AGLN A 310 " occ=0.20 ... (16 atoms not shown) pdb=" NE2BGLN A 310 " occ=0.20 residue: pdb=" N APHE B 87 " occ=0.20 ... (20 atoms not shown) pdb=" CZ BPHE B 87 " occ=0.20 residue: pdb=" N AASP B 168 " occ=0.20 ... (14 atoms not shown) pdb=" OD2BASP B 168 " occ=0.20 residue: pdb=" N AASP B 182 " occ=0.20 ... (14 atoms not shown) pdb=" OD2BASP B 182 " occ=0.20 residue: pdb=" N AGLN B 310 " occ=0.20 ... (16 atoms not shown) pdb=" NE2BGLN B 310 " occ=0.20 Time building chain proxies: 17.75, per 1000 atoms: 1.05 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.67 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: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 Processing helix chain 'A' and resid 16 through 21 Processing helix chain 'A' and resid 24 through 37 Processing helix chain 'A' and resid 54 through 62 removed outlier: 4.256A pdb=" N GLU A 60 " --> pdb=" O ARG A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 83 removed outlier: 3.899A pdb=" N ASP A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N PHE A 81 " --> pdb=" O PHE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 4.065A pdb=" N LYS A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 107 No H-bonds generated for 'chain 'A' and resid 105 through 107' Processing helix chain 'A' and resid 108 through 132 removed outlier: 4.760A pdb=" N ALA A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N MET A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 159 Processing helix chain 'A' and resid 163 through 167 Processing helix chain 'A' and resid 171 through 188 removed outlier: 3.650A pdb=" N LEU A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 198 through 226 Processing helix chain 'A' and resid 232 through 240 Processing helix chain 'A' and resid 250 through 265 Processing helix chain 'A' and resid 266 through 283 Processing helix chain 'A' and resid 283 through 298 Processing helix chain 'A' and resid 304 through 311 Processing helix chain 'A' and resid 311 through 325 Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 375 through 380 Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 402 through 420 Processing helix chain 'A' and resid 491 through 506 removed outlier: 3.553A pdb=" N SER A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 519 No H-bonds generated for 'chain 'A' and resid 517 through 519' Processing helix chain 'A' and resid 544 through 553 Processing helix chain 'A' and resid 574 through 578 removed outlier: 3.783A pdb=" N TYR A 578 " --> pdb=" O ALA A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 591 Processing helix chain 'A' and resid 608 through 628 Processing helix chain 'A' and resid 653 through 659 Processing helix chain 'A' and resid 707 through 719 Processing helix chain 'A' and resid 746 through 750 Processing helix chain 'A' and resid 751 through 753 No H-bonds generated for 'chain 'A' and resid 751 through 753' Processing helix chain 'A' and resid 760 through 770 Processing helix chain 'A' and resid 773 through 783 Processing helix chain 'A' and resid 785 through 793 Processing helix chain 'A' and resid 799 through 807 Processing helix chain 'A' and resid 813 through 820 removed outlier: 3.611A pdb=" N ALA A 819 " --> pdb=" O SER A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 871 Processing helix chain 'A' and resid 903 through 905 No H-bonds generated for 'chain 'A' and resid 903 through 905' Processing helix chain 'A' and resid 906 through 923 removed outlier: 4.702A pdb=" N PHE A 910 " --> pdb=" O GLY A 906 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 912 " --> pdb=" O ALA A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 955 Processing helix chain 'A' and resid 974 through 982 Processing helix chain 'A' and resid 982 through 992 Processing helix chain 'A' and resid 1004 through 1021 Processing helix chain 'A' and resid 1024 through 1036 Processing helix chain 'B' and resid 11 through 15 Processing helix chain 'B' and resid 16 through 21 Processing helix chain 'B' and resid 24 through 37 Processing helix chain 'B' and resid 54 through 62 removed outlier: 4.256A pdb=" N GLU B 60 " --> pdb=" O ARG B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 83 removed outlier: 3.899A pdb=" N ASP B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N PHE B 81 " --> pdb=" O PHE B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 4.065A pdb=" N LYS B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 107 No H-bonds generated for 'chain 'B' and resid 105 through 107' Processing helix chain 'B' and resid 108 through 132 removed outlier: 4.760A pdb=" N ALA B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N MET B 118 " --> pdb=" O GLY B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 171 through 188 removed outlier: 3.650A pdb=" N LEU B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 198 through 226 Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'B' and resid 250 through 265 Processing helix chain 'B' and resid 266 through 283 Processing helix chain 'B' and resid 283 through 298 Processing helix chain 'B' and resid 304 through 311 Processing helix chain 'B' and resid 311 through 325 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 363 through 368 Processing helix chain 'B' and resid 375 through 380 Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 395 through 399 Processing helix chain 'B' and resid 402 through 420 Processing helix chain 'B' and resid 491 through 506 removed outlier: 3.554A pdb=" N SER B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 519 No H-bonds generated for 'chain 'B' and resid 517 through 519' Processing helix chain 'B' and resid 544 through 553 Processing helix chain 'B' and resid 574 through 578 removed outlier: 3.784A pdb=" N TYR B 578 " --> pdb=" O ALA B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 591 Processing helix chain 'B' and resid 608 through 628 Processing helix chain 'B' and resid 634 through 638 removed outlier: 3.526A pdb=" N ASP B 637 " --> pdb=" O ASN B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 659 Processing helix chain 'B' and resid 707 through 719 Processing helix chain 'B' and resid 746 through 750 Processing helix chain 'B' and resid 751 through 753 No H-bonds generated for 'chain 'B' and resid 751 through 753' Processing helix chain 'B' and resid 760 through 770 Processing helix chain 'B' and resid 773 through 783 Processing helix chain 'B' and resid 785 through 793 Processing helix chain 'B' and resid 799 through 807 Processing helix chain 'B' and resid 813 through 820 removed outlier: 3.611A pdb=" N ALA B 819 " --> pdb=" O SER B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 871 Processing helix chain 'B' and resid 903 through 905 No H-bonds generated for 'chain 'B' and resid 903 through 905' Processing helix chain 'B' and resid 906 through 923 removed outlier: 4.703A pdb=" N PHE B 910 " --> pdb=" O GLY B 906 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY B 912 " --> pdb=" O ALA B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 955 Processing helix chain 'B' and resid 974 through 982 Processing helix chain 'B' and resid 982 through 992 Processing helix chain 'B' and resid 1004 through 1021 Processing helix chain 'B' and resid 1024 through 1036 Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 44 removed outlier: 4.840A pdb=" N GLU A 352 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N SER A 332 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 139 through 140 Processing sheet with id=AA3, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AA4, first strand: chain 'A' and resid 433 through 435 Processing sheet with id=AA5, first strand: chain 'A' and resid 512 through 515 removed outlier: 6.476A pdb=" N LEU A 483 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL A 532 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU A 485 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL A 529 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N PHE A 567 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE A 531 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N CYS A 569 " --> pdb=" O ILE A 531 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR A 533 " --> pdb=" O CYS A 569 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP A 599 " --> pdb=" O TYR A 564 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N VAL A 566 " --> pdb=" O ASP A 599 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 827 through 830 removed outlier: 4.840A pdb=" N THR A 878 " --> pdb=" O ILE A 703 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN A 665 " --> pdb=" O GLU A 687 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU A 685 " --> pdb=" O VAL A 667 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER A 669 " --> pdb=" O HIS A 683 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N HIS A 683 " --> pdb=" O SER A 669 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLU A 671 " --> pdb=" O THR A 681 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR A 681 " --> pdb=" O GLU A 671 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 743 through 745 removed outlier: 3.586A pdb=" N LEU A 728 " --> pdb=" O GLN B 645 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN B 645 " --> pdb=" O LEU A 728 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 850 through 852 Processing sheet with id=AA9, first strand: chain 'A' and resid 959 through 964 removed outlier: 6.368A pdb=" N ALA A 930 " --> pdb=" O THR A 959 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N HIS A 961 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU A 932 " --> pdb=" O HIS A 961 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ALA A 963 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE A 934 " --> pdb=" O ALA A 963 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU A 898 " --> pdb=" O HIS A 931 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N TYR A 933 " --> pdb=" O LEU A 898 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N MET A 900 " --> pdb=" O TYR A 933 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N GLY A 935 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 39 through 44 removed outlier: 4.840A pdb=" N GLU B 352 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N SER B 332 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 139 through 140 Processing sheet with id=AB3, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AB4, first strand: chain 'B' and resid 433 through 435 Processing sheet with id=AB5, first strand: chain 'B' and resid 512 through 515 removed outlier: 6.475A pdb=" N LEU B 483 " --> pdb=" O LEU B 530 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL B 532 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU B 485 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL B 529 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N PHE B 567 " --> pdb=" O VAL B 529 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE B 531 " --> pdb=" O PHE B 567 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N CYS B 569 " --> pdb=" O ILE B 531 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR B 533 " --> pdb=" O CYS B 569 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP B 599 " --> pdb=" O TYR B 564 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N VAL B 566 " --> pdb=" O ASP B 599 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 827 through 830 removed outlier: 4.841A pdb=" N THR B 878 " --> pdb=" O ILE B 703 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASN B 665 " --> pdb=" O GLU B 687 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLU B 685 " --> pdb=" O VAL B 667 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER B 669 " --> pdb=" O HIS B 683 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N HIS B 683 " --> pdb=" O SER B 669 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLU B 671 " --> pdb=" O THR B 681 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR B 681 " --> pdb=" O GLU B 671 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 725 through 727 Processing sheet with id=AB8, first strand: chain 'B' and resid 850 through 852 Processing sheet with id=AB9, first strand: chain 'B' and resid 959 through 964 removed outlier: 6.367A pdb=" N ALA B 930 " --> pdb=" O THR B 959 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N HIS B 961 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU B 932 " --> pdb=" O HIS B 961 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ALA B 963 " --> pdb=" O LEU B 932 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE B 934 " --> pdb=" O ALA B 963 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU B 898 " --> pdb=" O HIS B 931 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N TYR B 933 " --> pdb=" O LEU B 898 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET B 900 " --> pdb=" O TYR B 933 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N GLY B 935 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE B 899 " --> pdb=" O TYR B 997 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N CYS B 999 " --> pdb=" O ILE B 899 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL B 901 " --> pdb=" O CYS B 999 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ASP B1001 " --> pdb=" O VAL B 901 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N PHE B 996 " --> pdb=" O ALA B1042 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ASP B1044 " --> pdb=" O PHE B 996 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE B 998 " --> pdb=" O ASP B1044 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N TRP B1046 " --> pdb=" O ILE B 998 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLY B1000 " --> pdb=" O TRP B1046 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 800 hydrogen bonds defined for protein. 2263 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.22 Time building geometry restraints manager: 5.23 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 - 20.26: 9288 20.26 - 40.52: 731 40.52 - 60.79: 231 60.79 - 81.05: 44 81.05 - 101.31: 13 Dihedral angle restraints: 10307 sinusoidal: 4242 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 10304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.228: 2370 0.228 - 0.456: 99 0.456 - 0.683: 10 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: 3023 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 " 0.007 2.00e-02 2.50e+03 6.83e-02 2.21e+02 pdb=" C10 FMN B1103 " 0.107 2.00e-02 2.50e+03 pdb=" C2 FMN B1103 " -0.001 2.00e-02 2.50e+03 pdb=" C4 FMN B1103 " -0.055 2.00e-02 2.50e+03 pdb=" C4A FMN B1103 " 0.108 2.00e-02 2.50e+03 pdb=" C5A FMN B1103 " 0.007 2.00e-02 2.50e+03 pdb=" C6 FMN B1103 " 0.053 2.00e-02 2.50e+03 pdb=" C7 FMN B1103 " 0.020 2.00e-02 2.50e+03 pdb=" C7M FMN B1103 " 0.052 2.00e-02 2.50e+03 pdb=" C8 FMN B1103 " -0.053 2.00e-02 2.50e+03 pdb=" C8M FMN B1103 " -0.101 2.00e-02 2.50e+03 pdb=" C9 FMN B1103 " -0.053 2.00e-02 2.50e+03 pdb=" C9A FMN B1103 " -0.028 2.00e-02 2.50e+03 pdb=" N1 FMN B1103 " 0.097 2.00e-02 2.50e+03 pdb=" N10 FMN B1103 " -0.007 2.00e-02 2.50e+03 pdb=" N3 FMN B1103 " -0.086 2.00e-02 2.50e+03 pdb=" N5 FMN B1103 " 0.086 2.00e-02 2.50e+03 pdb=" O2 FMN B1103 " -0.031 2.00e-02 2.50e+03 pdb=" O4 FMN B1103 " -0.121 2.00e-02 2.50e+03 ... (remaining 3020 not shown) Histogram of nonbonded interaction distances: 0.31 - 1.17: 7 1.17 - 2.03: 81 2.03 - 2.88: 7678 2.88 - 3.74: 36578 3.74 - 4.60: 69867 Warning: very small nonbonded interaction distances. Nonbonded interactions: 114211 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=" NZ LYS A 472 " pdb=" CB ASP B 231 " model vdw 0.819 3.250 nonbonded pdb=" NE2 GLN A 546 " pdb=" ND2 ASN B 381 " model vdw 0.898 3.100 ... (remaining 114206 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.240 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: 0.470 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 50.190 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.090 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.290 ------------------------------------------------------------------------------- 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 : 0.029 1.558 17037 Z= 1.792 Angle : 2.330 58.209 23153 Z= 1.418 Chirality : 0.122 1.139 2484 Planarity : 0.014 0.274 2995 Dihedral : 16.954 101.311 6333 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 *********************** 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 fitting. rotamer outliers: 116 poor density : 246 time to evaluate : 2.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP A1044 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 LEU cc_start: 0.7743 (tp) cc_final: 0.7529 (tp) REVERT: A 177 MET cc_start: 0.7413 (ttp) cc_final: 0.6763 (tmm) REVERT: A 272 LEU cc_start: 0.7757 (tp) cc_final: 0.7486 (tt) REVERT: A 314 VAL cc_start: 0.8500 (t) cc_final: 0.7883 (t) REVERT: A 357 ILE cc_start: 0.7172 (mt) cc_final: 0.6781 (mm) REVERT: A 411 THR cc_start: 0.8551 (m) cc_final: 0.7866 (t) REVERT: A 644 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6438 (pt) REVERT: A 913 PHE cc_start: 0.6518 (m-10) cc_final: 0.5984 (m-10) REVERT: A 1016 SER cc_start: 0.7616 (m) cc_final: 0.6909 (t) REVERT: B 62 CYS cc_start: 0.2999 (m) cc_final: 0.2569 (m) REVERT: B 216 VAL cc_start: 0.8727 (t) cc_final: 0.8400 (t) REVERT: B 471 ARG cc_start: 0.6184 (OUTLIER) cc_final: 0.5465 (ptt180) REVERT: B 629 ASN cc_start: 0.7530 (OUTLIER) cc_final: 0.6982 (p0) REVERT: B 659 HIS cc_start: 0.6522 (m-70) cc_final: 0.6051 (m-70) REVERT: B 793 VAL cc_start: 0.5659 (t) cc_final: 0.5043 (t) REVERT: B 847 SER cc_start: 0.6713 (OUTLIER) cc_final: 0.6101 (p) outliers start: 116 outliers final: 33 residues processed: 343 average time/residue: 0.3280 time to fit residues: 164.8434 Evaluate side-chains 180 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 143 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 161 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 27 GLN A 73 GLN 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 319 ASN B 388 HIS B 403 GLN ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 699 HIS B 923 GLN B 992 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17037 Z= 0.227 Angle : 0.753 24.303 23153 Z= 0.376 Chirality : 0.041 0.217 2484 Planarity : 0.007 0.193 2995 Dihedral : 8.666 89.538 2401 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 37.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.61 % Favored : 95.15 % Rotamer: Outliers : 0.23 % Allowed : 1.11 % 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: -0.27 (0.18), residues: 2086 helix: 0.58 (0.16), residues: 966 sheet: -0.33 (0.29), residues: 297 loop : -0.94 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 96 HIS 0.008 0.001 HIS A 478 PHE 0.015 0.001 PHE B 82 TYR 0.023 0.001 TYR A 613 ARG 0.011 0.001 ARG A 296 *********************** 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 173 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 169 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP A1044 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 MET cc_start: 0.7025 (mmp) cc_final: 0.6744 (mmp) REVERT: A 314 VAL cc_start: 0.8466 (t) cc_final: 0.8204 (t) REVERT: A 357 ILE cc_start: 0.7387 (mt) cc_final: 0.7162 (mm) REVERT: A 996 PHE cc_start: 0.5679 (t80) cc_final: 0.5424 (t80) REVERT: B 86 LEU cc_start: 0.7384 (mt) cc_final: 0.7080 (tp) outliers start: 4 outliers final: 3 residues processed: 173 average time/residue: 0.2939 time to fit residues: 78.3132 Evaluate side-chains 120 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 117 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 187 optimal weight: 9.9990 chunk 202 optimal weight: 0.7980 chunk 166 optimal weight: 9.9990 chunk 185 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 GLN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 645 GLN B 992 GLN B1021 HIS B1034 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 17037 Z= 0.339 Angle : 0.898 33.816 23153 Z= 0.395 Chirality : 0.041 0.218 2484 Planarity : 0.007 0.176 2995 Dihedral : 7.634 86.271 2401 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 58.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.82 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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: 0.02 (0.18), residues: 2086 helix: 0.85 (0.16), residues: 964 sheet: -0.05 (0.30), residues: 277 loop : -0.87 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 550 HIS 0.017 0.002 HIS A 388 PHE 0.019 0.002 PHE B 107 TYR 0.052 0.003 TYR B 305 ARG 0.008 0.001 ARG B 471 *********************** 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 123 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.999 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 ILE cc_start: 0.7259 (mt) cc_final: 0.6892 (mt) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.3054 time to fit residues: 57.3115 Evaluate side-chains 86 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 188 optimal weight: 5.9990 chunk 199 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 841 GLN A 951 ASN B 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 17037 Z= 0.220 Angle : 0.647 19.333 23153 Z= 0.303 Chirality : 0.038 0.190 2484 Planarity : 0.006 0.167 2995 Dihedral : 7.031 72.834 2401 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 56.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.66 % Favored : 95.20 % Rotamer: Outliers : 0.06 % Allowed : 0.70 % Favored : 99.24 % 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: 1.13 (0.16), residues: 976 sheet: -0.02 (0.30), residues: 269 loop : -0.87 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 96 HIS 0.005 0.001 HIS A 961 PHE 0.015 0.001 PHE B 158 TYR 0.019 0.001 TYR A 997 ARG 0.003 0.001 ARG A 617 *********************** 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 107 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 1.781 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 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: A 357 ILE cc_start: 0.7067 (mt) cc_final: 0.6860 (mt) REVERT: A 482 LEU cc_start: 0.7143 (tt) cc_final: 0.6694 (tt) REVERT: B 212 MET cc_start: 0.7974 (mmp) cc_final: 0.7241 (mmm) REVERT: B 712 ASN cc_start: 0.8410 (m-40) cc_final: 0.8052 (p0) outliers start: 1 outliers final: 1 residues processed: 107 average time/residue: 0.2822 time to fit residues: 48.3898 Evaluate side-chains 87 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 8.9990 chunk 113 optimal weight: 0.6980 chunk 2 optimal weight: 0.3980 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 169 optimal weight: 9.9990 chunk 137 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 0.8980 chunk 178 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 GLN A ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN B 841 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 17037 Z= 0.172 Angle : 0.575 19.281 23153 Z= 0.271 Chirality : 0.037 0.189 2484 Planarity : 0.005 0.163 2995 Dihedral : 6.624 65.200 2401 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 55.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.00 % Favored : 94.86 % Rotamer: Outliers : 0.06 % Allowed : 0.70 % Favored : 99.24 % 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: 0.70 (0.19), residues: 2086 helix: 1.59 (0.17), residues: 969 sheet: 0.06 (0.31), residues: 266 loop : -0.69 (0.23), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 96 HIS 0.003 0.001 HIS B 977 PHE 0.013 0.001 PHE A 158 TYR 0.015 0.001 TYR B 305 ARG 0.002 0.000 ARG A 617 *********************** 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 106 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 2.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP A1044 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 ILE cc_start: 0.6469 (mt) cc_final: 0.6264 (mm) REVERT: A 482 LEU cc_start: 0.7382 (tt) cc_final: 0.6872 (tt) REVERT: B 212 MET cc_start: 0.7861 (mmp) cc_final: 0.7617 (mmp) outliers start: 1 outliers final: 1 residues processed: 106 average time/residue: 0.2738 time to fit residues: 47.1239 Evaluate side-chains 83 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 9.9990 chunk 179 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 49 optimal weight: 0.4980 chunk 199 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 chunk 65 optimal weight: 6.9990 chunk 104 optimal weight: 0.5980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 665 ASN ** A 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN B 204 GLN ** B 310 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** B1034 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.5868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 17037 Z= 0.223 Angle : 0.665 23.926 23153 Z= 0.299 Chirality : 0.037 0.182 2484 Planarity : 0.006 0.154 2995 Dihedral : 6.622 65.737 2401 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 63.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.38 % Favored : 94.47 % 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 : 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: 0.59 (0.19), residues: 2086 helix: 1.45 (0.17), residues: 964 sheet: -0.01 (0.32), residues: 267 loop : -0.65 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 96 HIS 0.005 0.001 HIS B 931 PHE 0.027 0.002 PHE B 82 TYR 0.021 0.002 TYR B 829 ARG 0.005 0.001 ARG B1029 *********************** 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 92 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.916 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: B 890 LEU cc_start: 0.7103 (tp) cc_final: 0.6827 (tp) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2885 time to fit residues: 43.9139 Evaluate side-chains 70 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 112 optimal weight: 0.5980 chunk 167 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 198 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.6000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 17037 Z= 0.161 Angle : 0.517 12.547 23153 Z= 0.253 Chirality : 0.036 0.139 2484 Planarity : 0.004 0.048 2995 Dihedral : 6.469 64.508 2401 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 59.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.75 % Favored : 95.20 % 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: 0.84 (0.19), residues: 2086 helix: 1.75 (0.17), residues: 964 sheet: -0.05 (0.32), residues: 269 loop : -0.59 (0.23), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 96 HIS 0.003 0.001 HIS B 961 PHE 0.011 0.001 PHE A 261 TYR 0.013 0.001 TYR A 613 ARG 0.003 0.000 ARG B1029 *********************** 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 93 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP A1044 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 ILE cc_start: 0.5981 (mm) cc_final: 0.5468 (mm) REVERT: B 890 LEU cc_start: 0.7081 (tp) cc_final: 0.6769 (tp) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.2783 time to fit residues: 41.8621 Evaluate side-chains 78 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 0.0870 chunk 79 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 59 optimal weight: 0.0060 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 126 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 98 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 156 optimal weight: 0.7980 overall best weight: 0.4774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.6051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 17037 Z= 0.116 Angle : 0.476 9.430 23153 Z= 0.238 Chirality : 0.036 0.158 2484 Planarity : 0.004 0.045 2995 Dihedral : 6.207 58.799 2401 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 55.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.88 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z (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: 1.16 (0.19), residues: 2086 helix: 2.04 (0.17), residues: 965 sheet: 0.04 (0.32), residues: 268 loop : -0.44 (0.23), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 550 HIS 0.002 0.000 HIS B 995 PHE 0.011 0.001 PHE B 82 TYR 0.012 0.001 TYR A 613 ARG 0.002 0.000 ARG B1029 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.873 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 357 ILE cc_start: 0.5271 (mm) cc_final: 0.4555 (mm) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.2821 time to fit residues: 44.3360 Evaluate side-chains 83 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 180 optimal weight: 0.4980 chunk 190 optimal weight: 0.8980 chunk 173 optimal weight: 7.9990 chunk 185 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 80 optimal weight: 0.0040 chunk 145 optimal weight: 9.9990 chunk 56 optimal weight: 0.7980 chunk 167 optimal weight: 0.6980 chunk 174 optimal weight: 4.9990 chunk 184 optimal weight: 8.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 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 310 GLN A Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.6146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 17037 Z= 0.122 Angle : 0.474 8.828 23153 Z= 0.236 Chirality : 0.036 0.145 2484 Planarity : 0.003 0.045 2995 Dihedral : 6.031 55.573 2401 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 55.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.46 % Favored : 95.49 % 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: 1.26 (0.20), residues: 2086 helix: 2.12 (0.17), residues: 965 sheet: 0.12 (0.32), residues: 266 loop : -0.39 (0.23), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1031 HIS 0.002 0.000 HIS A 116 PHE 0.011 0.001 PHE B 82 TYR 0.013 0.001 TYR A 613 ARG 0.002 0.000 ARG B1029 *********************** 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 97 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 357 ILE cc_start: 0.5189 (mm) cc_final: 0.4571 (mm) REVERT: A 767 MET cc_start: 0.8010 (ptp) cc_final: 0.7637 (ptp) REVERT: B 5 MET cc_start: 0.5906 (ttp) cc_final: 0.5487 (ttp) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2812 time to fit residues: 43.7361 Evaluate side-chains 82 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 0.4980 chunk 195 optimal weight: 0.3980 chunk 119 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 205 optimal weight: 0.9990 chunk 188 optimal weight: 6.9990 chunk 163 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 126 optimal weight: 0.0970 chunk 100 optimal weight: 6.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.6242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 17037 Z= 0.119 Angle : 0.461 10.234 23153 Z= 0.229 Chirality : 0.036 0.165 2484 Planarity : 0.003 0.044 2995 Dihedral : 5.856 52.329 2401 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 55.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.22 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z (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: 1.41 (0.20), residues: 2086 helix: 2.25 (0.17), residues: 961 sheet: 0.18 (0.32), residues: 265 loop : -0.29 (0.23), residues: 860 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 0.015 0.001 PHE A 261 TYR 0.014 0.001 TYR A 256 ARG 0.003 0.000 ARG A 255 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.737 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: A 357 ILE cc_start: 0.5186 (mm) cc_final: 0.4506 (mm) REVERT: B 5 MET cc_start: 0.5925 (ttp) cc_final: 0.5523 (ttp) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2696 time to fit residues: 43.0822 Evaluate side-chains 82 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 129 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 150 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 168 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 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 573 ASN A 724 GLN ** A 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.038466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.025825 restraints weight = 519029.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.027851 restraints weight = 208769.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.029279 restraints weight = 121386.311| |-----------------------------------------------------------------------------| r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2673 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.7022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 17037 Z= 0.378 Angle : 0.904 30.484 23153 Z= 0.407 Chirality : 0.041 0.168 2484 Planarity : 0.005 0.053 2995 Dihedral : 6.834 77.436 2401 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 84.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.03 % Favored : 92.92 % 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 : 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: -0.13 (0.19), residues: 2086 helix: 0.66 (0.16), residues: 963 sheet: -0.38 (0.33), residues: 255 loop : -0.74 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 96 HIS 0.011 0.002 HIS A 266 PHE 0.026 0.003 PHE B 107 TYR 0.036 0.003 TYR B 829 ARG 0.014 0.001 ARG A 765 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2954.13 seconds wall clock time: 54 minutes 55.15 seconds (3295.15 seconds total)