Starting phenix.real_space_refine on Sun Mar 17 05:57:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmg_27536/03_2024/8dmg_27536_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmg_27536/03_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_27536/03_2024/8dmg_27536.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmg_27536/03_2024/8dmg_27536.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmg_27536/03_2024/8dmg_27536_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmg_27536/03_2024/8dmg_27536_updated.pdb" } 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 Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 56": "NH1" <-> "NH2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 475": "OE1" <-> "OE2" Residue "A GLU 633": "OE1" <-> "OE2" Residue "A ARG 705": "NH1" <-> "NH2" Residue "A GLU 747": "OE1" <-> "OE2" Residue "A GLU 779": "OE1" <-> "OE2" Residue "A ARG 917": "NH1" <-> "NH2" Residue "A GLU 948": "OE1" <-> "OE2" Residue "A GLU 1010": "OE1" <-> "OE2" Residue "A GLU 1036": "OE1" <-> "OE2" Residue "A ARG 1040": "NH1" <-> "NH2" Residue "B PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 56": "NH1" <-> "NH2" Residue "B GLU 228": "OE1" <-> "OE2" Residue "B TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 633": "OE1" <-> "OE2" Residue "B ARG 705": "NH1" <-> "NH2" Residue "B GLU 747": "OE1" <-> "OE2" Residue "B GLU 779": "OE1" <-> "OE2" Residue "B ARG 917": "NH1" <-> "NH2" Residue "B GLU 948": "OE1" <-> "OE2" Residue "B GLU 1010": "OE1" <-> "OE2" Residue "B GLU 1036": "OE1" <-> "OE2" Residue "B ARG 1040": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 16.47, per 1000 atoms: 0.98 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 - 3.50 Amino acid : False - 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: 6.84 Conformation dependent library (CDL) restraints added in 5.8 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... running ksdssp... Secondary structure from input PDB file: 89 helices and 20 sheets defined 44.3% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.08 Creating SS restraints... Processing helix chain 'A' and resid 12 through 14 No H-bonds generated for 'chain 'A' and resid 12 through 14' Processing helix chain 'A' and resid 17 through 20 Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 55 through 61 removed outlier: 4.256A pdb=" N GLU A 60 " --> pdb=" O ARG A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 82 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 94 through 107 Proline residue: A 105 - end of helix Processing helix chain 'A' and resid 109 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 158 Processing helix chain 'A' and resid 164 through 166 No H-bonds generated for 'chain 'A' and resid 164 through 166' Processing helix chain 'A' and resid 172 through 189 removed outlier: 3.650A pdb=" N LEU A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLN A 189 " --> pdb=" O MET A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 225 removed outlier: 4.570A pdb=" N GLU A 200 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP A 222 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 251 through 264 Processing helix chain 'A' and resid 267 through 282 Processing helix chain 'A' and resid 284 through 297 Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 364 through 367 No H-bonds generated for 'chain 'A' and resid 364 through 367' Processing helix chain 'A' and resid 376 through 379 Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 396 through 398 No H-bonds generated for 'chain 'A' and resid 396 through 398' Processing helix chain 'A' and resid 403 through 420 Processing helix chain 'A' and resid 492 through 507 removed outlier: 3.553A pdb=" N SER A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 545 through 552 Processing helix chain 'A' and resid 575 through 577 No H-bonds generated for 'chain 'A' and resid 575 through 577' Processing helix chain 'A' and resid 580 through 590 Processing helix chain 'A' and resid 609 through 627 Processing helix chain 'A' and resid 654 through 658 Processing helix chain 'A' and resid 708 through 718 Processing helix chain 'A' and resid 746 through 752 removed outlier: 3.567A pdb=" N GLN A 751 " --> pdb=" O GLU A 747 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 770 Processing helix chain 'A' and resid 774 through 784 removed outlier: 3.990A pdb=" N LEU A 784 " --> pdb=" O LEU A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 792 Processing helix chain 'A' and resid 800 through 806 Processing helix chain 'A' and resid 814 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 863 through 870 Processing helix chain 'A' and resid 904 through 923 Proline residue: A 909 - end of helix removed outlier: 3.586A pdb=" N LYS A 918 " --> pdb=" O GLN A 915 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A 921 " --> pdb=" O LYS A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 954 Processing helix chain 'A' and resid 975 through 981 Processing helix chain 'A' and resid 983 through 992 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1025 through 1035 Processing helix chain 'B' and resid 12 through 14 No H-bonds generated for 'chain 'B' and resid 12 through 14' Processing helix chain 'B' and resid 17 through 20 Processing helix chain 'B' and resid 25 through 36 Processing helix chain 'B' and resid 55 through 61 removed outlier: 4.256A pdb=" N GLU B 60 " --> pdb=" O ARG B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 82 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 94 through 107 Proline residue: B 105 - end of helix Processing helix chain 'B' and resid 109 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 158 Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 172 through 189 removed outlier: 3.650A pdb=" N LEU B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLN B 189 " --> pdb=" O MET B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 225 removed outlier: 4.571A pdb=" N GLU B 200 " --> pdb=" O ALA B 197 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP B 222 " --> pdb=" O ILE B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 239 Processing helix chain 'B' and resid 251 through 264 Processing helix chain 'B' and resid 267 through 282 Processing helix chain 'B' and resid 284 through 297 Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 312 through 324 Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 364 through 367 No H-bonds generated for 'chain 'B' and resid 364 through 367' Processing helix chain 'B' and resid 376 through 379 Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 403 through 420 Processing helix chain 'B' and resid 492 through 507 removed outlier: 3.554A pdb=" N SER B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 545 through 552 Processing helix chain 'B' and resid 575 through 577 No H-bonds generated for 'chain 'B' and resid 575 through 577' Processing helix chain 'B' and resid 580 through 590 Processing helix chain 'B' and resid 609 through 627 Processing helix chain 'B' and resid 635 through 637 No H-bonds generated for 'chain 'B' and resid 635 through 637' Processing helix chain 'B' and resid 654 through 658 Processing helix chain 'B' and resid 708 through 718 Processing helix chain 'B' and resid 746 through 752 removed outlier: 3.567A pdb=" N GLN B 751 " --> pdb=" O GLU B 747 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 770 Processing helix chain 'B' and resid 774 through 784 removed outlier: 3.990A pdb=" N LEU B 784 " --> pdb=" O LEU B 780 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 792 Processing helix chain 'B' and resid 800 through 806 Processing helix chain 'B' and resid 814 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 863 through 870 Processing helix chain 'B' and resid 904 through 923 Proline residue: B 909 - end of helix removed outlier: 3.586A pdb=" N LYS B 918 " --> pdb=" O GLN B 915 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS B 921 " --> pdb=" O LYS B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 954 Processing helix chain 'B' and resid 975 through 981 Processing helix chain 'B' and resid 983 through 992 Processing helix chain 'B' and resid 1005 through 1020 Processing helix chain 'B' and resid 1025 through 1035 Processing sheet with id= A, 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= B, first strand: chain 'A' and resid 339 through 341 Processing sheet with id= C, first strand: chain 'A' and resid 421 through 424 Processing sheet with id= D, first strand: chain 'A' and resid 433 through 436 Processing sheet with id= E, first strand: chain 'A' and resid 512 through 515 removed outlier: 6.619A pdb=" N ALA A 528 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N LEU A 485 " --> pdb=" O ALA A 528 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU A 530 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N GLY A 487 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL A 532 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLY A 601 " --> pdb=" O GLY A 568 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N GLY A 570 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ALA A 603 " --> pdb=" O GLY A 570 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 662 through 665 removed outlier: 4.840A pdb=" N THR A 878 " --> pdb=" O ILE A 703 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 841 through 847 removed outlier: 6.549A pdb=" N GLU A 687 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL A 666 " --> pdb=" O GLU A 687 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 725 through 727 Processing sheet with id= I, first strand: chain 'A' and resid 850 through 852 Processing sheet with id= J, first strand: chain 'A' and resid 995 through 998 removed outlier: 6.483A pdb=" N THR A 959 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N PHE A 934 " --> pdb=" O THR A 959 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N HIS A 961 " --> pdb=" O PHE A 934 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N CYS A 936 " --> pdb=" O HIS A 961 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ALA A 963 " --> pdb=" O CYS A 936 " (cutoff:3.500A) Processing sheet with id= K, 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= L, first strand: chain 'B' and resid 339 through 341 Processing sheet with id= M, first strand: chain 'B' and resid 421 through 424 Processing sheet with id= N, first strand: chain 'B' and resid 433 through 436 Processing sheet with id= O, first strand: chain 'B' and resid 512 through 515 removed outlier: 6.618A pdb=" N ALA B 528 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LEU B 485 " --> pdb=" O ALA B 528 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU B 530 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N GLY B 487 " --> pdb=" O LEU B 530 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL B 532 " --> pdb=" O GLY B 487 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY B 601 " --> pdb=" O GLY B 568 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLY B 570 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ALA B 603 " --> pdb=" O GLY B 570 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 662 through 665 removed outlier: 4.841A pdb=" N THR B 878 " --> pdb=" O ILE B 703 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 841 through 847 removed outlier: 6.550A pdb=" N GLU B 687 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL B 666 " --> pdb=" O GLU B 687 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 725 through 727 Processing sheet with id= S, first strand: chain 'B' and resid 850 through 852 Processing sheet with id= T, first strand: chain 'B' and resid 1041 through 1046 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) removed outlier: 6.482A pdb=" N THR B 959 " --> pdb=" O LEU B 932 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N PHE B 934 " --> pdb=" O THR B 959 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N HIS B 961 " --> pdb=" O PHE B 934 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N CYS B 936 " --> pdb=" O HIS B 961 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ALA B 963 " --> pdb=" O CYS B 936 " (cutoff:3.500A) 687 hydrogen bonds defined for protein. 1775 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: 5.95 Time building geometry restraints manager: 7.29 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: 65.98 - 86.97: 16 86.97 - 107.97: 1630 107.97 - 128.96: 21799 128.96 - 149.96: 170 149.96 - 170.95: 6 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: 7707 2.88 - 3.74: 36697 3.74 - 4.60: 70175 Warning: very small nonbonded interaction distances. Nonbonded interactions: 114667 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 114662 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.250 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: 0.400 Extract box with map and model: 2.200 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 56.790 Find NCS groups from input model: 0.870 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.710 ------------------------------------------------------------------------------- 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= 1.870 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 : 2.189 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: 0.3114 time to fit residues: 156.5491 Evaluate side-chains 180 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 143 time to evaluate : 1.523 ------------------------------------------------------------------------------- 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: 0.6980 chunk 156 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 187 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 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 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: 0.6555 moved from start: 0.3159 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= 0.228 Angle : 0.733 25.214 23153 Z= 0.364 Chirality : 0.040 0.217 2484 Planarity : 0.007 0.195 2995 Dihedral : 8.563 89.688 2401 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 38.86 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.12 % Favored : 95.64 % Rotamer: Outliers : 0.23 % Allowed : 1.06 % Favored : 98.71 % 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: -0.61 (0.18), residues: 2086 helix: 0.15 (0.16), residues: 973 sheet: -0.18 (0.30), residues: 269 loop : -1.03 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 96 HIS 0.009 0.001 HIS B 478 PHE 0.014 0.001 PHE B 82 TYR 0.018 0.001 TYR B 613 ARG 0.012 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 177 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 173 time to evaluate : 1.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP A1044 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 996 PHE cc_start: 0.5894 (t80) cc_final: 0.5619 (t80) REVERT: B 86 LEU cc_start: 0.7431 (mt) cc_final: 0.7103 (tp) outliers start: 4 outliers final: 3 residues processed: 177 average time/residue: 0.2990 time to fit residues: 82.1418 Evaluate side-chains 119 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 116 time to evaluate : 1.947 ------------------------------------------------------------------------------- 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: 1.9990 chunk 155 optimal weight: 4.9990 chunk 127 optimal weight: 0.0870 chunk 51 optimal weight: 6.9990 chunk 187 optimal weight: 10.0000 chunk 202 optimal weight: 0.7980 chunk 166 optimal weight: 10.0000 chunk 185 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 150 optimal weight: 3.9990 overall best weight: 2.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 27 GLN A 109 GLN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN B 213 ASN B 645 GLN B 992 GLN B1021 HIS ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17037 Z= 0.272 Angle : 0.783 26.827 23153 Z= 0.349 Chirality : 0.039 0.198 2484 Planarity : 0.007 0.177 2995 Dihedral : 7.493 87.917 2401 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 54.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.29 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: -0.25 (0.18), residues: 2086 helix: 0.37 (0.16), residues: 976 sheet: -0.12 (0.29), residues: 287 loop : -0.70 (0.23), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP A 550 HIS 0.013 0.002 HIS A 408 PHE 0.020 0.002 PHE A 405 TYR 0.022 0.002 TYR A 997 ARG 0.004 0.001 ARG A 296 *********************** 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 135 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 0.7150 (mm) cc_final: 0.6427 (mm) REVERT: B 890 LEU cc_start: 0.7599 (mt) cc_final: 0.7354 (tp) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2916 time to fit residues: 60.3744 Evaluate side-chains 93 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.870 ------------------------------------------------------------------------------- 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: 7.9990 chunk 140 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 125 optimal weight: 8.9990 chunk 188 optimal weight: 10.0000 chunk 199 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 665 ASN ** A 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 841 GLN ** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 HIS B 109 GLN ** B 310 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 17037 Z= 0.266 Angle : 0.691 19.880 23153 Z= 0.323 Chirality : 0.038 0.184 2484 Planarity : 0.006 0.169 2995 Dihedral : 7.010 66.535 2401 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 63.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.14 % Favored : 94.71 % 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 : 0.00 % 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: -0.26 (0.18), residues: 2086 helix: 0.40 (0.16), residues: 976 sheet: -0.12 (0.30), residues: 273 loop : -0.73 (0.23), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 550 HIS 0.005 0.001 HIS B 977 PHE 0.016 0.002 PHE A 158 TYR 0.019 0.002 TYR A 829 ARG 0.004 0.001 ARG B 679 *********************** 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 114 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.778 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 ILE cc_start: 0.7186 (mm) cc_final: 0.6508 (mm) REVERT: B 369 ASP cc_start: 0.5923 (p0) cc_final: 0.5670 (p0) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.2757 time to fit residues: 49.6109 Evaluate side-chains 84 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 2.052 ------------------------------------------------------------------------------- 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: 4.9990 chunk 2 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 169 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 178 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** 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 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN B 665 ASN ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 841 GLN ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.6619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.140 17037 Z= 0.504 Angle : 1.057 29.139 23153 Z= 0.493 Chirality : 0.044 0.223 2484 Planarity : 0.007 0.141 2995 Dihedral : 8.152 89.538 2401 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 104.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.95 % Favored : 91.90 % Rotamer: Outliers : 0.12 % Allowed : 1.35 % Favored : 98.53 % 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: -1.81 (0.17), residues: 2086 helix: -1.04 (0.15), residues: 942 sheet: -0.59 (0.31), residues: 257 loop : -1.43 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP B 96 HIS 0.012 0.003 HIS B 266 PHE 0.030 0.003 PHE B 107 TYR 0.032 0.003 TYR B 829 ARG 0.009 0.001 ARG B1029 *********************** 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 94 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP A1044 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 SER cc_start: 0.9091 (m) cc_final: 0.8818 (t) REVERT: A 357 ILE cc_start: 0.7295 (mm) cc_final: 0.6731 (mm) REVERT: B 369 ASP cc_start: 0.6306 (p0) cc_final: 0.6011 (p0) REVERT: B 471 ARG cc_start: 0.4485 (ptt180) cc_final: 0.4120 (ptt-90) outliers start: 2 outliers final: 2 residues processed: 94 average time/residue: 0.3059 time to fit residues: 44.8616 Evaluate side-chains 72 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 70 time to evaluate : 2.067 ------------------------------------------------------------------------------- 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: 0.9980 chunk 179 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 165 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 16 optimal weight: 0.4980 chunk 65 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 GLN ** 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** ** A 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1022 GLN ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.6447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 17037 Z= 0.180 Angle : 0.596 17.528 23153 Z= 0.279 Chirality : 0.036 0.198 2484 Planarity : 0.006 0.157 2995 Dihedral : 7.084 87.981 2401 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 74.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.43 % Favored : 94.42 % 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: -0.69 (0.18), residues: 2086 helix: 0.06 (0.17), residues: 949 sheet: -0.42 (0.32), residues: 258 loop : -0.93 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 96 HIS 0.004 0.001 HIS A 388 PHE 0.023 0.001 PHE B 82 TYR 0.014 0.001 TYR A 613 ARG 0.003 0.000 ARG A1029 *********************** 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 96 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP A1044 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 SER cc_start: 0.9016 (m) cc_final: 0.8775 (p) REVERT: A 357 ILE cc_start: 0.6892 (mm) cc_final: 0.6505 (mm) REVERT: B 212 MET cc_start: 0.8189 (mmp) cc_final: 0.7896 (mmm) REVERT: B 369 ASP cc_start: 0.6436 (p0) cc_final: 0.6087 (p0) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.3040 time to fit residues: 45.5878 Evaluate side-chains 77 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.726 ------------------------------------------------------------------------------- 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: 0.0370 chunk 22 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 198 optimal weight: 0.0000 chunk 124 optimal weight: 0.6980 chunk 121 optimal weight: 0.4980 chunk 91 optimal weight: 9.9990 overall best weight: 0.4464 ------------------------------------------------------------------------------- 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 388 HIS ** 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 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.6418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 17037 Z= 0.140 Angle : 0.495 12.875 23153 Z= 0.244 Chirality : 0.036 0.137 2484 Planarity : 0.004 0.052 2995 Dihedral : 6.562 84.776 2401 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 65.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.61 % Favored : 95.34 % 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: 0.17 (0.19), residues: 2086 helix: 0.92 (0.17), residues: 946 sheet: -0.24 (0.32), residues: 255 loop : -0.58 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 96 HIS 0.003 0.000 HIS B 995 PHE 0.010 0.001 PHE A 261 TYR 0.013 0.001 TYR A 613 ARG 0.006 0.000 ARG B 471 *********************** 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 101 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 2.012 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: A 274 SER cc_start: 0.9033 (m) cc_final: 0.8726 (p) REVERT: A 357 ILE cc_start: 0.7097 (mm) cc_final: 0.6404 (mm) REVERT: B 212 MET cc_start: 0.8159 (mmp) cc_final: 0.7837 (mmm) REVERT: B 369 ASP cc_start: 0.6446 (p0) cc_final: 0.6060 (p0) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2854 time to fit residues: 45.8010 Evaluate side-chains 81 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 2.040 ------------------------------------------------------------------------------- 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: 0.0370 chunk 79 optimal weight: 0.3980 chunk 118 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 38 optimal weight: 0.3980 chunk 126 optimal weight: 0.4980 chunk 135 optimal weight: 0.4980 chunk 98 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 156 optimal weight: 0.0970 overall best weight: 0.2856 ------------------------------------------------------------------------------- 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 388 HIS ** 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 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.6455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 17037 Z= 0.122 Angle : 0.458 9.171 23153 Z= 0.231 Chirality : 0.036 0.162 2484 Planarity : 0.004 0.048 2995 Dihedral : 6.095 79.481 2401 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 61.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.03 % Favored : 95.88 % 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: 0.61 (0.20), residues: 2086 helix: 1.37 (0.18), residues: 950 sheet: -0.01 (0.33), residues: 250 loop : -0.47 (0.23), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 96 HIS 0.006 0.000 HIS A 776 PHE 0.010 0.001 PHE B 173 TYR 0.011 0.001 TYR A 613 ARG 0.005 0.000 ARG A 563 *********************** 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 103 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP A1044 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 SER cc_start: 0.9009 (m) cc_final: 0.8737 (p) REVERT: A 357 ILE cc_start: 0.6367 (mm) cc_final: 0.5475 (mm) REVERT: B 369 ASP cc_start: 0.6432 (p0) cc_final: 0.6011 (p0) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.2740 time to fit residues: 45.0939 Evaluate side-chains 83 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.773 ------------------------------------------------------------------------------- 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: 1.9990 chunk 190 optimal weight: 0.0170 chunk 173 optimal weight: 0.0000 chunk 185 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 80 optimal weight: 0.0470 chunk 145 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 174 optimal weight: 0.3980 chunk 184 optimal weight: 4.9990 overall best weight: 0.4922 ------------------------------------------------------------------------------- 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 388 HIS ** 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 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.6551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 17037 Z= 0.123 Angle : 0.449 8.826 23153 Z= 0.223 Chirality : 0.035 0.150 2484 Planarity : 0.004 0.043 2995 Dihedral : 5.874 76.514 2401 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 62.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.46 % Favored : 95.49 % 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: 0.77 (0.20), residues: 2086 helix: 1.55 (0.18), residues: 949 sheet: 0.02 (0.33), residues: 252 loop : -0.42 (0.23), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 96 HIS 0.002 0.000 HIS A 388 PHE 0.011 0.001 PHE B 173 TYR 0.010 0.001 TYR A 613 ARG 0.003 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.842 Fit side-chains 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 274 SER cc_start: 0.9062 (m) cc_final: 0.8725 (p) REVERT: A 357 ILE cc_start: 0.6434 (mm) cc_final: 0.5472 (mm) REVERT: B 118 MET cc_start: 0.8209 (mpp) cc_final: 0.7946 (mpp) REVERT: B 369 ASP cc_start: 0.6473 (p0) cc_final: 0.6042 (p0) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2838 time to fit residues: 45.5157 Evaluate side-chains 83 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.858 ------------------------------------------------------------------------------- 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: 7.9990 chunk 195 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 205 optimal weight: 1.9990 chunk 188 optimal weight: 7.9990 chunk 163 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 126 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** 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 724 GLN ** A 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.6811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 17037 Z= 0.179 Angle : 0.529 17.111 23153 Z= 0.249 Chirality : 0.035 0.161 2484 Planarity : 0.004 0.043 2995 Dihedral : 6.014 78.602 2401 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 69.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.85 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.20), residues: 2086 helix: 1.36 (0.18), residues: 959 sheet: 0.06 (0.33), residues: 256 loop : -0.41 (0.23), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 96 HIS 0.003 0.001 HIS A 266 PHE 0.011 0.001 PHE A 261 TYR 0.016 0.001 TYR B 829 ARG 0.005 0.000 ARG A 471 ********************** 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 96 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 2.116 Fit side-chains 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 274 SER cc_start: 0.9039 (m) cc_final: 0.8689 (p) REVERT: A 357 ILE cc_start: 0.6728 (mm) cc_final: 0.5948 (mm) REVERT: A 417 MET cc_start: 0.7017 (ptp) cc_final: 0.6349 (ptp) REVERT: A 516 LEU cc_start: 0.6577 (mt) cc_final: 0.6237 (mt) REVERT: B 118 MET cc_start: 0.8269 (mpp) cc_final: 0.8060 (mpp) REVERT: B 369 ASP cc_start: 0.6516 (p0) cc_final: 0.6094 (p0) REVERT: B 417 MET cc_start: 0.5795 (ptp) cc_final: 0.5189 (ptm) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2978 time to fit residues: 45.5115 Evaluate side-chains 76 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.844 ------------------------------------------------------------------------------- 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: 6.9990 chunk 174 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 150 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 168 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 0.0970 overall best weight: 2.3582 ------------------------------------------------------------------------------- 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 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1034 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 = 0.3050 r_free = 0.3050 target = 0.039167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.026456 restraints weight = 491299.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.028508 restraints weight = 202273.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.029971 restraints weight = 119188.611| |-----------------------------------------------------------------------------| r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.7377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 17037 Z= 0.272 Angle : 0.672 20.213 23153 Z= 0.312 Chirality : 0.037 0.181 2484 Planarity : 0.004 0.048 2995 Dihedral : 6.592 87.746 2401 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 87.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.84 % Favored : 93.11 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.04 (0.19), residues: 2086 helix: 0.74 (0.17), residues: 937 sheet: -0.20 (0.32), residues: 257 loop : -0.56 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 96 HIS 0.007 0.001 HIS A 266 PHE 0.016 0.002 PHE A 261 TYR 0.024 0.002 TYR B 829 ARG 0.005 0.001 ARG A 471 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2970.92 seconds wall clock time: 55 minutes 47.91 seconds (3347.91 seconds total)