Starting phenix.real_space_refine on Thu Nov 16 22:08:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmg_27536/11_2023/8dmg_27536_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmg_27536/11_2023/8dmg_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_27536/11_2023/8dmg_27536.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmg_27536/11_2023/8dmg_27536.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmg_27536/11_2023/8dmg_27536_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmg_27536/11_2023/8dmg_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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 4 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: 4 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: 7.98 Conformation dependent library (CDL) restraints added in 6.2 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: 4.54 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: 6.28 Time building geometry restraints manager: 8.29 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: 9185 20.26 - 40.52: 717 40.52 - 60.79: 216 60.79 - 81.05: 44 81.05 - 101.31: 13 Dihedral angle restraints: 10175 sinusoidal: 4110 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 10172 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: 0.330 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: 0.440 Extract box with map and model: 2.360 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 59.770 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.550 ------------------------------------------------------------------------------- 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 : 16.890 101.311 6237 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 *********************** 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 : 1.940 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 outliers start: 116 outliers final: 33 residues processed: 343 average time/residue: 0.3170 time to fit residues: 159.3053 Evaluate side-chains 173 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 140 time to evaluate : 1.934 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 5 residues processed: 33 average time/residue: 0.2522 time to fit residues: 15.3749 ------------------------------------------------------------------------------- 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: 1.9990 chunk 105 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 187 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 27 GLN ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 ASN A 134 ASN A 201 ASN A 236 HIS ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 ASN A 388 HIS 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: 0.6560 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17037 Z= 0.227 Angle : 0.718 25.874 23153 Z= 0.359 Chirality : 0.041 0.245 2484 Planarity : 0.007 0.192 2995 Dihedral : 7.955 89.430 2305 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 37.00 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.32 % Favored : 95.44 % Rotamer: Outliers : 0.23 % Allowed : 1.70 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.60 (0.18), residues: 2086 helix: 0.20 (0.16), residues: 969 sheet: -0.17 (0.30), residues: 267 loop : -1.07 (0.22), residues: 850 *********************** 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 : 1.824 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 outliers start: 4 outliers final: 3 residues processed: 177 average time/residue: 0.3022 time to fit residues: 82.2612 Evaluate side-chains 118 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 115 time to evaluate : 1.987 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 3 average time/residue: 0.1709 time to fit residues: 3.7174 ------------------------------------------------------------------------------- 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: 6.9990 chunk 127 optimal weight: 0.0010 chunk 51 optimal weight: 4.9990 chunk 187 optimal weight: 7.9990 chunk 202 optimal weight: 0.9990 chunk 166 optimal weight: 9.9990 chunk 185 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 overall best weight: 2.7994 ------------------------------------------------------------------------------- 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 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 GLN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN A 665 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: 0.6911 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 17037 Z= 0.302 Angle : 0.855 31.443 23153 Z= 0.377 Chirality : 0.040 0.218 2484 Planarity : 0.007 0.189 2995 Dihedral : 7.183 85.757 2305 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 61.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.43 % Favored : 94.42 % Rotamer: Outliers : 0.06 % Allowed : 0.88 % Favored : 99.06 % 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: -0.38 (0.18), residues: 2086 helix: 0.26 (0.16), residues: 969 sheet: -0.23 (0.28), residues: 293 loop : -0.72 (0.23), residues: 824 *********************** 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 130 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 1.989 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 outliers start: 1 outliers final: 1 residues processed: 130 average time/residue: 0.3158 time to fit residues: 62.9231 Evaluate side-chains 91 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 1.753 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1905 time to fit residues: 2.6887 ------------------------------------------------------------------------------- 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: 9.9990 chunk 140 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 188 optimal weight: 6.9990 chunk 199 optimal weight: 0.0010 chunk 98 optimal weight: 2.9990 chunk 178 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- 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 73 GLN ** 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 841 GLN ** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.4850 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= 0.181 Angle : 0.564 15.570 23153 Z= 0.273 Chirality : 0.037 0.200 2484 Planarity : 0.006 0.154 2995 Dihedral : 6.434 78.113 2305 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 55.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.66 % Favored : 95.20 % Rotamer: Outliers : 0.12 % Allowed : 1.06 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.19), residues: 2086 helix: 0.75 (0.17), residues: 971 sheet: -0.13 (0.29), residues: 291 loop : -0.54 (0.23), residues: 824 *********************** 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 117 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 1.957 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 outliers start: 2 outliers final: 2 residues processed: 117 average time/residue: 0.2895 time to fit residues: 53.8560 Evaluate side-chains 85 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 1.966 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.1511 time to fit residues: 3.2600 ------------------------------------------------------------------------------- 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: 0.0000 chunk 113 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 chunk 82 optimal weight: 0.6980 chunk 169 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 0.6980 chunk 178 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 overall best weight: 2.2788 ------------------------------------------------------------------------------- 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 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN ** A 310 GLN A ** 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 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 HIS B 109 GLN B 213 ASN ** B 310 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.5723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17037 Z= 0.268 Angle : 0.768 28.289 23153 Z= 0.335 Chirality : 0.038 0.185 2484 Planarity : 0.006 0.169 2995 Dihedral : 6.344 80.303 2305 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 73.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.82 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.35 (0.18), residues: 2086 helix: 0.36 (0.17), residues: 968 sheet: -0.28 (0.30), residues: 262 loop : -0.78 (0.22), residues: 856 *********************** 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 101 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.926 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 outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.3007 time to fit residues: 48.3150 Evaluate side-chains 75 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.870 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8158 ------------------------------------------------------------------------------- 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: 10.0000 chunk 179 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 116 optimal weight: 0.0970 chunk 49 optimal weight: 5.9990 chunk 199 optimal weight: 0.0070 chunk 165 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 104 optimal weight: 0.0270 overall best weight: 1.0056 ------------------------------------------------------------------------------- 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 73 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 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.5800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 17037 Z= 0.156 Angle : 0.517 13.786 23153 Z= 0.253 Chirality : 0.036 0.201 2484 Planarity : 0.005 0.142 2995 Dihedral : 5.855 72.658 2305 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 62.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.22 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: 0.31 (0.19), residues: 2086 helix: 0.98 (0.17), residues: 951 sheet: -0.21 (0.30), residues: 282 loop : -0.42 (0.23), residues: 853 *********************** 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 100 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.819 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 outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.2807 time to fit residues: 45.4063 Evaluate side-chains 78 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.801 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4752 ------------------------------------------------------------------------------- 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: 4.9990 chunk 22 optimal weight: 0.1980 chunk 113 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 198 optimal weight: 0.0270 chunk 124 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 overall best weight: 1.4442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 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 204 GLN ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 841 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.6088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 17037 Z= 0.189 Angle : 0.556 18.216 23153 Z= 0.262 Chirality : 0.036 0.158 2484 Planarity : 0.004 0.049 2995 Dihedral : 5.773 73.596 2305 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 68.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.29 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.19), residues: 2086 helix: 1.05 (0.17), residues: 948 sheet: -0.19 (0.31), residues: 272 loop : -0.44 (0.23), residues: 866 *********************** 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 97 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 2.062 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 outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2925 time to fit residues: 45.8264 Evaluate side-chains 76 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.985 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7001 ------------------------------------------------------------------------------- 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: 2.9990 chunk 79 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 59 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 126 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 98 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 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 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 420 HIS ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.6234 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= 0.174 Angle : 0.514 12.778 23153 Z= 0.252 Chirality : 0.035 0.135 2484 Planarity : 0.004 0.049 2995 Dihedral : 5.643 68.314 2305 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 67.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.00 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 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: 0.46 (0.19), residues: 2086 helix: 1.13 (0.18), residues: 947 sheet: -0.20 (0.31), residues: 283 loop : -0.35 (0.23), residues: 856 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.867 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 outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2768 time to fit residues: 42.6865 Evaluate side-chains 76 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.999 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.5198 > 50: distance: 86 - 93: 33.171 distance: 93 - 94: 39.629 distance: 94 - 95: 55.930 distance: 94 - 97: 57.216 distance: 95 - 96: 48.148 distance: 95 - 104: 57.088 distance: 96 - 130: 29.053 distance: 97 - 98: 41.202 distance: 98 - 99: 42.374 distance: 98 - 100: 33.844 distance: 99 - 101: 45.542 distance: 100 - 102: 3.702 distance: 101 - 103: 63.894 distance: 102 - 103: 67.713 distance: 104 - 105: 56.265 distance: 105 - 106: 41.706 distance: 105 - 108: 39.341 distance: 106 - 107: 44.519 distance: 106 - 110: 43.647 distance: 108 - 109: 67.967 distance: 110 - 111: 22.274 distance: 111 - 112: 41.897 distance: 111 - 114: 53.095 distance: 112 - 113: 28.826 distance: 112 - 119: 42.301 distance: 113 - 143: 44.486 distance: 114 - 115: 45.636 distance: 115 - 116: 33.615 distance: 116 - 117: 25.239 distance: 116 - 118: 24.497 distance: 119 - 120: 66.220 distance: 120 - 121: 56.881 distance: 120 - 123: 8.377 distance: 121 - 122: 57.879 distance: 121 - 130: 37.352 distance: 123 - 124: 29.707 distance: 124 - 125: 16.788 distance: 124 - 126: 34.184 distance: 125 - 127: 37.617 distance: 126 - 128: 36.471 distance: 127 - 129: 41.848 distance: 128 - 129: 31.681 distance: 130 - 131: 33.726 distance: 131 - 132: 7.762 distance: 131 - 134: 40.796 distance: 132 - 133: 40.198 distance: 132 - 138: 55.761 distance: 134 - 135: 70.356 distance: 134 - 136: 46.495 distance: 135 - 137: 42.820 distance: 138 - 139: 47.138 distance: 139 - 140: 41.837 distance: 139 - 142: 47.370 distance: 140 - 141: 41.633 distance: 140 - 143: 45.960 distance: 143 - 144: 68.709 distance: 144 - 145: 11.856 distance: 144 - 147: 41.442 distance: 145 - 146: 60.320 distance: 145 - 151: 15.107 distance: 147 - 148: 58.545 distance: 148 - 149: 55.787 distance: 148 - 150: 43.031 distance: 151 - 152: 17.427 distance: 152 - 153: 38.144 distance: 152 - 155: 42.470 distance: 153 - 154: 36.372 distance: 153 - 159: 52.133 distance: 155 - 156: 53.317 distance: 156 - 157: 40.298 distance: 156 - 158: 27.429 distance: 159 - 160: 44.784 distance: 159 - 165: 19.488 distance: 160 - 161: 28.620 distance: 160 - 163: 20.189 distance: 161 - 162: 14.356 distance: 161 - 166: 45.821 distance: 163 - 164: 43.130 distance: 164 - 165: 33.025 distance: 166 - 167: 40.327 distance: 167 - 168: 49.270 distance: 167 - 170: 56.210 distance: 168 - 169: 56.095 distance: 168 - 172: 30.798 distance: 170 - 171: 57.111