Starting phenix.real_space_refine on Mon Apr 15 20:14:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sod_40654/04_2024/8sod_40654_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sod_40654/04_2024/8sod_40654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sod_40654/04_2024/8sod_40654.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sod_40654/04_2024/8sod_40654.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sod_40654/04_2024/8sod_40654_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sod_40654/04_2024/8sod_40654_trim_updated.pdb" } resolution = 3.4 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= 0.003 sd= 0.988 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 107 5.16 5 C 11443 2.51 5 N 3139 2.21 5 O 3359 1.98 5 H 17995 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 36045 Number of models: 1 Model: "" Number of chains: 7 Chain: "E" Number of atoms: 5118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5118 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "C" Number of atoms: 5118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5118 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "A" Number of atoms: 15394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 941, 15394 Classifications: {'peptide': 941} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 895} Chain breaks: 12 Chain: "B" Number of atoms: 8364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 8364 Classifications: {'peptide': 524} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 497} Chain breaks: 8 Chain: "F" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1012 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 4, 'TRANS': 59} Chain: "D" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1012 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 4, 'TRANS': 59} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.35, per 1000 atoms: 0.45 Number of scatterers: 36045 At special positions: 0 Unit cell: (115.56, 142.56, 186.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 107 16.00 P 2 15.00 O 3359 8.00 N 3139 7.00 C 11443 6.00 H 17995 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=0, symmetry=0 Time building additional restraints: 27.73 Conformation dependent library (CDL) restraints added in 3.6 seconds 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4312 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 25 sheets defined 32.3% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.02 Creating SS restraints... Processing helix chain 'E' and resid 3 through 25 removed outlier: 3.906A pdb=" N ASN E 16 " --> pdb=" O GLU E 12 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N CYS E 25 " --> pdb=" O ALA E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 34 Processing helix chain 'C' and resid 3 through 25 removed outlier: 3.876A pdb=" N ASN C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'A' and resid 67 through 81 Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 145 through 158 Processing helix chain 'A' and resid 172 through 189 removed outlier: 4.074A pdb=" N VAL A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N THR A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Proline residue: A 183 - end of helix Processing helix chain 'A' and resid 193 through 198 Processing helix chain 'A' and resid 209 through 212 No H-bonds generated for 'chain 'A' and resid 209 through 212' Processing helix chain 'A' and resid 241 through 251 Processing helix chain 'A' and resid 291 through 299 Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 346 through 348 No H-bonds generated for 'chain 'A' and resid 346 through 348' Processing helix chain 'A' and resid 538 through 541 No H-bonds generated for 'chain 'A' and resid 538 through 541' Processing helix chain 'A' and resid 551 through 559 removed outlier: 3.595A pdb=" N ALA A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 558 " --> pdb=" O GLN A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 577 Processing helix chain 'A' and resid 586 through 592 Proline residue: A 590 - end of helix Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.626A pdb=" N LEU A 611 " --> pdb=" O THR A 607 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA A 612 " --> pdb=" O TYR A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 650 removed outlier: 4.234A pdb=" N SER A 650 " --> pdb=" O GLN A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 658 Processing helix chain 'A' and resid 660 through 666 Processing helix chain 'A' and resid 676 through 685 Processing helix chain 'A' and resid 690 through 705 Processing helix chain 'A' and resid 710 through 721 Processing helix chain 'A' and resid 726 through 751 Processing helix chain 'A' and resid 761 through 776 Processing helix chain 'A' and resid 798 through 800 No H-bonds generated for 'chain 'A' and resid 798 through 800' Processing helix chain 'A' and resid 840 through 857 removed outlier: 3.573A pdb=" N LEU A 845 " --> pdb=" O ASP A 841 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 846 " --> pdb=" O MET A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 892 Processing helix chain 'A' and resid 906 through 914 Processing helix chain 'A' and resid 918 through 942 removed outlier: 4.227A pdb=" N SER A 931 " --> pdb=" O ARG A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 994 Processing helix chain 'A' and resid 1005 through 1035 removed outlier: 4.330A pdb=" N HIS A1023 " --> pdb=" O ALA A1019 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR A1024 " --> pdb=" O LEU A1020 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ASN A1025 " --> pdb=" O ARG A1021 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU A1026 " --> pdb=" O HIS A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1055 removed outlier: 3.680A pdb=" N ASP A1053 " --> pdb=" O TYR A1050 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA A1054 " --> pdb=" O ILE A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1075 Processing helix chain 'B' and resid 10 through 20 Processing helix chain 'B' and resid 40 through 50 Processing helix chain 'B' and resid 52 through 72 removed outlier: 3.798A pdb=" N GLU B 71 " --> pdb=" O GLU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 91 removed outlier: 4.137A pdb=" N ALA B 79 " --> pdb=" O ASP B 76 " (cutoff:3.500A) Proline residue: B 80 - end of helix removed outlier: 3.684A pdb=" N VAL B 89 " --> pdb=" O TYR B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 111 removed outlier: 4.274A pdb=" N ARG B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 135 Processing helix chain 'B' and resid 139 through 149 Processing helix chain 'B' and resid 173 through 183 Processing helix chain 'B' and resid 189 through 204 removed outlier: 3.850A pdb=" N THR B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 219 Processing helix chain 'B' and resid 223 through 239 removed outlier: 3.773A pdb=" N ALA B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 264 removed outlier: 3.892A pdb=" N LYS B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 524 through 542 Processing helix chain 'B' and resid 605 through 610 Processing helix chain 'B' and resid 614 through 619 Processing helix chain 'B' and resid 651 through 662 removed outlier: 3.648A pdb=" N CYS B 660 " --> pdb=" O LEU B 656 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 704 Processing helix chain 'B' and resid 708 through 712 Processing helix chain 'B' and resid 820 through 822 No H-bonds generated for 'chain 'B' and resid 820 through 822' Processing helix chain 'F' and resid 5 through 23 Processing helix chain 'F' and resid 30 through 44 Processing helix chain 'F' and resid 56 through 58 No H-bonds generated for 'chain 'F' and resid 56 through 58' Processing helix chain 'D' and resid 5 through 23 removed outlier: 3.503A pdb=" N LYS D 14 " --> pdb=" O ALA D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 44 Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'D' and resid 60 through 63 No H-bonds generated for 'chain 'D' and resid 60 through 63' Processing sheet with id= A, first strand: chain 'E' and resid 58 through 63 removed outlier: 6.581A pdb=" N ALA E 73 " --> pdb=" O TYR E 59 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N MET E 61 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL E 71 " --> pdb=" O MET E 61 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N TRP E 63 " --> pdb=" O LEU E 69 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LEU E 69 " --> pdb=" O TRP E 63 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASP E 83 " --> pdb=" O LYS E 89 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LYS E 89 " --> pdb=" O ASP E 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 100 through 105 removed outlier: 6.922A pdb=" N GLY E 115 " --> pdb=" O MET E 101 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N CYS E 103 " --> pdb=" O ALA E 113 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA E 113 " --> pdb=" O CYS E 103 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N TYR E 105 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N TYR E 111 " --> pdb=" O TYR E 105 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ASN E 125 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N VAL E 135 " --> pdb=" O ASN E 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 178 through 180 removed outlier: 3.548A pdb=" N CYS E 148 " --> pdb=" O SER E 160 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 187 through 192 removed outlier: 6.976A pdb=" N GLY E 202 " --> pdb=" O MET E 188 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU E 190 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL E 200 " --> pdb=" O LEU E 190 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LEU E 192 " --> pdb=" O LEU E 198 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N LEU E 198 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN E 220 " --> pdb=" O LEU E 210 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASP E 212 " --> pdb=" O CYS E 218 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N CYS E 218 " --> pdb=" O ASP E 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 229 through 234 removed outlier: 6.843A pdb=" N GLY E 244 " --> pdb=" O ASN E 230 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE E 232 " --> pdb=" O ALA E 242 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA E 242 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE E 234 " --> pdb=" O ALA E 240 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA E 240 " --> pdb=" O PHE E 234 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR E 249 " --> pdb=" O SER E 245 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET E 262 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ASP E 254 " --> pdb=" O GLU E 260 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N GLU E 260 " --> pdb=" O ASP E 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 273 through 278 removed outlier: 6.463A pdb=" N GLY E 288 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL E 276 " --> pdb=" O LEU E 286 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU E 286 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N PHE E 278 " --> pdb=" O LEU E 284 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU E 284 " --> pdb=" O PHE E 278 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASP E 298 " --> pdb=" O ARG E 304 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ARG E 304 " --> pdb=" O ASP E 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 317 through 320 removed outlier: 6.785A pdb=" N ASN E 340 " --> pdb=" O THR E 47 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N THR E 47 " --> pdb=" O ASN E 340 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.408A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.780A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.484A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.585A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.321A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.300A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 317 through 320 removed outlier: 3.616A pdb=" N LEU C 336 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 41 through 43 Processing sheet with id= P, first strand: chain 'A' and resid 136 through 139 Processing sheet with id= Q, first strand: chain 'A' and resid 229 through 236 Processing sheet with id= R, first strand: chain 'A' and resid 412 through 415 removed outlier: 4.000A pdb=" N VAL A 412 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG A 366 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N SER A 517 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ILE A 368 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N SER A 515 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 367 through 369 Processing sheet with id= T, first strand: chain 'A' and resid 428 through 435 Processing sheet with id= U, first strand: chain 'A' and resid 811 through 814 Processing sheet with id= V, first strand: chain 'B' and resid 288 through 292 removed outlier: 8.862A pdb=" N TYR B 289 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR B 162 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N TYR B 291 " --> pdb=" O THR B 162 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU B 164 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N THR B 514 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N VAL B 163 " --> pdb=" O THR B 514 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ARG B 516 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU B 165 " --> pdb=" O ARG B 516 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL B 518 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N LYS B 551 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL B 517 " --> pdb=" O LYS B 551 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLN B 553 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL B 519 " --> pdb=" O GLN B 553 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE B 555 " --> pdb=" O VAL B 519 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLY B 521 " --> pdb=" O PHE B 555 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL B 557 " --> pdb=" O GLY B 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'B' and resid 692 through 695 removed outlier: 3.701A pdb=" N ALA B 813 " --> pdb=" O GLY B 695 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 740 through 748 removed outlier: 4.254A pdb=" N LYS B 801 " --> pdb=" O SER B 731 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR B 677 " --> pdb=" O ILE B 828 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N CYS B 830 " --> pdb=" O GLU B 675 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLU B 675 " --> pdb=" O CYS B 830 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N VAL B 832 " --> pdb=" O GLN B 673 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N GLN B 673 " --> pdb=" O VAL B 832 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 751 through 755 removed outlier: 3.652A pdb=" N ILE B 797 " --> pdb=" O LEU B 772 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU B 776 " --> pdb=" O SER B 793 " (cutoff:3.500A) 666 hydrogen bonds defined for protein. 1773 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: 14.54 Time building geometry restraints manager: 28.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 17931 1.03 - 1.23: 65 1.23 - 1.42: 7642 1.42 - 1.62: 10619 1.62 - 1.81: 150 Bond restraints: 36407 Sorted by residual: bond pdb=" CD ARG A 684 " pdb=" NE ARG A 684 " ideal model delta sigma weight residual 1.458 1.438 0.020 1.40e-02 5.10e+03 2.08e+00 bond pdb=" C4 ADP A1201 " pdb=" C5 ADP A1201 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.68e+00 bond pdb=" CB GLN A 432 " pdb=" CG GLN A 432 " ideal model delta sigma weight residual 1.520 1.484 0.036 3.00e-02 1.11e+03 1.43e+00 bond pdb=" CA LEU B 253 " pdb=" C LEU B 253 " ideal model delta sigma weight residual 1.519 1.507 0.012 1.22e-02 6.72e+03 1.03e+00 bond pdb=" CA TYR B 75 " pdb=" CB TYR B 75 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.69e-02 3.50e+03 9.58e-01 ... (remaining 36402 not shown) Histogram of bond angle deviations from ideal: 100.16 - 107.31: 1263 107.31 - 114.47: 44269 114.47 - 121.63: 13244 121.63 - 128.79: 6814 128.79 - 135.94: 161 Bond angle restraints: 65751 Sorted by residual: angle pdb=" N LEU B 253 " pdb=" CA LEU B 253 " pdb=" C LEU B 253 " ideal model delta sigma weight residual 113.55 108.31 5.24 1.26e+00 6.30e-01 1.73e+01 angle pdb=" N ARG B 254 " pdb=" CA ARG B 254 " pdb=" C ARG B 254 " ideal model delta sigma weight residual 111.33 107.33 4.00 1.21e+00 6.83e-01 1.09e+01 angle pdb=" CA TYR B 75 " pdb=" CB TYR B 75 " pdb=" CG TYR B 75 " ideal model delta sigma weight residual 113.90 119.13 -5.23 1.80e+00 3.09e-01 8.46e+00 angle pdb=" N ARG A 927 " pdb=" CA ARG A 927 " pdb=" C ARG A 927 " ideal model delta sigma weight residual 113.19 109.77 3.42 1.19e+00 7.06e-01 8.25e+00 angle pdb=" N GLN B 45 " pdb=" CA GLN B 45 " pdb=" C GLN B 45 " ideal model delta sigma weight residual 111.82 108.62 3.20 1.16e+00 7.43e-01 7.62e+00 ... (remaining 65746 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.74: 16597 29.74 - 59.47: 447 59.47 - 89.21: 30 89.21 - 118.94: 0 118.94 - 148.68: 3 Dihedral angle restraints: 17077 sinusoidal: 9317 harmonic: 7760 Sorted by residual: dihedral pdb=" CD ARG A 684 " pdb=" NE ARG A 684 " pdb=" CZ ARG A 684 " pdb=" NH1 ARG A 684 " ideal model delta sinusoidal sigma weight residual 0.00 -74.16 74.16 1 1.00e+01 1.00e-02 6.98e+01 dihedral pdb=" C5' ADP A1201 " pdb=" O5' ADP A1201 " pdb=" PA ADP A1201 " pdb=" O2A ADP A1201 " ideal model delta sinusoidal sigma weight residual 300.00 151.33 148.68 1 2.00e+01 2.50e-03 4.45e+01 dihedral pdb=" O2A ADP A1201 " pdb=" O3A ADP A1201 " pdb=" PA ADP A1201 " pdb=" PB ADP A1201 " ideal model delta sinusoidal sigma weight residual -60.00 70.00 -130.00 1 2.00e+01 2.50e-03 3.94e+01 ... (remaining 17074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1840 0.031 - 0.063: 666 0.063 - 0.094: 178 0.094 - 0.125: 119 0.125 - 0.156: 33 Chirality restraints: 2836 Sorted by residual: chirality pdb=" CA VAL B 117 " pdb=" N VAL B 117 " pdb=" C VAL B 117 " pdb=" CB VAL B 117 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.12e-01 chirality pdb=" CA VAL E 296 " pdb=" N VAL E 296 " pdb=" C VAL E 296 " pdb=" CB VAL E 296 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA ILE E 81 " pdb=" N ILE E 81 " pdb=" C ILE E 81 " pdb=" CB ILE E 81 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.86e-01 ... (remaining 2833 not shown) Planarity restraints: 5337 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 684 " 0.965 9.50e-02 1.11e+02 3.23e-01 1.18e+02 pdb=" NE ARG A 684 " -0.055 2.00e-02 2.50e+03 pdb=" CZ ARG A 684 " 0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG A 684 " -0.031 2.00e-02 2.50e+03 pdb=" NH2 ARG A 684 " -0.021 2.00e-02 2.50e+03 pdb="HH11 ARG A 684 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 684 " 0.016 2.00e-02 2.50e+03 pdb="HH21 ARG A 684 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 684 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 252 " -0.028 2.00e-02 2.50e+03 5.55e-02 3.08e+01 pdb=" C TRP B 252 " 0.096 2.00e-02 2.50e+03 pdb=" O TRP B 252 " -0.036 2.00e-02 2.50e+03 pdb=" N LEU B 253 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 655 " 0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C MET B 655 " -0.058 2.00e-02 2.50e+03 pdb=" O MET B 655 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU B 656 " 0.020 2.00e-02 2.50e+03 ... (remaining 5334 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.06: 542 2.06 - 2.69: 58026 2.69 - 3.33: 103743 3.33 - 3.96: 132655 3.96 - 4.60: 209442 Nonbonded interactions: 504408 Sorted by model distance: nonbonded pdb=" OD1 ASP B 131 " pdb=" HZ3 LYS B 135 " model vdw 1.421 1.850 nonbonded pdb=" HG SER E 147 " pdb=" O VAL E 187 " model vdw 1.500 1.850 nonbonded pdb=" H GLY B 521 " pdb=" O VAL B 557 " model vdw 1.504 1.850 nonbonded pdb=" O VAL B 814 " pdb=" H LEU B 824 " model vdw 1.529 1.850 nonbonded pdb=" HE ARG A 397 " pdb=" O GLU A 415 " model vdw 1.536 1.850 ... (remaining 504403 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 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.410 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: 0.520 Extract box with map and model: 8.840 Check model and map are aligned: 0.580 Set scattering table: 0.360 Process input model: 113.440 Find NCS groups from input model: 0.920 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: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5748 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 : 0.003 0.047 18412 Z= 0.183 Angle : 0.589 8.801 24943 Z= 0.323 Chirality : 0.041 0.156 2836 Planarity : 0.009 0.416 3181 Dihedral : 13.236 148.676 6780 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.73 % Allowed : 6.36 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -2.70 (0.16), residues: 2219 helix: -1.57 (0.17), residues: 774 sheet: -1.38 (0.22), residues: 470 loop : -2.07 (0.18), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 42 HIS 0.003 0.001 HIS A 199 PHE 0.021 0.002 PHE B 129 TYR 0.041 0.002 TYR B 658 ARG 0.047 0.001 ARG A 684 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 338 time to evaluate : 3.103 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 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: 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: 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: 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: E 126 LEU cc_start: 0.5318 (mt) cc_final: 0.4978 (tt) REVERT: A 99 LEU cc_start: 0.8339 (mt) cc_final: 0.7765 (mp) REVERT: A 207 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7563 (tt) REVERT: A 652 GLU cc_start: 0.7063 (mm-30) cc_final: 0.6488 (pt0) REVERT: A 878 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.6905 (ptm) REVERT: A 883 LYS cc_start: 0.7985 (mttt) cc_final: 0.7758 (pttt) REVERT: A 1068 PHE cc_start: 0.5283 (t80) cc_final: 0.4859 (t80) REVERT: B 127 LEU cc_start: 0.8893 (mt) cc_final: 0.8413 (tt) REVERT: B 270 LEU cc_start: 0.7338 (mt) cc_final: 0.7078 (tp) REVERT: B 691 SER cc_start: 0.6860 (OUTLIER) cc_final: 0.5812 (m) outliers start: 54 outliers final: 20 residues processed: 382 average time/residue: 0.8834 time to fit residues: 472.1316 Evaluate side-chains 235 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 212 time to evaluate : 3.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 749 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 0.2980 chunk 169 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 203 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 9 GLN E 13 GLN E 295 ASN C 259 GLN C 295 ASN B 45 GLN B 219 GLN B 295 GLN B 825 GLN F 4 ASN F 18 GLN D 4 ASN ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5811 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18412 Z= 0.222 Angle : 0.576 6.236 24943 Z= 0.302 Chirality : 0.041 0.155 2836 Planarity : 0.005 0.093 3181 Dihedral : 7.234 123.855 2496 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.27 % Allowed : 11.26 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -2.03 (0.17), residues: 2219 helix: -0.71 (0.18), residues: 780 sheet: -1.32 (0.22), residues: 489 loop : -1.80 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 910 HIS 0.005 0.001 HIS B 690 PHE 0.014 0.001 PHE B 129 TYR 0.032 0.002 TYR B 658 ARG 0.009 0.000 ARG A 684 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 222 time to evaluate : 2.912 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 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 126 LEU cc_start: 0.5280 (mt) cc_final: 0.4941 (tt) REVERT: E 335 PHE cc_start: 0.3678 (OUTLIER) cc_final: 0.3462 (m-80) REVERT: C 105 TYR cc_start: 0.2815 (OUTLIER) cc_final: 0.0163 (t80) REVERT: A 207 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7503 (tt) REVERT: A 741 MET cc_start: 0.8890 (mtm) cc_final: 0.8618 (mtp) REVERT: A 1052 ARG cc_start: 0.7869 (mtp-110) cc_final: 0.7651 (tpt170) REVERT: B 127 LEU cc_start: 0.8943 (mt) cc_final: 0.8440 (tt) REVERT: B 771 THR cc_start: 0.8041 (OUTLIER) cc_final: 0.7815 (p) outliers start: 45 outliers final: 22 residues processed: 252 average time/residue: 0.8634 time to fit residues: 308.5681 Evaluate side-chains 222 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 196 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 335 PHE Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 556 TYR Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 752 ASN Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 872 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 20.0000 chunk 169 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 203 optimal weight: 5.9990 chunk 220 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 chunk 202 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 163 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN A 231 GLN A 396 GLN ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5860 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18412 Z= 0.253 Angle : 0.572 6.461 24943 Z= 0.301 Chirality : 0.041 0.153 2836 Planarity : 0.004 0.051 3181 Dihedral : 6.708 119.726 2478 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.37 % Allowed : 12.87 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -1.75 (0.17), residues: 2219 helix: -0.42 (0.17), residues: 786 sheet: -1.23 (0.21), residues: 515 loop : -1.65 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 339 HIS 0.005 0.001 HIS B 54 PHE 0.017 0.001 PHE B 129 TYR 0.022 0.002 TYR B 658 ARG 0.004 0.000 ARG B 829 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 202 time to evaluate : 2.987 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 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: 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: 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: E 126 LEU cc_start: 0.5064 (mt) cc_final: 0.4721 (tt) REVERT: E 188 MET cc_start: 0.1002 (mtt) cc_final: -0.2467 (mmm) REVERT: C 105 TYR cc_start: 0.2489 (OUTLIER) cc_final: -0.0073 (t80) REVERT: A 207 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7547 (tt) REVERT: A 702 GLU cc_start: 0.6726 (mm-30) cc_final: 0.6493 (mm-30) REVERT: A 878 MET cc_start: 0.6649 (ptm) cc_final: 0.6246 (ptm) REVERT: B 127 LEU cc_start: 0.8949 (mt) cc_final: 0.8433 (tt) outliers start: 47 outliers final: 33 residues processed: 235 average time/residue: 0.8297 time to fit residues: 284.7371 Evaluate side-chains 227 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 192 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 556 TYR Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 752 ASN Chi-restraints excluded: chain B residue 812 PHE Chi-restraints excluded: chain B residue 872 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 8.9990 chunk 153 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 22 optimal weight: 30.0000 chunk 97 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 204 optimal weight: 9.9990 chunk 216 optimal weight: 7.9990 chunk 106 optimal weight: 0.7980 chunk 193 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 259 GLN ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 HIS ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5899 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18412 Z= 0.273 Angle : 0.583 6.843 24943 Z= 0.307 Chirality : 0.042 0.158 2836 Planarity : 0.004 0.054 3181 Dihedral : 6.492 125.006 2475 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.57 % Allowed : 14.13 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -1.70 (0.17), residues: 2219 helix: -0.31 (0.18), residues: 789 sheet: -1.26 (0.22), residues: 496 loop : -1.66 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 339 HIS 0.006 0.001 HIS A 225 PHE 0.021 0.001 PHE B 129 TYR 0.021 0.002 TYR B 658 ARG 0.006 0.000 ARG A 712 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 194 time to evaluate : 2.898 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 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: 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: E 188 MET cc_start: 0.0939 (mtt) cc_final: -0.2402 (mmm) REVERT: C 105 TYR cc_start: 0.2610 (OUTLIER) cc_final: 0.0145 (t80) REVERT: A 207 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7482 (tt) REVERT: A 702 GLU cc_start: 0.6783 (mm-30) cc_final: 0.6254 (mm-30) REVERT: B 127 LEU cc_start: 0.8946 (mt) cc_final: 0.8442 (tt) outliers start: 51 outliers final: 42 residues processed: 231 average time/residue: 0.8360 time to fit residues: 286.5922 Evaluate side-chains 226 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 182 time to evaluate : 3.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 556 TYR Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 752 ASN Chi-restraints excluded: chain B residue 812 PHE Chi-restraints excluded: chain B residue 872 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 161 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 184 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 110 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5857 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18412 Z= 0.170 Angle : 0.517 6.356 24943 Z= 0.268 Chirality : 0.040 0.155 2836 Planarity : 0.004 0.051 3181 Dihedral : 6.200 125.058 2475 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.17 % Allowed : 14.84 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -1.25 (0.17), residues: 2219 helix: 0.27 (0.18), residues: 789 sheet: -1.19 (0.22), residues: 508 loop : -1.50 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.004 0.001 HIS E 311 PHE 0.014 0.001 PHE A 249 TYR 0.025 0.001 TYR A 100 ARG 0.003 0.000 ARG B 829 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 190 time to evaluate : 3.105 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 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: 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: E 126 LEU cc_start: 0.5129 (mt) cc_final: 0.4733 (tt) REVERT: E 188 MET cc_start: 0.0890 (mtt) cc_final: -0.2309 (mmm) REVERT: C 105 TYR cc_start: 0.2641 (OUTLIER) cc_final: 0.0017 (t80) REVERT: A 695 LEU cc_start: 0.6426 (OUTLIER) cc_final: 0.6025 (tt) REVERT: A 702 GLU cc_start: 0.6699 (mm-30) cc_final: 0.6355 (mm-30) REVERT: A 878 MET cc_start: 0.6324 (ptm) cc_final: 0.6026 (ptm) REVERT: B 127 LEU cc_start: 0.8898 (mt) cc_final: 0.8381 (tt) outliers start: 43 outliers final: 36 residues processed: 220 average time/residue: 0.8231 time to fit residues: 268.5098 Evaluate side-chains 216 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 178 time to evaluate : 3.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 556 TYR Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 752 ASN Chi-restraints excluded: chain B residue 812 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 216 optimal weight: 6.9990 chunk 179 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 18 optimal weight: 20.0000 chunk 71 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 818 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5900 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18412 Z= 0.233 Angle : 0.545 6.787 24943 Z= 0.284 Chirality : 0.040 0.147 2836 Planarity : 0.004 0.046 3181 Dihedral : 6.173 125.640 2473 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.68 % Allowed : 15.14 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -1.29 (0.17), residues: 2219 helix: 0.28 (0.18), residues: 788 sheet: -1.19 (0.22), residues: 485 loop : -1.58 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 339 HIS 0.004 0.001 HIS E 311 PHE 0.017 0.001 PHE B 129 TYR 0.014 0.002 TYR B 658 ARG 0.004 0.000 ARG A 712 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 179 time to evaluate : 2.928 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 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: 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: E 126 LEU cc_start: 0.5087 (mt) cc_final: 0.4654 (tt) REVERT: E 188 MET cc_start: 0.0712 (mtt) cc_final: -0.2443 (mmm) REVERT: C 105 TYR cc_start: 0.2615 (OUTLIER) cc_final: 0.0157 (t80) REVERT: C 337 LYS cc_start: 0.7907 (ttmt) cc_final: 0.7671 (ttmt) REVERT: A 695 LEU cc_start: 0.6386 (OUTLIER) cc_final: 0.5996 (tt) REVERT: A 702 GLU cc_start: 0.6796 (mm-30) cc_final: 0.6265 (mm-30) REVERT: A 881 ILE cc_start: 0.5483 (OUTLIER) cc_final: 0.5243 (mt) REVERT: B 127 LEU cc_start: 0.8930 (mt) cc_final: 0.8413 (tt) outliers start: 53 outliers final: 41 residues processed: 218 average time/residue: 0.7798 time to fit residues: 247.5753 Evaluate side-chains 218 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 174 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 556 TYR Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 812 PHE Chi-restraints excluded: chain B residue 872 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 0.8980 chunk 24 optimal weight: 20.0000 chunk 123 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 182 optimal weight: 7.9990 chunk 121 optimal weight: 0.9980 chunk 215 optimal weight: 20.0000 chunk 135 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5857 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18412 Z= 0.152 Angle : 0.500 6.518 24943 Z= 0.257 Chirality : 0.040 0.155 2836 Planarity : 0.004 0.046 3181 Dihedral : 5.835 126.150 2470 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.17 % Allowed : 15.70 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -0.92 (0.18), residues: 2219 helix: 0.72 (0.19), residues: 782 sheet: -1.11 (0.22), residues: 495 loop : -1.40 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 339 HIS 0.005 0.001 HIS E 311 PHE 0.017 0.001 PHE A 993 TYR 0.016 0.001 TYR A 100 ARG 0.002 0.000 ARG B 829 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 183 time to evaluate : 3.159 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 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: 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: E 126 LEU cc_start: 0.5169 (mt) cc_final: 0.4673 (tt) REVERT: E 188 MET cc_start: 0.0619 (mtt) cc_final: -0.2485 (mmm) REVERT: A 684 ARG cc_start: 0.6370 (tpp-160) cc_final: 0.6073 (ttm-80) REVERT: A 695 LEU cc_start: 0.6431 (OUTLIER) cc_final: 0.6040 (tt) REVERT: A 702 GLU cc_start: 0.6634 (mm-30) cc_final: 0.6269 (mm-30) REVERT: A 881 ILE cc_start: 0.5467 (OUTLIER) cc_final: 0.5232 (mt) REVERT: B 127 LEU cc_start: 0.8924 (mt) cc_final: 0.8409 (tt) outliers start: 43 outliers final: 33 residues processed: 212 average time/residue: 0.8028 time to fit residues: 250.3431 Evaluate side-chains 207 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 172 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 556 TYR Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 772 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 chunk 169 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 818 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5877 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18412 Z= 0.184 Angle : 0.512 6.646 24943 Z= 0.265 Chirality : 0.040 0.151 2836 Planarity : 0.004 0.041 3181 Dihedral : 5.796 125.049 2468 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.27 % Allowed : 15.60 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -0.94 (0.18), residues: 2219 helix: 0.70 (0.19), residues: 789 sheet: -1.06 (0.22), residues: 489 loop : -1.46 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 339 HIS 0.005 0.001 HIS E 311 PHE 0.016 0.001 PHE A 249 TYR 0.014 0.001 TYR A 100 ARG 0.003 0.000 ARG A 712 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 177 time to evaluate : 2.921 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 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: 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: E 126 LEU cc_start: 0.5130 (mt) cc_final: 0.4622 (tt) REVERT: E 188 MET cc_start: 0.0601 (mtt) cc_final: -0.2421 (mmm) REVERT: C 105 TYR cc_start: 0.2939 (OUTLIER) cc_final: 0.0187 (t80) REVERT: A 684 ARG cc_start: 0.6425 (tpp-160) cc_final: 0.5821 (ttm-80) REVERT: A 695 LEU cc_start: 0.6482 (OUTLIER) cc_final: 0.6074 (tt) REVERT: A 702 GLU cc_start: 0.6659 (mm-30) cc_final: 0.6287 (mm-30) REVERT: A 881 ILE cc_start: 0.5472 (OUTLIER) cc_final: 0.5232 (mt) REVERT: A 940 PHE cc_start: 0.8523 (t80) cc_final: 0.8265 (t80) REVERT: B 127 LEU cc_start: 0.8973 (mt) cc_final: 0.8409 (tt) outliers start: 45 outliers final: 36 residues processed: 208 average time/residue: 0.7938 time to fit residues: 242.1676 Evaluate side-chains 209 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 170 time to evaluate : 3.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 556 TYR Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 772 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 5.9990 chunk 206 optimal weight: 0.5980 chunk 188 optimal weight: 6.9990 chunk 201 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 181 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 chunk 200 optimal weight: 8.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 GLN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 GLN A 775 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5993 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 18412 Z= 0.428 Angle : 0.695 8.937 24943 Z= 0.372 Chirality : 0.045 0.191 2836 Planarity : 0.006 0.054 3181 Dihedral : 6.523 124.521 2466 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.83 % Favored : 91.12 % Rotamer: Outliers : 2.68 % Allowed : 15.65 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -1.86 (0.17), residues: 2219 helix: -0.40 (0.18), residues: 785 sheet: -1.19 (0.23), residues: 471 loop : -1.88 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 413 HIS 0.007 0.002 HIS C 183 PHE 0.027 0.002 PHE B 129 TYR 0.023 0.003 TYR B 289 ARG 0.011 0.001 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 171 time to evaluate : 3.167 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 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 105 TYR cc_start: 0.2868 (OUTLIER) cc_final: 0.0326 (t80) REVERT: A 695 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.6162 (tt) REVERT: A 702 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6266 (mm-30) REVERT: A 881 ILE cc_start: 0.5470 (OUTLIER) cc_final: 0.5226 (mt) REVERT: A 1052 ARG cc_start: 0.7597 (mtp-110) cc_final: 0.7365 (tpt170) REVERT: B 127 LEU cc_start: 0.8955 (mt) cc_final: 0.8433 (tt) REVERT: B 744 MET cc_start: 0.6703 (mmt) cc_final: 0.6219 (mmp) outliers start: 53 outliers final: 44 residues processed: 209 average time/residue: 0.8084 time to fit residues: 246.9789 Evaluate side-chains 206 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 159 time to evaluate : 3.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 556 TYR Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 872 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 1.9990 chunk 212 optimal weight: 20.0000 chunk 129 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 223 optimal weight: 0.5980 chunk 205 optimal weight: 2.9990 chunk 177 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 137 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 HIS ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5890 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18412 Z= 0.164 Angle : 0.536 7.389 24943 Z= 0.277 Chirality : 0.040 0.160 2836 Planarity : 0.004 0.049 3181 Dihedral : 6.021 128.045 2466 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.87 % Allowed : 16.76 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -1.19 (0.18), residues: 2219 helix: 0.39 (0.19), residues: 788 sheet: -1.10 (0.23), residues: 488 loop : -1.58 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 697 HIS 0.006 0.001 HIS E 311 PHE 0.016 0.001 PHE A 249 TYR 0.017 0.001 TYR A 100 ARG 0.003 0.000 ARG E 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 165 time to evaluate : 2.754 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 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: 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: E 188 MET cc_start: 0.0590 (mtt) cc_final: -0.1970 (mmt) REVERT: C 105 TYR cc_start: 0.3091 (OUTLIER) cc_final: 0.0141 (t80) REVERT: C 155 ASN cc_start: 0.8401 (t0) cc_final: 0.7792 (t0) REVERT: A 684 ARG cc_start: 0.6367 (tpp-160) cc_final: 0.6099 (ttm-80) REVERT: A 695 LEU cc_start: 0.6304 (OUTLIER) cc_final: 0.5893 (tt) REVERT: A 702 GLU cc_start: 0.6810 (mm-30) cc_final: 0.6260 (mm-30) REVERT: A 881 ILE cc_start: 0.5364 (OUTLIER) cc_final: 0.5045 (mt) REVERT: B 127 LEU cc_start: 0.8955 (mt) cc_final: 0.8382 (tt) outliers start: 37 outliers final: 32 residues processed: 191 average time/residue: 0.7869 time to fit residues: 221.2357 Evaluate side-chains 196 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 161 time to evaluate : 2.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 556 TYR Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 772 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 163 optimal weight: 3.9990 chunk 26 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 chunk 177 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 182 optimal weight: 0.0370 chunk 22 optimal weight: 40.0000 chunk 32 optimal weight: 8.9990 overall best weight: 2.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 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 = 0.4761 r_free = 0.4761 target = 0.136719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.097142 restraints weight = 159020.498| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 4.12 r_work: 0.3812 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18412 Z= 0.266 Angle : 0.581 6.725 24943 Z= 0.305 Chirality : 0.041 0.175 2836 Planarity : 0.005 0.047 3181 Dihedral : 6.115 124.197 2466 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 2.02 % Allowed : 16.86 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -1.42 (0.17), residues: 2219 helix: 0.13 (0.18), residues: 787 sheet: -1.10 (0.23), residues: 482 loop : -1.70 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 413 HIS 0.006 0.001 HIS A1022 PHE 0.017 0.002 PHE B 129 TYR 0.015 0.002 TYR A 463 ARG 0.005 0.000 ARG A 178 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8421.36 seconds wall clock time: 151 minutes 3.00 seconds (9063.00 seconds total)