Starting phenix.real_space_refine on Sun Oct 12 20:27:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9f_37367/10_2025/8w9f_37367_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9f_37367/10_2025/8w9f_37367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8w9f_37367/10_2025/8w9f_37367_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9f_37367/10_2025/8w9f_37367_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w9f_37367/10_2025/8w9f_37367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9f_37367/10_2025/8w9f_37367.map" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.000 sd= 0.003 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 Zn 7 6.06 5 P 292 5.49 5 S 104 5.16 5 C 16800 2.51 5 N 4889 2.21 5 O 5776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 277 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27868 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 5066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 5066 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2884 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 333} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3057 Classifications: {'peptide': 385} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 366} Chain: "C" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1483 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 175} Chain: "D" Number of atoms: 1497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1497 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 176} Chain: "F" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1282 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 147} Chain breaks: 1 Chain: "a" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "b" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "c" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "d" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "e" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "f" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "g" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "h" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "i" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3011 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "j" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3010 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "G" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 570 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain breaks: 2 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5538 SG CYS E 263 92.341 97.136 91.981 1.00 63.46 S ATOM 5555 SG CYS E 266 89.928 95.114 93.570 1.00 53.02 S ATOM 5708 SG CYS E 286 93.231 93.681 92.999 1.00 38.07 S ATOM 5619 SG CYS E 275 100.350 102.730 82.033 1.00 87.52 S ATOM 5640 SG CYS E 278 96.846 101.994 81.535 1.00 89.24 S ATOM 5843 SG CYS E 303 98.070 98.765 80.999 1.00 84.64 S ATOM 5866 SG CYS E 306 98.964 101.341 78.710 1.00 85.05 S ATOM 6956 SG CYS E 440 60.182 85.037 111.606 1.00 27.99 S ATOM 6982 SG CYS E 443 58.098 82.201 111.670 1.00 23.37 S ATOM 7170 SG CYS E 466 59.127 83.512 115.391 1.00 25.28 S ATOM 6795 SG CYS E 420 53.575 85.172 126.282 1.00 30.63 S ATOM 7051 SG CYS E 451 57.050 84.408 125.918 1.00 26.14 S ATOM 14065 SG CYS F 263 43.423 37.948 66.888 1.00 95.21 S ATOM 14082 SG CYS F 266 44.744 34.700 67.224 1.00 88.26 S ATOM 14235 SG CYS F 286 42.230 36.473 69.982 1.00 90.91 S ATOM 14146 SG CYS F 275 40.471 50.443 63.991 1.00 96.38 S ATOM 14167 SG CYS F 278 43.804 49.392 64.497 1.00 89.68 S ATOM 14370 SG CYS F 303 43.056 49.359 68.089 1.00 96.28 S ATOM 14393 SG CYS F 306 42.764 52.457 65.952 1.00 88.14 S Time building chain proxies: 5.56, per 1000 atoms: 0.20 Number of scatterers: 27868 At special positions: 0 Unit cell: (144.571, 183.703, 168.485, 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) Zn 7 29.99 S 104 16.00 P 292 15.00 O 5776 8.00 N 4889 7.00 C 16800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 977.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1000 " pdb="ZN ZN B1000 " - pdb=" ND1 HIS B 188 " pdb=" ZN E1000 " pdb="ZN ZN E1000 " - pdb=" ND1 HIS E 283 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 266 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 263 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 286 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 303 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 275 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 306 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 278 " pdb=" ZN E1002 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 440 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 443 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 466 " pdb=" ZN E1003 " pdb="ZN ZN E1003 " - pdb=" ND1 HIS E 448 " pdb="ZN ZN E1003 " - pdb=" SG CYS E 420 " pdb="ZN ZN E1003 " - pdb=" SG CYS E 451 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" ND1 HIS F 283 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 286 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 266 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 263 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 306 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 303 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 278 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 275 " Number of angles added : 18 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5110 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 22 sheets defined 60.5% alpha, 4.7% beta 145 base pairs and 258 stacking pairs defined. Time for finding SS restraints: 3.43 Creating SS restraints... Processing helix chain 'A' and resid 663 through 677 removed outlier: 3.543A pdb=" N THR A 667 " --> pdb=" O ASN A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 694 removed outlier: 3.535A pdb=" N TYR A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 711 removed outlier: 3.748A pdb=" N PHE A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TYR A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 724 Processing helix chain 'A' and resid 772 through 777 removed outlier: 3.506A pdb=" N GLU A 776 " --> pdb=" O ASP A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 840 removed outlier: 3.767A pdb=" N ILE A 810 " --> pdb=" O THR A 806 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS A 830 " --> pdb=" O ARG A 826 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN A 840 " --> pdb=" O ASN A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 849 removed outlier: 3.578A pdb=" N ASN A 848 " --> pdb=" O ASN A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 872 through 886 Processing helix chain 'A' and resid 886 through 925 Proline residue: A 892 - end of helix removed outlier: 4.978A pdb=" N VAL A 915 " --> pdb=" O GLU A 911 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 917 " --> pdb=" O ASN A 913 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE A 925 " --> pdb=" O GLN A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 928 No H-bonds generated for 'chain 'A' and resid 926 through 928' Processing helix chain 'A' and resid 930 through 934 removed outlier: 3.501A pdb=" N LEU A 933 " --> pdb=" O HIS A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 964 removed outlier: 3.899A pdb=" N ILE A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 999 removed outlier: 3.859A pdb=" N TYR A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1022 Processing helix chain 'A' and resid 1025 through 1039 Processing helix chain 'A' and resid 1064 through 1070 Processing helix chain 'A' and resid 1070 through 1081 removed outlier: 3.626A pdb=" N ASN A1081 " --> pdb=" O LEU A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1127 Processing helix chain 'A' and resid 1141 through 1173 removed outlier: 5.041A pdb=" N GLU A1166 " --> pdb=" O LYS A1162 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ARG A1167 " --> pdb=" O GLN A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1184 removed outlier: 3.833A pdb=" N LEU A1184 " --> pdb=" O PHE A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1194 Processing helix chain 'A' and resid 1202 through 1217 removed outlier: 3.753A pdb=" N GLN A1206 " --> pdb=" O ASP A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1232 Processing helix chain 'A' and resid 1237 through 1240 Processing helix chain 'A' and resid 1241 through 1259 removed outlier: 3.768A pdb=" N THR A1246 " --> pdb=" O ILE A1242 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A1256 " --> pdb=" O HIS A1252 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET A1257 " --> pdb=" O ALA A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1275 removed outlier: 3.509A pdb=" N ALA A1275 " --> pdb=" O LYS A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1294 removed outlier: 3.593A pdb=" N HIS A1293 " --> pdb=" O GLN A1289 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET A1294 " --> pdb=" O VAL A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1329 through 1343 removed outlier: 3.992A pdb=" N LEU A1343 " --> pdb=" O THR A1339 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 313 Processing helix chain 'E' and resid 315 through 330 Processing helix chain 'E' and resid 331 through 334 Processing helix chain 'E' and resid 336 through 343 Processing helix chain 'E' and resid 344 through 346 No H-bonds generated for 'chain 'E' and resid 344 through 346' Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.547A pdb=" N LYS E 358 " --> pdb=" O PRO E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 390 Processing helix chain 'E' and resid 430 through 434 removed outlier: 3.731A pdb=" N ASN E 433 " --> pdb=" O HIS E 430 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER E 434 " --> pdb=" O PRO E 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 430 through 434' Processing helix chain 'E' and resid 543 through 580 Processing helix chain 'B' and resid 28 through 32 removed outlier: 4.148A pdb=" N TYR B 32 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 55 removed outlier: 3.703A pdb=" N ARG B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.622A pdb=" N LYS B 59 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET B 61 " --> pdb=" O TYR B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 79 through 89 Processing helix chain 'B' and resid 94 through 98 removed outlier: 3.849A pdb=" N LYS B 98 " --> pdb=" O GLU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 104 Processing helix chain 'B' and resid 115 through 136 Processing helix chain 'B' and resid 164 through 175 removed outlier: 3.580A pdb=" N LEU B 168 " --> pdb=" O ASN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 243 through 262 Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 287 through 301 removed outlier: 4.425A pdb=" N CYS B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE B 301 " --> pdb=" O TYR B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 330 Processing helix chain 'B' and resid 343 through 347 Processing helix chain 'B' and resid 365 through 381 Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'C' and resid 225 through 239 Processing helix chain 'C' and resid 253 through 267 Processing helix chain 'C' and resid 271 through 297 removed outlier: 5.390A pdb=" N GLY C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ASN C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 317 Processing helix chain 'C' and resid 321 through 325 Processing helix chain 'C' and resid 327 through 344 removed outlier: 3.923A pdb=" N LEU C 331 " --> pdb=" O GLY C 327 " (cutoff:3.500A) Proline residue: C 339 - end of helix Processing helix chain 'C' and resid 348 through 369 Processing helix chain 'C' and resid 391 through 400 Processing helix chain 'D' and resid 225 through 241 Processing helix chain 'D' and resid 253 through 266 Processing helix chain 'D' and resid 271 through 294 removed outlier: 3.536A pdb=" N GLN D 275 " --> pdb=" O SER D 271 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLY D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 316 removed outlier: 4.171A pdb=" N GLN D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 327 through 344 removed outlier: 3.764A pdb=" N LEU D 331 " --> pdb=" O GLY D 327 " (cutoff:3.500A) Proline residue: D 339 - end of helix Processing helix chain 'D' and resid 348 through 369 Processing helix chain 'D' and resid 369 through 375 removed outlier: 3.716A pdb=" N TYR D 373 " --> pdb=" O HIS D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 385 removed outlier: 3.565A pdb=" N ASP D 384 " --> pdb=" O ARG D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 399 removed outlier: 3.576A pdb=" N GLU D 395 " --> pdb=" O SER D 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 313 Processing helix chain 'F' and resid 315 through 330 Processing helix chain 'F' and resid 333 through 344 removed outlier: 4.647A pdb=" N LYS F 338 " --> pdb=" O LYS F 334 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LEU F 339 " --> pdb=" O ILE F 335 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN F 342 " --> pdb=" O LYS F 338 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE F 343 " --> pdb=" O LEU F 339 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP F 344 " --> pdb=" O LEU F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 544 through 577 removed outlier: 3.606A pdb=" N LEU F 577 " --> pdb=" O LEU F 573 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 57 removed outlier: 3.898A pdb=" N LEU a 48 " --> pdb=" O GLY a 44 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER a 57 " --> pdb=" O ARG a 53 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 79 removed outlier: 3.688A pdb=" N PHE a 67 " --> pdb=" O ARG a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 removed outlier: 3.585A pdb=" N ALA a 114 " --> pdb=" O CYS a 110 " (cutoff:3.500A) Processing helix chain 'a' and resid 120 through 131 removed outlier: 3.539A pdb=" N ILE a 124 " --> pdb=" O MET a 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 49 through 76 removed outlier: 3.839A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP b 68 " --> pdb=" O ASN b 64 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA b 76 " --> pdb=" O TYR b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 93 removed outlier: 3.670A pdb=" N VAL b 86 " --> pdb=" O THR b 82 " (cutoff:3.500A) Processing helix chain 'c' and resid 16 through 21 Processing helix chain 'c' and resid 26 through 37 Processing helix chain 'c' and resid 45 through 73 removed outlier: 4.554A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN c 73 " --> pdb=" O ALA c 69 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 90 removed outlier: 3.645A pdb=" N ASP c 90 " --> pdb=" O ALA c 86 " (cutoff:3.500A) Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'c' and resid 112 through 116 removed outlier: 3.569A pdb=" N LEU c 115 " --> pdb=" O GLN c 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 37 through 49 Processing helix chain 'd' and resid 55 through 84 removed outlier: 3.719A pdb=" N ASN d 84 " --> pdb=" O LEU d 80 " (cutoff:3.500A) Processing helix chain 'd' and resid 90 through 102 Processing helix chain 'd' and resid 104 through 124 removed outlier: 4.104A pdb=" N ALA d 124 " --> pdb=" O LYS d 120 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 57 removed outlier: 3.897A pdb=" N LEU e 48 " --> pdb=" O GLY e 44 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER e 57 " --> pdb=" O ARG e 53 " (cutoff:3.500A) Processing helix chain 'e' and resid 63 through 79 removed outlier: 3.688A pdb=" N PHE e 67 " --> pdb=" O ARG e 63 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 114 removed outlier: 3.583A pdb=" N ALA e 114 " --> pdb=" O CYS e 110 " (cutoff:3.500A) Processing helix chain 'e' and resid 120 through 131 removed outlier: 3.540A pdb=" N ILE e 124 " --> pdb=" O MET e 120 " (cutoff:3.500A) Processing helix chain 'f' and resid 25 through 29 removed outlier: 3.505A pdb=" N ILE f 29 " --> pdb=" O ILE f 26 " (cutoff:3.500A) Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 49 through 76 removed outlier: 3.806A pdb=" N GLU f 53 " --> pdb=" O LEU f 49 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG f 67 " --> pdb=" O GLU f 63 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASP f 68 " --> pdb=" O ASN f 64 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 93 Processing helix chain 'g' and resid 16 through 21 Processing helix chain 'g' and resid 26 through 37 Processing helix chain 'g' and resid 45 through 73 removed outlier: 4.531A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 89 Processing helix chain 'g' and resid 90 through 97 Processing helix chain 'g' and resid 112 through 116 Processing helix chain 'h' and resid 37 through 49 Processing helix chain 'h' and resid 55 through 84 removed outlier: 3.694A pdb=" N ASN h 84 " --> pdb=" O LEU h 80 " (cutoff:3.500A) Processing helix chain 'h' and resid 90 through 102 removed outlier: 3.595A pdb=" N ILE h 94 " --> pdb=" O THR h 90 " (cutoff:3.500A) Processing helix chain 'h' and resid 103 through 124 removed outlier: 3.752A pdb=" N SER h 123 " --> pdb=" O THR h 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 756 through 757 Processing sheet with id=AA2, first strand: chain 'A' and resid 975 through 978 removed outlier: 4.610A pdb=" N MET A1300 " --> pdb=" O ILE A1317 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 178 through 179 removed outlier: 3.808A pdb=" N GLU B 62 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA B 22 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ALA B 142 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU B 181 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLN B 270 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE B 183 " --> pdb=" O GLN B 270 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL B 180 " --> pdb=" O MET B 204 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N CYS B 206 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TYR B 182 " --> pdb=" O CYS B 206 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N PHE B 208 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ASP B 184 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N LYS B 210 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL B 234 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N THR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL B 236 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER B 207 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU B 238 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N HIS B 209 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 273 through 274 Processing sheet with id=AA5, first strand: chain 'E' and resid 365 through 366 Processing sheet with id=AA6, first strand: chain 'E' and resid 437 through 439 Processing sheet with id=AA7, first strand: chain 'E' and resid 521 through 522 removed outlier: 6.181A pdb=" N GLN E 521 " --> pdb=" O ILE E 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 244 through 246 Processing sheet with id=AA9, first strand: chain 'D' and resid 244 through 246 Processing sheet with id=AB1, first strand: chain 'F' and resid 272 through 274 Processing sheet with id=AB2, first strand: chain 'F' and resid 364 through 366 Processing sheet with id=AB3, first strand: chain 'a' and resid 83 through 84 removed outlier: 7.140A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'a' and resid 118 through 119 Processing sheet with id=AB5, first strand: chain 'b' and resid 97 through 98 Processing sheet with id=AB6, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.194A pdb=" N ARG c 42 " --> pdb=" O ILE d 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'c' and resid 77 through 78 removed outlier: 3.719A pdb=" N ILE c 78 " --> pdb=" O GLY d 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'c' and resid 101 through 102 removed outlier: 6.680A pdb=" N THR c 101 " --> pdb=" O TYR f 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.832A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AC2, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.373A pdb=" N ARG g 42 " --> pdb=" O ILE h 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'g' and resid 77 through 78 removed outlier: 3.608A pdb=" N ILE g 78 " --> pdb=" O GLY h 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'G' and resid 90 through 93 removed outlier: 6.853A pdb=" N CYS G 76 " --> pdb=" O ILE G 30 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE G 30 " --> pdb=" O CYS G 76 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE G 78 " --> pdb=" O LEU G 28 " (cutoff:3.500A) 1150 hydrogen bonds defined for protein. 3372 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 349 hydrogen bonds 698 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 258 stacking parallelities Total time for adding SS restraints: 7.45 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.45: 13581 1.45 - 1.77: 15291 1.77 - 2.08: 159 2.08 - 2.40: 1 2.40 - 2.72: 1 Bond restraints: 29033 Sorted by residual: bond pdb=" CB TYR F 372 " pdb=" CG TYR F 372 " ideal model delta sigma weight residual 1.512 2.718 -1.206 2.20e-02 2.07e+03 3.00e+03 bond pdb=" CE3 TRP D 236 " pdb=" CZ3 TRP D 236 " ideal model delta sigma weight residual 1.382 2.269 -0.887 3.00e-02 1.11e+03 8.74e+02 bond pdb=" CE2 TRP D 236 " pdb=" CZ2 TRP D 236 " ideal model delta sigma weight residual 1.394 1.823 -0.429 2.10e-02 2.27e+03 4.18e+02 bond pdb=" CZ3 TRP D 236 " pdb=" CH2 TRP D 236 " ideal model delta sigma weight residual 1.400 1.853 -0.453 2.50e-02 1.60e+03 3.28e+02 bond pdb=" N PRO c 117 " pdb=" CA PRO c 117 " ideal model delta sigma weight residual 1.466 1.690 -0.224 1.24e-02 6.50e+03 3.26e+02 ... (remaining 29028 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.48: 40342 6.48 - 12.96: 90 12.96 - 19.44: 13 19.44 - 25.92: 1 25.92 - 32.40: 1 Bond angle restraints: 40447 Sorted by residual: angle pdb=" C ARG E 384 " pdb=" CA ARG E 384 " pdb=" CB ARG E 384 " ideal model delta sigma weight residual 109.65 142.05 -32.40 1.74e+00 3.30e-01 3.47e+02 angle pdb=" C LEU c 116 " pdb=" N PRO c 117 " pdb=" CA PRO c 117 " ideal model delta sigma weight residual 119.78 138.57 -18.79 1.03e+00 9.43e-01 3.33e+02 angle pdb=" C LYS B 67 " pdb=" N PRO B 68 " pdb=" CA PRO B 68 " ideal model delta sigma weight residual 119.89 134.57 -14.68 1.02e+00 9.61e-01 2.07e+02 angle pdb=" C LYS B 41 " pdb=" N PRO B 42 " pdb=" CA PRO B 42 " ideal model delta sigma weight residual 119.87 133.85 -13.98 1.04e+00 9.25e-01 1.81e+02 angle pdb=" CA TYR F 372 " pdb=" CB TYR F 372 " pdb=" CG TYR F 372 " ideal model delta sigma weight residual 113.90 136.95 -23.05 1.80e+00 3.09e-01 1.64e+02 ... (remaining 40442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 12580 17.88 - 35.77: 2320 35.77 - 53.65: 1420 53.65 - 71.53: 475 71.53 - 89.42: 43 Dihedral angle restraints: 16838 sinusoidal: 8930 harmonic: 7908 Sorted by residual: dihedral pdb=" C ARG E 384 " pdb=" N ARG E 384 " pdb=" CA ARG E 384 " pdb=" CB ARG E 384 " ideal model delta harmonic sigma weight residual -122.60 -155.40 32.80 0 2.50e+00 1.60e-01 1.72e+02 dihedral pdb=" C THR E 169 " pdb=" N THR E 169 " pdb=" CA THR E 169 " pdb=" CB THR E 169 " ideal model delta harmonic sigma weight residual -122.00 -152.32 30.32 0 2.50e+00 1.60e-01 1.47e+02 dihedral pdb=" N THR E 169 " pdb=" C THR E 169 " pdb=" CA THR E 169 " pdb=" CB THR E 169 " ideal model delta harmonic sigma weight residual 123.40 151.08 -27.68 0 2.50e+00 1.60e-01 1.23e+02 ... (remaining 16835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.239: 4425 0.239 - 0.479: 32 0.479 - 0.718: 5 0.718 - 0.957: 2 0.957 - 1.197: 2 Chirality restraints: 4466 Sorted by residual: chirality pdb=" CA THR E 169 " pdb=" N THR E 169 " pdb=" C THR E 169 " pdb=" CB THR E 169 " both_signs ideal model delta sigma weight residual False 2.53 1.33 1.20 2.00e-01 2.50e+01 3.58e+01 chirality pdb=" CA ARG E 384 " pdb=" N ARG E 384 " pdb=" C ARG E 384 " pdb=" CB ARG E 384 " both_signs ideal model delta sigma weight residual False 2.51 1.35 1.16 2.00e-01 2.50e+01 3.35e+01 chirality pdb=" CA ASP E 383 " pdb=" N ASP E 383 " pdb=" C ASP E 383 " pdb=" CB ASP E 383 " both_signs ideal model delta sigma weight residual False 2.51 1.60 0.91 2.00e-01 2.50e+01 2.08e+01 ... (remaining 4463 not shown) Planarity restraints: 4129 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 157 " 0.029 2.00e-02 2.50e+03 5.82e-02 3.39e+01 pdb=" C ALA B 157 " -0.101 2.00e-02 2.50e+03 pdb=" O ALA B 157 " 0.039 2.00e-02 2.50e+03 pdb=" N SER B 158 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 66 " 0.025 2.00e-02 2.50e+03 4.98e-02 2.48e+01 pdb=" C ALA B 66 " -0.086 2.00e-02 2.50e+03 pdb=" O ALA B 66 " 0.033 2.00e-02 2.50e+03 pdb=" N LYS B 67 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 470 " 0.075 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO E 471 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO E 471 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO E 471 " 0.061 5.00e-02 4.00e+02 ... (remaining 4126 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.91: 10 1.91 - 2.65: 757 2.65 - 3.40: 37779 3.40 - 4.15: 71081 4.15 - 4.90: 119842 Nonbonded interactions: 229469 Sorted by model distance: nonbonded pdb=" CB SER E 179 " pdb=" OE2 GLU B 129 " model vdw 1.158 3.440 nonbonded pdb=" OE2 GLU A 904 " pdb=" ND2 ASN E 116 " model vdw 1.174 3.120 nonbonded pdb=" NZ LYS B 41 " pdb=" SD MET B 315 " model vdw 1.548 3.480 nonbonded pdb=" CG2 THR E 169 " pdb=" CB MET B 53 " model vdw 1.581 3.860 nonbonded pdb=" O SER E 179 " pdb=" OE1 GLU B 129 " model vdw 1.728 3.040 ... (remaining 229464 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'D' and resid 219 through 401) } ncs_group { reference = chain 'a' selection = (chain 'e' and resid 38 through 134) } ncs_group { reference = chain 'b' selection = (chain 'f' and resid 24 through 102) } ncs_group { reference = chain 'c' selection = chain 'g' } ncs_group { reference = chain 'd' selection = chain 'h' } ncs_group { reference = (chain 'i' and (resid -73 through -1 or resid 1 through 73)) selection = (chain 'j' and (resid -73 through -1 or resid 1 through 73)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 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: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 31.780 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4241 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 : 0.013 1.206 29056 Z= 0.618 Angle : 1.092 53.767 40465 Z= 0.629 Chirality : 0.064 1.197 4466 Planarity : 0.006 0.114 4129 Dihedral : 24.101 89.417 11728 Min Nonbonded Distance : 1.158 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.57 % Favored : 94.90 % Rotamer: Outliers : 7.51 % Allowed : 16.82 % Favored : 75.67 % Cbeta Deviations : 0.94 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.06 (0.14), residues: 2646 helix: -0.63 (0.12), residues: 1500 sheet: -1.14 (0.45), residues: 125 loop : -2.46 (0.16), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 98 TYR 0.053 0.002 TYR G 100 PHE 0.048 0.002 PHE E 387 TRP 0.051 0.004 TRP G 31 HIS 0.009 0.001 HIS G 18 Details of bonding type rmsd covalent geometry : bond 0.01243 (29033) covalent geometry : angle 0.98301 (40447) hydrogen bonds : bond 0.13941 ( 1499) hydrogen bonds : angle 5.67426 ( 4070) metal coordination : bond 0.15145 ( 23) metal coordination : angle 22.58577 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 457 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 778 LEU cc_start: 0.6060 (mm) cc_final: 0.5119 (mm) REVERT: A 903 GLU cc_start: 0.1730 (OUTLIER) cc_final: 0.0965 (mt-10) REVERT: A 1065 LEU cc_start: -0.4742 (OUTLIER) cc_final: -0.5547 (mp) REVERT: A 1332 ASP cc_start: 0.0726 (t0) cc_final: 0.0448 (m-30) REVERT: A 1345 HIS cc_start: -0.1069 (t-90) cc_final: -0.1314 (m170) REVERT: E 108 VAL cc_start: 0.2626 (OUTLIER) cc_final: 0.2260 (m) REVERT: E 123 ILE cc_start: -0.1158 (OUTLIER) cc_final: -0.1537 (mm) REVERT: E 272 PHE cc_start: 0.2359 (OUTLIER) cc_final: 0.2004 (p90) REVERT: E 387 PHE cc_start: 0.1003 (OUTLIER) cc_final: 0.0553 (p90) REVERT: E 388 ASN cc_start: 0.2422 (OUTLIER) cc_final: 0.1934 (t0) REVERT: B 2 VAL cc_start: 0.5121 (OUTLIER) cc_final: 0.3199 (t) REVERT: B 14 LYS cc_start: -0.0227 (OUTLIER) cc_final: -0.1075 (mtpt) REVERT: B 32 TYR cc_start: 0.2204 (OUTLIER) cc_final: 0.0788 (m-80) REVERT: B 38 HIS cc_start: 0.3201 (OUTLIER) cc_final: 0.2342 (m170) REVERT: B 93 ASN cc_start: 0.3600 (p0) cc_final: 0.3359 (p0) REVERT: B 111 PRO cc_start: -0.0664 (OUTLIER) cc_final: -0.0940 (Cg_exo) REVERT: B 112 VAL cc_start: 0.1354 (OUTLIER) cc_final: 0.0973 (m) REVERT: B 187 VAL cc_start: 0.5049 (p) cc_final: 0.4335 (p) REVERT: B 204 MET cc_start: 0.3062 (ttt) cc_final: 0.2678 (ttm) REVERT: C 222 LEU cc_start: 0.0502 (OUTLIER) cc_final: 0.0091 (tp) REVERT: C 235 ASP cc_start: -0.1351 (OUTLIER) cc_final: -0.2217 (t0) REVERT: C 241 LYS cc_start: -0.0648 (OUTLIER) cc_final: -0.1226 (mttt) REVERT: C 376 ASP cc_start: -0.1500 (OUTLIER) cc_final: -0.2453 (p0) REVERT: D 332 LEU cc_start: 0.2591 (OUTLIER) cc_final: 0.1976 (mp) REVERT: F 343 ILE cc_start: 0.0584 (mt) cc_final: -0.0316 (mp) REVERT: F 369 ARG cc_start: 0.0844 (ptm160) cc_final: 0.0644 (tpt90) REVERT: a 86 SER cc_start: 0.8520 (OUTLIER) cc_final: 0.7961 (t) REVERT: a 89 VAL cc_start: 0.8842 (OUTLIER) cc_final: 0.8596 (m) REVERT: b 58 LEU cc_start: 0.8296 (tp) cc_final: 0.8078 (tt) REVERT: b 88 TYR cc_start: 0.6500 (m-10) cc_final: 0.6236 (m-10) REVERT: c 30 VAL cc_start: 0.8496 (t) cc_final: 0.8223 (p) REVERT: c 62 ILE cc_start: 0.8790 (tt) cc_final: 0.8214 (mt) REVERT: c 90 ASP cc_start: 0.7134 (t0) cc_final: 0.6908 (t0) REVERT: c 107 VAL cc_start: 0.8332 (m) cc_final: 0.8051 (t) REVERT: d 79 ARG cc_start: 0.8176 (mtt180) cc_final: 0.7804 (mmm160) REVERT: e 60 LEU cc_start: 0.8374 (mt) cc_final: 0.8173 (mm) REVERT: e 87 SER cc_start: 0.9150 (OUTLIER) cc_final: 0.8399 (t) REVERT: f 84 MET cc_start: 0.7618 (mmm) cc_final: 0.6637 (tpp) REVERT: h 83 TYR cc_start: 0.7780 (m-10) cc_final: 0.7357 (m-10) REVERT: h 101 LEU cc_start: 0.8847 (mt) cc_final: 0.8410 (tp) outliers start: 180 outliers final: 25 residues processed: 607 average time/residue: 0.2191 time to fit residues: 200.6050 Evaluate side-chains 232 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 186 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.0770 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 overall best weight: 2.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 857 HIS A 884 HIS A 965 HIS A1004 ASN A1081 ASN A1315 GLN E 304 ASN E 314 ASN E 346 HIS E 347 ASN E 350 GLN E 352 GLN E 376 ASN E 541 GLN E 580 ASN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 HIS C 305 GLN C 380 ASN C 389 ASN C 393 GLN D 369 HIS D 375 ASN D 380 ASN D 393 GLN F 346 HIS F 355 ASN d 49 HIS d 95 GLN e 125 GLN f 25 ASN f 93 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.086976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.060848 restraints weight = 257908.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.062531 restraints weight = 141662.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.063621 restraints weight = 95444.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.064332 restraints weight = 73421.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.064791 restraints weight = 62238.825| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.204 29056 Z= 0.468 Angle : 0.714 23.051 40465 Z= 0.400 Chirality : 0.041 0.280 4466 Planarity : 0.005 0.094 4129 Dihedral : 26.206 89.794 6239 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.50 % Favored : 95.35 % Rotamer: Outliers : 0.21 % Allowed : 3.67 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.15), residues: 2646 helix: 0.79 (0.13), residues: 1549 sheet: -0.73 (0.45), residues: 123 loop : -2.05 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG e 40 TYR 0.032 0.002 TYR E 514 PHE 0.026 0.002 PHE A 819 TRP 0.052 0.003 TRP A 916 HIS 0.010 0.002 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.01067 (29033) covalent geometry : angle 0.71005 (40447) hydrogen bonds : bond 0.04894 ( 1499) hydrogen bonds : angle 4.14776 ( 4070) metal coordination : bond 0.00886 ( 23) metal coordination : angle 3.49476 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 245 time to evaluate : 1.007 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: A 939 ASP cc_start: 0.4825 (m-30) cc_final: 0.4575 (p0) REVERT: A 948 LEU cc_start: 0.6762 (mp) cc_final: 0.6440 (mm) REVERT: A 1294 MET cc_start: 0.1291 (mtm) cc_final: 0.0651 (mtt) REVERT: A 1345 HIS cc_start: -0.1173 (t-90) cc_final: -0.1734 (m170) REVERT: B 38 HIS cc_start: 0.4045 (p-80) cc_final: 0.3661 (m170) REVERT: D 387 TYR cc_start: -0.0647 (m-80) cc_final: -0.0937 (m-10) REVERT: a 105 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7802 (mt-10) REVERT: a 120 MET cc_start: 0.8404 (mtm) cc_final: 0.8108 (mtm) REVERT: a 126 LEU cc_start: 0.8111 (tp) cc_final: 0.7846 (tp) REVERT: a 134 ARG cc_start: 0.6723 (mmm-85) cc_final: 0.6451 (ptt180) REVERT: c 38 ASN cc_start: 0.8594 (m110) cc_final: 0.8305 (m-40) REVERT: c 62 ILE cc_start: 0.8825 (tt) cc_final: 0.8447 (mt) REVERT: e 60 LEU cc_start: 0.7955 (mt) cc_final: 0.7448 (pp) REVERT: e 120 MET cc_start: 0.7805 (mtp) cc_final: 0.7243 (tpp) REVERT: f 43 VAL cc_start: 0.6327 (t) cc_final: 0.6111 (p) REVERT: g 38 ASN cc_start: 0.7390 (m-40) cc_final: 0.7018 (p0) REVERT: h 62 MET cc_start: 0.8418 (mmm) cc_final: 0.8215 (mmm) REVERT: h 101 LEU cc_start: 0.8833 (mt) cc_final: 0.8476 (tp) outliers start: 5 outliers final: 1 residues processed: 250 average time/residue: 0.2037 time to fit residues: 79.4134 Evaluate side-chains 147 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 191 optimal weight: 10.0000 chunk 200 optimal weight: 9.9990 chunk 173 optimal weight: 20.0000 chunk 232 optimal weight: 0.9990 chunk 271 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 187 optimal weight: 5.9990 chunk 78 optimal weight: 0.2980 chunk 169 optimal weight: 9.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 798 HIS A 857 HIS A1163 GLN A1216 ASN E 174 ASN E 346 HIS E 347 ASN E 393 GLN E 499 ASN ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 HIS c 38 ASN ** c 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 82 HIS f 93 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.085575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.059662 restraints weight = 259370.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.061397 restraints weight = 145019.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.062414 restraints weight = 98821.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.063120 restraints weight = 76861.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.063379 restraints weight = 65658.617| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.204 29056 Z= 0.458 Angle : 0.655 23.865 40465 Z= 0.369 Chirality : 0.039 0.198 4466 Planarity : 0.005 0.059 4129 Dihedral : 26.271 88.079 6239 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.04 % Favored : 95.92 % Rotamer: Outliers : 0.13 % Allowed : 3.92 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.16), residues: 2646 helix: 1.19 (0.13), residues: 1553 sheet: -0.50 (0.44), residues: 124 loop : -1.72 (0.18), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 496 TYR 0.026 0.002 TYR F 372 PHE 0.024 0.002 PHE E 387 TRP 0.042 0.002 TRP D 236 HIS 0.006 0.001 HIS B 151 Details of bonding type rmsd covalent geometry : bond 0.01051 (29033) covalent geometry : angle 0.65220 (40447) hydrogen bonds : bond 0.04480 ( 1499) hydrogen bonds : angle 3.93143 ( 4070) metal coordination : bond 0.00363 ( 23) metal coordination : angle 3.10325 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 205 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 939 ASP cc_start: 0.4982 (m-30) cc_final: 0.4418 (p0) REVERT: A 948 LEU cc_start: 0.6454 (mp) cc_final: 0.6253 (mm) REVERT: A 1014 LEU cc_start: 0.7526 (mt) cc_final: 0.7250 (tp) REVERT: A 1257 MET cc_start: 0.4700 (mtp) cc_final: 0.4355 (mtp) REVERT: A 1345 HIS cc_start: -0.0482 (t-90) cc_final: -0.1127 (m170) REVERT: E 496 ARG cc_start: 0.5906 (mpp-170) cc_final: 0.4929 (tpm170) REVERT: B 128 MET cc_start: 0.6624 (mtm) cc_final: 0.6279 (mtt) REVERT: C 380 ASN cc_start: 0.7291 (m-40) cc_final: 0.7085 (m-40) REVERT: b 85 ASP cc_start: 0.8636 (m-30) cc_final: 0.8288 (m-30) REVERT: b 88 TYR cc_start: 0.6460 (m-10) cc_final: 0.5727 (m-10) REVERT: c 38 ASN cc_start: 0.8648 (m-40) cc_final: 0.8274 (m110) REVERT: c 90 ASP cc_start: 0.7338 (t0) cc_final: 0.6520 (t0) REVERT: d 62 MET cc_start: 0.8715 (mmm) cc_final: 0.8510 (mmm) REVERT: e 60 LEU cc_start: 0.7894 (mt) cc_final: 0.7319 (pp) REVERT: e 105 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7637 (tm-30) REVERT: g 38 ASN cc_start: 0.7544 (m-40) cc_final: 0.7251 (p0) REVERT: g 56 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8307 (mm-30) REVERT: h 62 MET cc_start: 0.8698 (mmm) cc_final: 0.8252 (mmm) REVERT: h 101 LEU cc_start: 0.8908 (mt) cc_final: 0.8520 (tp) outliers start: 3 outliers final: 0 residues processed: 208 average time/residue: 0.1748 time to fit residues: 59.0664 Evaluate side-chains 142 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 268 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 233 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 248 optimal weight: 4.9990 chunk 55 optimal weight: 20.0000 chunk 113 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 chunk 217 optimal weight: 9.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1004 ASN E 267 ASN E 393 GLN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN C 305 GLN C 350 GLN D 277 GLN D 330 HIS F 346 HIS a 113 HIS ** a 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.083194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.057770 restraints weight = 265910.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.059373 restraints weight = 153325.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.060353 restraints weight = 105928.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.061009 restraints weight = 83328.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.061280 restraints weight = 71611.946| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.6653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.205 29056 Z= 0.473 Angle : 0.708 23.597 40465 Z= 0.396 Chirality : 0.041 0.203 4466 Planarity : 0.005 0.060 4129 Dihedral : 26.642 89.310 6239 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.91 % Favored : 95.05 % Rotamer: Outliers : 0.13 % Allowed : 2.92 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.16), residues: 2646 helix: 0.97 (0.13), residues: 1532 sheet: -0.36 (0.45), residues: 119 loop : -1.64 (0.19), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 384 TYR 0.029 0.002 TYR g 50 PHE 0.039 0.003 PHE E 387 TRP 0.044 0.003 TRP D 236 HIS 0.012 0.002 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.01083 (29033) covalent geometry : angle 0.70425 (40447) hydrogen bonds : bond 0.05750 ( 1499) hydrogen bonds : angle 4.21065 ( 4070) metal coordination : bond 0.01430 ( 23) metal coordination : angle 3.44622 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 189 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 948 LEU cc_start: 0.6687 (mp) cc_final: 0.6356 (mm) REVERT: A 1071 ARG cc_start: 0.3928 (ptp90) cc_final: 0.3725 (ttt90) REVERT: A 1345 HIS cc_start: -0.0294 (t-90) cc_final: -0.1079 (m170) REVERT: E 387 PHE cc_start: 0.1808 (OUTLIER) cc_final: 0.1194 (m-10) REVERT: B 247 TYR cc_start: 0.8319 (t80) cc_final: 0.8106 (t80) REVERT: C 347 MET cc_start: -0.4406 (tpt) cc_final: -0.4841 (tmm) REVERT: F 560 MET cc_start: 0.2952 (tpt) cc_final: 0.2617 (ttp) REVERT: a 105 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7930 (mt-10) REVERT: b 58 LEU cc_start: 0.9002 (tp) cc_final: 0.8769 (tp) REVERT: b 74 GLU cc_start: 0.8002 (pp20) cc_final: 0.7692 (pt0) REVERT: b 81 VAL cc_start: 0.6190 (t) cc_final: 0.5802 (t) REVERT: b 85 ASP cc_start: 0.8524 (m-30) cc_final: 0.8177 (p0) REVERT: b 88 TYR cc_start: 0.7503 (m-10) cc_final: 0.6431 (m-10) REVERT: c 38 ASN cc_start: 0.8525 (m-40) cc_final: 0.8105 (m-40) REVERT: c 90 ASP cc_start: 0.7405 (t0) cc_final: 0.6983 (t0) REVERT: e 60 LEU cc_start: 0.7782 (mt) cc_final: 0.7165 (pp) REVERT: e 120 MET cc_start: 0.7439 (mtp) cc_final: 0.6918 (tpp) REVERT: g 56 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8108 (mt-10) REVERT: h 101 LEU cc_start: 0.8919 (mt) cc_final: 0.8588 (tp) outliers start: 3 outliers final: 0 residues processed: 190 average time/residue: 0.1733 time to fit residues: 54.6551 Evaluate side-chains 140 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 116 optimal weight: 20.0000 chunk 112 optimal weight: 5.9990 chunk 241 optimal weight: 0.8980 chunk 8 optimal weight: 0.1980 chunk 18 optimal weight: 10.0000 chunk 180 optimal weight: 50.0000 chunk 119 optimal weight: 7.9990 chunk 164 optimal weight: 8.9990 chunk 242 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 271 optimal weight: 10.0000 overall best weight: 4.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 302 HIS ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 495 GLN B 38 HIS ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.085342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.059597 restraints weight = 254853.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.061183 restraints weight = 144929.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.062165 restraints weight = 99977.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.062771 restraints weight = 79628.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.063005 restraints weight = 69489.965| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.7543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.209 29056 Z= 0.474 Angle : 0.694 23.553 40465 Z= 0.389 Chirality : 0.041 0.166 4466 Planarity : 0.005 0.059 4129 Dihedral : 26.761 89.507 6239 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.88 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.16), residues: 2646 helix: 0.92 (0.13), residues: 1531 sheet: -0.44 (0.48), residues: 121 loop : -1.64 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 384 TYR 0.026 0.002 TYR F 372 PHE 0.045 0.002 PHE E 567 TRP 0.043 0.002 TRP D 236 HIS 0.014 0.002 HIS E 448 Details of bonding type rmsd covalent geometry : bond 0.01088 (29033) covalent geometry : angle 0.69139 (40447) hydrogen bonds : bond 0.05409 ( 1499) hydrogen bonds : angle 4.21233 ( 4070) metal coordination : bond 0.00562 ( 23) metal coordination : angle 3.14173 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1071 ARG cc_start: 0.4190 (ptp90) cc_final: 0.3987 (ttt90) REVERT: A 1345 HIS cc_start: -0.0123 (t-90) cc_final: -0.1082 (m170) REVERT: E 387 PHE cc_start: 0.1921 (p90) cc_final: 0.1458 (m-10) REVERT: B 128 MET cc_start: 0.7174 (mtm) cc_final: 0.6775 (mtt) REVERT: C 347 MET cc_start: -0.4425 (tpt) cc_final: -0.4827 (tmm) REVERT: F 560 MET cc_start: 0.3306 (tpt) cc_final: 0.2748 (ptt) REVERT: a 52 ARG cc_start: 0.8095 (mtt90) cc_final: 0.7850 (mmt90) REVERT: b 58 LEU cc_start: 0.9114 (tp) cc_final: 0.8818 (tp) REVERT: b 74 GLU cc_start: 0.7730 (pp20) cc_final: 0.7419 (pt0) REVERT: b 81 VAL cc_start: 0.6467 (t) cc_final: 0.5914 (t) REVERT: b 85 ASP cc_start: 0.8664 (m-30) cc_final: 0.8388 (p0) REVERT: c 38 ASN cc_start: 0.8539 (m-40) cc_final: 0.8062 (m-40) REVERT: e 60 LEU cc_start: 0.7762 (mt) cc_final: 0.7169 (pp) REVERT: e 120 MET cc_start: 0.7503 (mtp) cc_final: 0.6922 (tpp) REVERT: h 93 GLU cc_start: 0.8654 (mp0) cc_final: 0.8101 (mp0) REVERT: h 101 LEU cc_start: 0.8961 (mt) cc_final: 0.8633 (tp) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1875 time to fit residues: 51.0464 Evaluate side-chains 132 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 102 optimal weight: 20.0000 chunk 226 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 89 optimal weight: 0.2980 chunk 188 optimal weight: 8.9990 chunk 198 optimal weight: 1.9990 chunk 229 optimal weight: 0.8980 chunk 284 optimal weight: 9.9990 chunk 219 optimal weight: 10.0000 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 680 HIS E 302 HIS ** E 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 495 GLN ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN C 350 GLN F 346 HIS h 49 HIS h 109 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.082295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.057203 restraints weight = 269166.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.058697 restraints weight = 155375.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.059687 restraints weight = 108475.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.060231 restraints weight = 85926.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.060481 restraints weight = 74551.534| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.7887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.205 29056 Z= 0.459 Angle : 0.641 23.600 40465 Z= 0.363 Chirality : 0.039 0.157 4466 Planarity : 0.004 0.054 4129 Dihedral : 26.533 89.917 6239 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.88 % Favored : 95.09 % Rotamer: Outliers : 0.08 % Allowed : 1.92 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.16), residues: 2646 helix: 1.25 (0.13), residues: 1508 sheet: -0.54 (0.47), residues: 121 loop : -1.56 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 384 TYR 0.026 0.001 TYR F 372 PHE 0.019 0.002 PHE h 65 TRP 0.043 0.002 TRP D 236 HIS 0.007 0.001 HIS E 448 Details of bonding type rmsd covalent geometry : bond 0.01053 (29033) covalent geometry : angle 0.63757 (40447) hydrogen bonds : bond 0.04711 ( 1499) hydrogen bonds : angle 3.97941 ( 4070) metal coordination : bond 0.00519 ( 23) metal coordination : angle 3.24616 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 180 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1071 ARG cc_start: 0.4123 (ptp90) cc_final: 0.3876 (ttt90) REVERT: A 1331 GLU cc_start: 0.4649 (pm20) cc_final: 0.4407 (tp30) REVERT: A 1345 HIS cc_start: 0.0208 (t-90) cc_final: -0.0952 (m170) REVERT: E 395 ILE cc_start: 0.3411 (pt) cc_final: 0.3089 (mp) REVERT: E 438 MET cc_start: 0.2191 (mtm) cc_final: 0.1984 (mmm) REVERT: B 168 LEU cc_start: 0.4816 (mt) cc_final: 0.4394 (tt) REVERT: a 52 ARG cc_start: 0.7993 (mtt90) cc_final: 0.7780 (mmt90) REVERT: a 120 MET cc_start: 0.8577 (mtp) cc_final: 0.8300 (mtm) REVERT: b 58 LEU cc_start: 0.9132 (tp) cc_final: 0.8791 (tp) REVERT: b 81 VAL cc_start: 0.6384 (t) cc_final: 0.6126 (t) REVERT: c 38 ASN cc_start: 0.8445 (m-40) cc_final: 0.8087 (m-40) REVERT: d 116 LYS cc_start: 0.7895 (tttm) cc_final: 0.7686 (mtpp) REVERT: e 60 LEU cc_start: 0.7633 (mt) cc_final: 0.7085 (pp) REVERT: g 56 GLU cc_start: 0.9024 (mp0) cc_final: 0.8229 (mp0) REVERT: h 93 GLU cc_start: 0.8281 (mp0) cc_final: 0.7751 (mp0) REVERT: h 101 LEU cc_start: 0.8929 (mt) cc_final: 0.8614 (tp) outliers start: 2 outliers final: 1 residues processed: 181 average time/residue: 0.1856 time to fit residues: 53.7588 Evaluate side-chains 137 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 2 optimal weight: 6.9990 chunk 283 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 220 optimal weight: 9.9990 chunk 176 optimal weight: 0.8980 chunk 100 optimal weight: 30.0000 chunk 242 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 171 optimal weight: 0.7980 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 HIS ** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 495 GLN ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.081238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.056481 restraints weight = 269718.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.058055 restraints weight = 151926.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.059022 restraints weight = 104938.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.059559 restraints weight = 82873.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.059980 restraints weight = 72142.293| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.8490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.207 29056 Z= 0.469 Angle : 0.677 24.007 40465 Z= 0.380 Chirality : 0.041 0.263 4466 Planarity : 0.005 0.059 4129 Dihedral : 26.692 89.146 6239 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.40 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.16), residues: 2646 helix: 1.02 (0.13), residues: 1515 sheet: -0.61 (0.49), residues: 110 loop : -1.64 (0.18), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 182 TYR 0.028 0.002 TYR F 372 PHE 0.020 0.002 PHE E 361 TRP 0.061 0.003 TRP A1151 HIS 0.010 0.001 HIS E 448 Details of bonding type rmsd covalent geometry : bond 0.01075 (29033) covalent geometry : angle 0.67260 (40447) hydrogen bonds : bond 0.05487 ( 1499) hydrogen bonds : angle 4.12313 ( 4070) metal coordination : bond 0.00573 ( 23) metal coordination : angle 3.54161 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1071 ARG cc_start: 0.4091 (ptp90) cc_final: 0.3865 (ttt90) REVERT: A 1145 TYR cc_start: 0.5744 (t80) cc_final: 0.5470 (t80) REVERT: A 1345 HIS cc_start: 0.0431 (t-90) cc_final: -0.0773 (m170) REVERT: E 258 GLU cc_start: 0.1921 (tp30) cc_final: 0.1277 (mp0) REVERT: E 438 MET cc_start: 0.2469 (mtm) cc_final: 0.2260 (mmm) REVERT: B 128 MET cc_start: 0.7179 (mtm) cc_final: 0.6821 (mtt) REVERT: B 204 MET cc_start: 0.0881 (mpp) cc_final: -0.0991 (mpp) REVERT: C 311 LYS cc_start: -0.2670 (mttt) cc_final: -0.2947 (tptm) REVERT: a 52 ARG cc_start: 0.8010 (mtt90) cc_final: 0.7778 (mmt90) REVERT: b 88 TYR cc_start: 0.7039 (m-10) cc_final: 0.6819 (m-10) REVERT: c 92 GLU cc_start: 0.6558 (pm20) cc_final: 0.6186 (pm20) REVERT: e 60 LEU cc_start: 0.7672 (mt) cc_final: 0.7079 (pp) REVERT: h 93 GLU cc_start: 0.8395 (mp0) cc_final: 0.7794 (mp0) REVERT: h 101 LEU cc_start: 0.8897 (mt) cc_final: 0.8532 (tp) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1882 time to fit residues: 53.9689 Evaluate side-chains 139 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 218 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 130 optimal weight: 40.0000 chunk 126 optimal weight: 3.9990 chunk 133 optimal weight: 8.9990 chunk 270 optimal weight: 10.0000 chunk 200 optimal weight: 20.0000 chunk 103 optimal weight: 7.9990 chunk 167 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 HIS E 393 GLN ** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 495 GLN ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 GLN ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.080566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.056078 restraints weight = 271259.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.057530 restraints weight = 153623.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.058488 restraints weight = 107057.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.059076 restraints weight = 85029.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.059308 restraints weight = 73762.892| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.9241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.205 29056 Z= 0.476 Angle : 0.709 24.087 40465 Z= 0.396 Chirality : 0.042 0.218 4466 Planarity : 0.005 0.073 4129 Dihedral : 26.942 89.812 6239 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.59 % Favored : 94.37 % Rotamer: Outliers : 0.04 % Allowed : 1.21 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.16), residues: 2646 helix: 0.80 (0.13), residues: 1503 sheet: -0.93 (0.48), residues: 110 loop : -1.64 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG d 79 TYR 0.026 0.002 TYR F 372 PHE 0.026 0.002 PHE E 361 TRP 0.041 0.003 TRP D 236 HIS 0.007 0.002 HIS E 448 Details of bonding type rmsd covalent geometry : bond 0.01090 (29033) covalent geometry : angle 0.70495 (40447) hydrogen bonds : bond 0.05788 ( 1499) hydrogen bonds : angle 4.30516 ( 4070) metal coordination : bond 0.01403 ( 23) metal coordination : angle 3.81747 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 785 HIS cc_start: 0.1705 (t-90) cc_final: 0.1452 (t-90) REVERT: A 1257 MET cc_start: 0.4961 (mtp) cc_final: 0.2974 (ppp) REVERT: A 1345 HIS cc_start: 0.0560 (t-90) cc_final: -0.0769 (m-70) REVERT: E 258 GLU cc_start: 0.1384 (tp30) cc_final: 0.0858 (mp0) REVERT: E 395 ILE cc_start: 0.3663 (pt) cc_final: 0.3302 (mp) REVERT: B 128 MET cc_start: 0.7326 (mtm) cc_final: 0.6985 (tpp) REVERT: B 204 MET cc_start: 0.1545 (mpp) cc_final: 0.0202 (mpp) REVERT: C 347 MET cc_start: -0.3811 (tpt) cc_final: -0.4248 (tmm) REVERT: a 52 ARG cc_start: 0.7990 (mtt90) cc_final: 0.7755 (mmt90) REVERT: e 60 LEU cc_start: 0.7634 (mt) cc_final: 0.7018 (pp) REVERT: h 101 LEU cc_start: 0.8815 (mt) cc_final: 0.8520 (tp) outliers start: 1 outliers final: 0 residues processed: 175 average time/residue: 0.1828 time to fit residues: 52.2184 Evaluate side-chains 135 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 83 optimal weight: 20.0000 chunk 110 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 186 optimal weight: 0.8980 chunk 182 optimal weight: 10.0000 chunk 205 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 120 optimal weight: 20.0000 chunk 206 optimal weight: 8.9990 chunk 193 optimal weight: 6.9990 chunk 284 optimal weight: 40.0000 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 HIS E 371 GLN ** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 495 GLN ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 HIS ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 GLN ** F 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 31 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.080551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.055977 restraints weight = 271790.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.057477 restraints weight = 155650.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.058409 restraints weight = 108615.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.058931 restraints weight = 86531.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.059321 restraints weight = 75541.071| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.9545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.206 29056 Z= 0.469 Angle : 0.689 24.145 40465 Z= 0.385 Chirality : 0.041 0.193 4466 Planarity : 0.005 0.062 4129 Dihedral : 26.869 89.751 6239 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.67 % Favored : 94.29 % Rotamer: Outliers : 0.04 % Allowed : 0.38 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.16), residues: 2646 helix: 0.81 (0.13), residues: 1506 sheet: -0.92 (0.50), residues: 100 loop : -1.61 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1009 TYR 0.027 0.002 TYR F 372 PHE 0.031 0.002 PHE E 414 TRP 0.042 0.002 TRP D 236 HIS 0.008 0.001 HIS G 18 Details of bonding type rmsd covalent geometry : bond 0.01076 (29033) covalent geometry : angle 0.68227 (40447) hydrogen bonds : bond 0.05459 ( 1499) hydrogen bonds : angle 4.24676 ( 4070) metal coordination : bond 0.00693 ( 23) metal coordination : angle 4.49792 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 841 MET cc_start: 0.3359 (ptp) cc_final: 0.3152 (ptp) REVERT: A 1345 HIS cc_start: 0.0782 (t-90) cc_final: -0.0689 (m170) REVERT: E 258 GLU cc_start: 0.1659 (tp30) cc_final: 0.1048 (mp0) REVERT: E 298 LYS cc_start: 0.4164 (mppt) cc_final: 0.3823 (pttt) REVERT: B 47 MET cc_start: 0.2948 (tpp) cc_final: 0.2637 (tpp) REVERT: B 128 MET cc_start: 0.7310 (mtm) cc_final: 0.6995 (tpp) REVERT: B 204 MET cc_start: 0.1309 (mpp) cc_final: -0.0026 (mpp) REVERT: B 259 MET cc_start: 0.0537 (ppp) cc_final: -0.0062 (ptt) REVERT: B 298 VAL cc_start: 0.7542 (t) cc_final: 0.7253 (t) REVERT: a 52 ARG cc_start: 0.8014 (mtt90) cc_final: 0.7719 (mmt90) REVERT: b 88 TYR cc_start: 0.6758 (m-10) cc_final: 0.6477 (m-10) REVERT: d 71 GLU cc_start: 0.8606 (mp0) cc_final: 0.8397 (mp0) REVERT: e 60 LEU cc_start: 0.7693 (mt) cc_final: 0.7117 (pp) REVERT: h 101 LEU cc_start: 0.8714 (mt) cc_final: 0.8394 (tp) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.1825 time to fit residues: 54.0606 Evaluate side-chains 137 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 116 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 chunk 123 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 247 optimal weight: 0.9990 chunk 136 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 67 optimal weight: 0.5980 chunk 230 optimal weight: 9.9990 chunk 142 optimal weight: 7.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 HIS ** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 495 GLN ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 GLN F 346 HIS a 125 GLN G 18 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.081715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.056855 restraints weight = 270012.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.058461 restraints weight = 152807.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.059421 restraints weight = 105534.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.060112 restraints weight = 83633.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.060506 restraints weight = 71591.192| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.9569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.205 29056 Z= 0.452 Angle : 0.623 23.813 40465 Z= 0.352 Chirality : 0.038 0.166 4466 Planarity : 0.004 0.055 4129 Dihedral : 26.532 89.845 6239 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.69 % Favored : 95.28 % Rotamer: Outliers : 0.04 % Allowed : 0.25 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.16), residues: 2646 helix: 1.17 (0.13), residues: 1526 sheet: -0.81 (0.49), residues: 106 loop : -1.52 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d 79 TYR 0.023 0.001 TYR F 372 PHE 0.023 0.001 PHE E 414 TRP 0.040 0.002 TRP D 236 HIS 0.005 0.001 HIS C 369 Details of bonding type rmsd covalent geometry : bond 0.01037 (29033) covalent geometry : angle 0.61789 (40447) hydrogen bonds : bond 0.04174 ( 1499) hydrogen bonds : angle 3.89750 ( 4070) metal coordination : bond 0.00926 ( 23) metal coordination : angle 3.76484 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1257 MET cc_start: 0.5442 (mtp) cc_final: 0.3515 (ppp) REVERT: A 1345 HIS cc_start: 0.0136 (t-90) cc_final: -0.1140 (m170) REVERT: E 298 LYS cc_start: 0.3981 (mppt) cc_final: 0.3615 (pttt) REVERT: E 564 ARG cc_start: 0.3371 (mpt180) cc_final: 0.3122 (mmm160) REVERT: B 128 MET cc_start: 0.7285 (mtm) cc_final: 0.7016 (tpp) REVERT: B 204 MET cc_start: 0.1371 (mpp) cc_final: 0.0019 (mpp) REVERT: B 259 MET cc_start: 0.0617 (ppp) cc_final: 0.0009 (ptt) REVERT: a 52 ARG cc_start: 0.7912 (mtt90) cc_final: 0.7626 (mmt90) REVERT: b 88 TYR cc_start: 0.7015 (m-10) cc_final: 0.6784 (m-10) REVERT: c 90 ASP cc_start: 0.6876 (t0) cc_final: 0.6368 (t0) REVERT: d 59 MET cc_start: 0.8699 (ptm) cc_final: 0.8415 (ptp) REVERT: d 71 GLU cc_start: 0.8618 (mp0) cc_final: 0.8359 (mp0) REVERT: e 60 LEU cc_start: 0.7462 (mt) cc_final: 0.6952 (pp) REVERT: h 101 LEU cc_start: 0.8672 (mt) cc_final: 0.8412 (tp) outliers start: 1 outliers final: 1 residues processed: 187 average time/residue: 0.1864 time to fit residues: 56.8229 Evaluate side-chains 150 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 229 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 0.2980 chunk 26 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 247 optimal weight: 3.9990 chunk 11 optimal weight: 30.0000 chunk 180 optimal weight: 30.0000 chunk 182 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 HIS ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 495 GLN ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.080600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.055998 restraints weight = 267622.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.057581 restraints weight = 150125.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.058517 restraints weight = 103161.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.058915 restraints weight = 81990.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.059409 restraints weight = 72624.162| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.9860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.206 29056 Z= 0.465 Angle : 0.672 24.186 40465 Z= 0.376 Chirality : 0.040 0.320 4466 Planarity : 0.005 0.054 4129 Dihedral : 26.779 89.719 6239 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.82 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.16), residues: 2646 helix: 1.02 (0.13), residues: 1521 sheet: -0.76 (0.50), residues: 101 loop : -1.55 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG b 35 TYR 0.029 0.002 TYR F 372 PHE 0.021 0.002 PHE E 361 TRP 0.042 0.002 TRP D 236 HIS 0.006 0.001 HIS E 406 Details of bonding type rmsd covalent geometry : bond 0.01066 (29033) covalent geometry : angle 0.66590 (40447) hydrogen bonds : bond 0.05228 ( 1499) hydrogen bonds : angle 4.13346 ( 4070) metal coordination : bond 0.00959 ( 23) metal coordination : angle 4.19944 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9184.09 seconds wall clock time: 157 minutes 22.48 seconds (9442.48 seconds total)