Starting phenix.real_space_refine on Sat Apr 13 16:34:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tof_41449/04_2024/8tof_41449_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tof_41449/04_2024/8tof_41449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tof_41449/04_2024/8tof_41449.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tof_41449/04_2024/8tof_41449.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tof_41449/04_2024/8tof_41449_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tof_41449/04_2024/8tof_41449_neut_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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 5 6.06 5 P 352 5.49 5 S 106 5.16 5 C 17364 2.51 5 N 5145 2.21 5 O 6130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 804": "OE1" <-> "OE2" Residue "A GLU 805": "OE1" <-> "OE2" Residue "A GLU 812": "OE1" <-> "OE2" Residue "A GLU 845": "OE1" <-> "OE2" Residue "A GLU 874": "OE1" <-> "OE2" Residue "A GLU 885": "OE1" <-> "OE2" Residue "A GLU 904": "OE1" <-> "OE2" Residue "A GLU 1156": "OE1" <-> "OE2" Residue "A GLU 1201": "OE1" <-> "OE2" Residue "B TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 213": "OE1" <-> "OE2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "D GLU 308": "OE1" <-> "OE2" Residue "D GLU 340": "OE1" <-> "OE2" Residue "G GLU 359": "OE1" <-> "OE2" Residue "a GLU 50": "OE1" <-> "OE2" Residue "a GLU 59": "OE1" <-> "OE2" Residue "a GLU 94": "OE1" <-> "OE2" Residue "a GLU 105": "OE1" <-> "OE2" Residue "b GLU 53": "OE1" <-> "OE2" Residue "b GLU 74": "OE1" <-> "OE2" Residue "c GLU 64": "OE1" <-> "OE2" Residue "c GLU 91": "OE1" <-> "OE2" Residue "d GLU 68": "OE1" <-> "OE2" Residue "g GLU 41": "OE1" <-> "OE2" Residue "h GLU 68": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 29102 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 4572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4572 Classifications: {'peptide': 545} Link IDs: {'PTRANS': 12, 'TRANS': 532} Chain breaks: 2 Chain: "B" Number of atoms: 3057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3057 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 18, 'TRANS': 366} Chain: "D" Number of atoms: 2356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2356 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 277} Chain breaks: 2 Chain: "E" Number of atoms: 2080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2080 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 9, 'TRANS': 243} Chain breaks: 2 Chain: "F" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 724 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain breaks: 1 Chain: "G" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 3010 Classifications: {'peptide': 369} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 347} Chain breaks: 5 Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 31 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 3623 Classifications: {'DNA': 176} Link IDs: {'rna3p': 175} Chain: "T" Number of atoms: 3593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 3593 Classifications: {'DNA': 176} Link IDs: {'rna3p': 175} Chain: "a" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 836 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "c" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "d" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "e" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 836 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "g" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "h" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 39 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 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: "G" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13483 SG CYS G 263 62.286 92.071 104.064 1.00130.04 S ATOM 13500 SG CYS G 266 63.824 89.998 106.938 1.00119.58 S ATOM 13653 SG CYS G 286 60.707 92.300 107.591 1.00121.45 S ATOM 14713 SG CYS G 417 84.879 61.141 134.087 1.00108.79 S ATOM 14740 SG CYS G 420 85.278 57.617 135.012 1.00 91.61 S ATOM 14996 SG CYS G 451 81.929 59.290 135.694 1.00103.95 S ATOM 14901 SG CYS G 440 84.803 72.069 128.218 1.00106.26 S ATOM 14927 SG CYS G 443 87.496 72.672 130.949 1.00102.20 S ATOM 15116 SG CYS G 466 84.559 70.340 131.371 1.00116.46 S ATOM 13564 SG CYS G 275 57.244 98.911 94.446 1.00165.73 S ATOM 13585 SG CYS G 278 60.521 98.388 94.954 1.00166.34 S ATOM 13788 SG CYS G 303 60.415 101.428 96.372 1.00168.52 S Time building chain proxies: 14.94, per 1000 atoms: 0.51 Number of scatterers: 29102 At special positions: 0 Unit cell: (147.138, 160.29, 187.416, 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 5 29.99 S 106 16.00 P 352 15.00 O 6130 8.00 N 5145 7.00 C 17364 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.77 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 188 " pdb=" ZN G 701 " pdb="ZN ZN G 701 " - pdb=" ND1 HIS G 283 " pdb="ZN ZN G 701 " - pdb=" SG CYS G 263 " pdb="ZN ZN G 701 " - pdb=" SG CYS G 266 " pdb="ZN ZN G 701 " - pdb=" SG CYS G 286 " pdb=" ZN G 702 " pdb="ZN ZN G 702 " - pdb=" ND1 HIS G 448 " pdb="ZN ZN G 702 " - pdb=" SG CYS G 420 " pdb="ZN ZN G 702 " - pdb=" SG CYS G 417 " pdb="ZN ZN G 702 " - pdb=" SG CYS G 451 " pdb=" ZN G 703 " pdb="ZN ZN G 703 " - pdb=" NE2 HIS G 469 " pdb="ZN ZN G 703 " - pdb=" SG CYS G 466 " pdb="ZN ZN G 703 " - pdb=" SG CYS G 440 " pdb="ZN ZN G 703 " - pdb=" SG CYS G 443 " pdb=" ZN G 704 " pdb="ZN ZN G 704 " - pdb=" SG CYS G 278 " pdb="ZN ZN G 704 " - pdb=" SG CYS G 275 " pdb="ZN ZN G 704 " - pdb=" SG CYS G 303 " Number of angles added : 9 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5124 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 114 helices and 9 sheets defined 52.2% alpha, 3.6% beta 169 base pairs and 303 stacking pairs defined. Time for finding SS restraints: 14.20 Creating SS restraints... Processing helix chain 'A' and resid 665 through 675 removed outlier: 4.005A pdb=" N PHE A 669 " --> pdb=" O GLU A 665 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLU A 670 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 674 " --> pdb=" O GLU A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 691 Processing helix chain 'A' and resid 699 through 709 removed outlier: 3.527A pdb=" N PHE A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 724 Processing helix chain 'A' and resid 772 through 777 Processing helix chain 'A' and resid 788 through 790 No H-bonds generated for 'chain 'A' and resid 788 through 790' Processing helix chain 'A' and resid 802 through 839 removed outlier: 3.523A pdb=" N SER A 823 " --> pdb=" O PHE A 819 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN A 824 " --> pdb=" O TYR A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 Processing helix chain 'A' and resid 853 through 856 removed outlier: 4.171A pdb=" N GLY A 856 " --> pdb=" O PRO A 853 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 853 through 856' Processing helix chain 'A' and resid 862 through 870 Processing helix chain 'A' and resid 873 through 884 removed outlier: 3.596A pdb=" N HIS A 884 " --> pdb=" O ILE A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 927 removed outlier: 3.806A pdb=" N LYS A 914 " --> pdb=" O ARG A 910 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL A 915 " --> pdb=" O GLU A 911 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N PHE A 925 " --> pdb=" O GLN A 921 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LYS A 926 " --> pdb=" O LYS A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 933 No H-bonds generated for 'chain 'A' and resid 930 through 933' Processing helix chain 'A' and resid 938 through 942 Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.598A pdb=" N ILE A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 998 Processing helix chain 'A' and resid 1004 through 1021 removed outlier: 3.697A pdb=" N ARG A1009 " --> pdb=" O PRO A1005 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A1018 " --> pdb=" O LEU A1014 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER A1019 " --> pdb=" O LYS A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1038 removed outlier: 4.045A pdb=" N LEU A1033 " --> pdb=" O GLU A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1174 removed outlier: 3.591A pdb=" N PHE A1147 " --> pdb=" O ASN A1143 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A1152 " --> pdb=" O PHE A1148 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU A1160 " --> pdb=" O GLU A1156 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE A1161 " --> pdb=" O ARG A1157 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR A1174 " --> pdb=" O LYS A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1183 No H-bonds generated for 'chain 'A' and resid 1180 through 1183' Processing helix chain 'A' and resid 1190 through 1193 No H-bonds generated for 'chain 'A' and resid 1190 through 1193' Processing helix chain 'A' and resid 1206 through 1215 Processing helix chain 'A' and resid 1221 through 1229 removed outlier: 3.730A pdb=" N GLU A1225 " --> pdb=" O HIS A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1237 through 1239 No H-bonds generated for 'chain 'A' and resid 1237 through 1239' Processing helix chain 'A' and resid 1243 through 1257 Processing helix chain 'A' and resid 1261 through 1273 Processing helix chain 'A' and resid 1280 through 1293 removed outlier: 3.515A pdb=" N HIS A1293 " --> pdb=" O GLN A1289 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 54 removed outlier: 3.645A pdb=" N MET B 53 " --> pdb=" O SER B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 60 No H-bonds generated for 'chain 'B' and resid 58 through 60' Processing helix chain 'B' and resid 71 through 76 removed outlier: 4.159A pdb=" N GLN B 76 " --> pdb=" O GLN B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 86 Processing helix chain 'B' and resid 95 through 104 removed outlier: 5.310A pdb=" N ARG B 99 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 104 " --> pdb=" O SER B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 135 Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 191 through 196 Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 244 through 261 Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 288 through 301 removed outlier: 3.924A pdb=" N CYS B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE B 301 " --> pdb=" O TYR B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 329 removed outlier: 3.762A pdb=" N THR B 321 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 328 " --> pdb=" O PHE B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 380 Processing helix chain 'D' and resid 69 through 72 No H-bonds generated for 'chain 'D' and resid 69 through 72' Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 102 through 130 Processing helix chain 'D' and resid 226 through 236 Processing helix chain 'D' and resid 254 through 265 Processing helix chain 'D' and resid 271 through 296 removed outlier: 3.642A pdb=" N SER D 279 " --> pdb=" O GLN D 275 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N GLY D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASN D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 316 removed outlier: 3.564A pdb=" N LEU D 304 " --> pdb=" O LEU D 301 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TYR D 306 " --> pdb=" O ARG D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 324 No H-bonds generated for 'chain 'D' and resid 322 through 324' Processing helix chain 'D' and resid 328 through 343 Proline residue: D 339 - end of helix Processing helix chain 'D' and resid 349 through 372 removed outlier: 5.393A pdb=" N ASP D 371 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLU D 372 " --> pdb=" O MET D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 398 removed outlier: 3.727A pdb=" N VAL D 397 " --> pdb=" O GLN D 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 72 No H-bonds generated for 'chain 'E' and resid 69 through 72' Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 102 through 130 Processing helix chain 'E' and resid 226 through 240 Processing helix chain 'E' and resid 254 through 265 Processing helix chain 'E' and resid 272 through 296 removed outlier: 6.237A pdb=" N GLY E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ASN E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 316 removed outlier: 3.635A pdb=" N LEU E 304 " --> pdb=" O LEU E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 324 No H-bonds generated for 'chain 'E' and resid 322 through 324' Processing helix chain 'E' and resid 328 through 344 Proline residue: E 339 - end of helix Processing helix chain 'E' and resid 349 through 368 Processing helix chain 'E' and resid 370 through 374 Processing helix chain 'F' and resid 304 through 312 Processing helix chain 'F' and resid 316 through 329 Processing helix chain 'F' and resid 334 through 345 removed outlier: 5.796A pdb=" N LYS F 338 " --> pdb=" O ILE F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 357 No H-bonds generated for 'chain 'F' and resid 355 through 357' Processing helix chain 'G' and resid 121 through 127 Processing helix chain 'G' and resid 164 through 166 No H-bonds generated for 'chain 'G' and resid 164 through 166' Processing helix chain 'G' and resid 293 through 295 No H-bonds generated for 'chain 'G' and resid 293 through 295' Processing helix chain 'G' and resid 304 through 312 Processing helix chain 'G' and resid 316 through 343 removed outlier: 3.780A pdb=" N ASN G 325 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ASN G 332 " --> pdb=" O LYS G 328 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL G 333 " --> pdb=" O GLN G 329 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ILE G 335 " --> pdb=" O ASN G 331 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N PHE G 336 " --> pdb=" O ASN G 332 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N LYS G 338 " --> pdb=" O LYS G 334 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU G 339 " --> pdb=" O ILE G 335 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE G 343 " --> pdb=" O LEU G 339 " (cutoff:3.500A) Processing helix chain 'G' and resid 355 through 360 removed outlier: 4.718A pdb=" N THR G 360 " --> pdb=" O TYR G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 383 through 386 No H-bonds generated for 'chain 'G' and resid 383 through 386' Processing helix chain 'G' and resid 394 through 396 No H-bonds generated for 'chain 'G' and resid 394 through 396' Processing helix chain 'G' and resid 401 through 403 No H-bonds generated for 'chain 'G' and resid 401 through 403' Processing helix chain 'G' and resid 431 through 433 No H-bonds generated for 'chain 'G' and resid 431 through 433' Processing helix chain 'G' and resid 545 through 564 Processing helix chain 'a' and resid 45 through 56 Processing helix chain 'a' and resid 64 through 77 removed outlier: 4.000A pdb=" N ASP a 77 " --> pdb=" O GLU a 73 " (cutoff:3.500A) Processing helix chain 'a' and resid 86 through 113 Processing helix chain 'a' and resid 121 through 131 Processing helix chain 'b' and resid 26 through 28 No H-bonds generated for 'chain 'b' and resid 26 through 28' Processing helix chain 'b' and resid 31 through 40 Processing helix chain 'b' and resid 48 through 75 removed outlier: 3.775A pdb=" N TYR b 51 " --> pdb=" O GLY b 48 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU b 52 " --> pdb=" O LEU b 49 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE b 66 " --> pdb=" O GLU b 63 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG b 67 " --> pdb=" O ASN b 64 " (cutoff:3.500A) Processing helix chain 'b' and resid 83 through 93 Processing helix chain 'c' and resid 17 through 21 Processing helix chain 'c' and resid 27 through 36 Processing helix chain 'c' and resid 45 through 72 removed outlier: 4.428A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 89 Processing helix chain 'c' and resid 91 through 96 Processing helix chain 'c' and resid 113 through 115 No H-bonds generated for 'chain 'c' and resid 113 through 115' Processing helix chain 'd' and resid 35 through 45 Processing helix chain 'd' and resid 53 through 80 Processing helix chain 'd' and resid 88 through 98 Processing helix chain 'd' and resid 101 through 120 Processing helix chain 'e' and resid 45 through 56 Processing helix chain 'e' and resid 64 through 78 removed outlier: 3.693A pdb=" N ASP e 77 " --> pdb=" O GLU e 73 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE e 78 " --> pdb=" O ILE e 74 " (cutoff:3.500A) Processing helix chain 'e' and resid 86 through 113 Processing helix chain 'e' and resid 121 through 131 Processing helix chain 'f' and resid 26 through 28 No H-bonds generated for 'chain 'f' and resid 26 through 28' Processing helix chain 'f' and resid 31 through 40 Processing helix chain 'f' and resid 48 through 75 removed outlier: 3.948A pdb=" N TYR f 51 " --> pdb=" O GLY f 48 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE f 66 " --> pdb=" O GLU f 63 " (cutoff:3.500A) Processing helix chain 'f' and resid 83 through 92 Processing helix chain 'g' and resid 17 through 21 Processing helix chain 'g' and resid 27 through 37 Processing helix chain 'g' and resid 45 through 72 removed outlier: 4.452A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU g 65 " --> pdb=" O GLU g 61 " (cutoff:3.500A) Processing helix chain 'g' and resid 80 through 89 Processing helix chain 'g' and resid 91 through 96 Processing helix chain 'g' and resid 113 through 115 No H-bonds generated for 'chain 'g' and resid 113 through 115' Processing helix chain 'h' and resid 35 through 45 Processing helix chain 'h' and resid 53 through 80 Processing helix chain 'h' and resid 88 through 98 Processing helix chain 'h' and resid 101 through 120 Processing sheet with id= A, first strand: chain 'A' and resid 1304 through 1306 removed outlier: 3.796A pdb=" N HIS A1311 " --> pdb=" O ASP A1306 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 62 through 64 removed outlier: 6.484A pdb=" N VAL B 141 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N PHE B 24 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL B 143 " --> pdb=" O PHE B 24 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N MET B 305 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ASN B 144 " --> pdb=" O MET B 305 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL B 307 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL B 267 " --> pdb=" O MET B 306 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL B 308 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU B 269 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LEU B 181 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLN B 270 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE B 183 " --> pdb=" O GLN B 270 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 97 through 99 removed outlier: 3.500A pdb=" N TYR D 23 " --> pdb=" O ALA D 16 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N HIS D 18 " --> pdb=" O LEU D 21 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU D 21 " --> pdb=" O HIS D 18 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE D 78 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU D 90 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 30 through 32 Processing sheet with id= E, first strand: chain 'D' and resid 244 through 246 Processing sheet with id= F, first strand: chain 'E' and resid 97 through 99 removed outlier: 6.469A pdb=" N PHE E 78 " --> pdb=" O LEU E 28 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 30 through 32 Processing sheet with id= H, first strand: chain 'F' and resid 272 through 274 Processing sheet with id= I, first strand: chain 'G' and resid 437 through 439 956 hydrogen bonds defined for protein. 2544 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 431 hydrogen bonds 858 hydrogen bond angles 0 basepair planarities 169 basepair parallelities 303 stacking parallelities Total time for adding SS restraints: 18.88 Time building geometry restraints manager: 14.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.89 - 1.24: 3049 1.24 - 1.58: 26494 1.58 - 1.92: 864 1.92 - 2.27: 0 2.27 - 2.61: 1 Bond restraints: 30408 Sorted by residual: bond pdb=" CB PRO F 279 " pdb=" CG PRO F 279 " ideal model delta sigma weight residual 1.492 2.612 -1.120 5.00e-02 4.00e+02 5.02e+02 bond pdb=" CG PRO F 279 " pdb=" CD PRO F 279 " ideal model delta sigma weight residual 1.503 0.894 0.609 3.40e-02 8.65e+02 3.20e+02 bond pdb=" CG PRO E 322 " pdb=" CD PRO E 322 " ideal model delta sigma weight residual 1.503 1.017 0.486 3.40e-02 8.65e+02 2.04e+02 bond pdb=" N ML3 a 36 " pdb=" CA ML3 a 36 " ideal model delta sigma weight residual 1.458 1.264 0.194 1.90e-02 2.77e+03 1.04e+02 bond pdb=" N ML3 e 36 " pdb=" CA ML3 e 36 " ideal model delta sigma weight residual 1.458 1.265 0.193 1.90e-02 2.77e+03 1.03e+02 ... (remaining 30403 not shown) Histogram of bond angle deviations from ideal: 8.51 - 35.14: 1 35.14 - 61.77: 0 61.77 - 88.40: 3 88.40 - 115.03: 20996 115.03 - 141.66: 21550 Bond angle restraints: 42550 Sorted by residual: angle pdb=" CB PRO F 279 " pdb=" CG PRO F 279 " pdb=" CD PRO F 279 " ideal model delta sigma weight residual 106.10 8.51 97.59 3.20e+00 9.77e-02 9.30e+02 angle pdb=" N PRO E 322 " pdb=" CD PRO E 322 " pdb=" CG PRO E 322 " ideal model delta sigma weight residual 103.20 72.21 30.99 1.50e+00 4.44e-01 4.27e+02 angle pdb=" CA PRO E 322 " pdb=" CB PRO E 322 " pdb=" CG PRO E 322 " ideal model delta sigma weight residual 104.50 73.46 31.04 1.90e+00 2.77e-01 2.67e+02 angle pdb=" N PRO F 279 " pdb=" CA PRO F 279 " pdb=" CB PRO F 279 " ideal model delta sigma weight residual 103.48 90.77 12.71 1.00e+00 1.00e+00 1.62e+02 angle pdb=" N PRO E 322 " pdb=" CA PRO E 322 " pdb=" CB PRO E 322 " ideal model delta sigma weight residual 103.25 92.43 10.82 1.05e+00 9.07e-01 1.06e+02 ... (remaining 42545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.41: 15038 33.41 - 66.83: 2308 66.83 - 100.24: 62 100.24 - 133.65: 5 133.65 - 167.07: 4 Dihedral angle restraints: 17417 sinusoidal: 9498 harmonic: 7919 Sorted by residual: dihedral pdb=" CA LEU E 248 " pdb=" C LEU E 248 " pdb=" N PRO E 249 " pdb=" CA PRO E 249 " ideal model delta harmonic sigma weight residual -180.00 -140.17 -39.83 0 5.00e+00 4.00e-02 6.35e+01 dihedral pdb=" CA LYS A 760 " pdb=" C LYS A 760 " pdb=" N SER A 761 " pdb=" CA SER A 761 " ideal model delta harmonic sigma weight residual -180.00 -150.18 -29.82 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA PRO F 279 " pdb=" CB PRO F 279 " pdb=" CG PRO F 279 " pdb=" CD PRO F 279 " ideal model delta sinusoidal sigma weight residual 38.00 152.70 -114.70 1 2.00e+01 2.50e-03 3.40e+01 ... (remaining 17414 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4518 0.098 - 0.195: 181 0.195 - 0.293: 1 0.293 - 0.391: 2 0.391 - 0.488: 1 Chirality restraints: 4703 Sorted by residual: chirality pdb=" CA ML3 a 36 " pdb=" N ML3 a 36 " pdb=" C ML3 a 36 " pdb=" CB ML3 a 36 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.96e+00 chirality pdb=" CA ML3 e 36 " pdb=" N ML3 e 36 " pdb=" C ML3 e 36 " pdb=" CB ML3 e 36 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CA PRO F 279 " pdb=" N PRO F 279 " pdb=" C PRO F 279 " pdb=" CB PRO F 279 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 4700 not shown) Planarity restraints: 4180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU G 507 " -0.081 5.00e-02 4.00e+02 1.22e-01 2.38e+01 pdb=" N PRO G 508 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO G 508 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO G 508 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN G 402 " 0.084 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO G 403 " -0.201 5.00e-02 4.00e+02 pdb=" CA PRO G 403 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO G 403 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 966 " -0.029 2.00e-02 2.50e+03 2.46e-02 1.52e+01 pdb=" CG TRP A 966 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP A 966 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 966 " -0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP A 966 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 966 " -0.018 2.00e-02 2.50e+03 pdb=" CE3 TRP A 966 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 966 " -0.015 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 966 " 0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP A 966 " 0.008 2.00e-02 2.50e+03 ... (remaining 4177 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 161 2.44 - 3.06: 19440 3.06 - 3.67: 48701 3.67 - 4.29: 74057 4.29 - 4.90: 112472 Nonbonded interactions: 254831 Sorted by model distance: nonbonded pdb=" OD2 ASP B 186 " pdb="ZN ZN B 501 " model vdw 1.828 2.230 nonbonded pdb=" C2 DG N 38 " pdb=" N2 DG T -37 " model vdw 1.904 3.340 nonbonded pdb=" O2 DT N 9 " pdb=" NH2 ARG e 40 " model vdw 1.922 2.520 nonbonded pdb=" OG SER E 313 " pdb=" O LYS E 318 " model vdw 1.963 2.440 nonbonded pdb=" C2 DA N 59 " pdb=" N2 DG T -58 " model vdw 2.010 3.420 ... (remaining 254826 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'D' and (resid 10 through 40 or resid 67 through 376)) selection = chain 'E' } ncs_group { reference = chain 'a' selection = chain 'e' } ncs_group { reference = (chain 'b' and resid 25 through 102) selection = chain 'f' } ncs_group { reference = chain 'c' selection = (chain 'g' and resid 16 through 118) } ncs_group { reference = (chain 'd' and resid 29 through 121) selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.960 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: 0.030 Extract box with map and model: 20.640 Check model and map are aligned: 0.520 Set scattering table: 0.250 Process input model: 98.930 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 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 : 0.010 1.120 30408 Z= 0.762 Angle : 1.002 97.589 42550 Z= 0.560 Chirality : 0.044 0.488 4703 Planarity : 0.005 0.135 4180 Dihedral : 24.373 167.067 12293 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.58 % Favored : 92.97 % Rotamer: Outliers : 3.09 % Allowed : 26.11 % Favored : 70.80 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.17), residues: 2631 helix: 1.18 (0.14), residues: 1435 sheet: -2.14 (0.48), residues: 114 loop : -1.24 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP D 236 HIS 0.006 0.001 HIS e 39 PHE 0.033 0.002 PHE E 362 TYR 0.018 0.002 TYR B 347 ARG 0.029 0.001 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 302 time to evaluate : 2.874 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: A 1291 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.6760 (tpt170) REVERT: B 220 GLU cc_start: 0.8418 (tm-30) cc_final: 0.7903 (tm-30) REVERT: D 78 PHE cc_start: 0.8227 (t80) cc_final: 0.7993 (t80) REVERT: G 552 PHE cc_start: 0.8263 (t80) cc_final: 0.8047 (t80) REVERT: a 56 LYS cc_start: 0.9136 (ttpp) cc_final: 0.8855 (ttpp) REVERT: g 90 ASP cc_start: 0.8695 (t0) cc_final: 0.8398 (t0) outliers start: 74 outliers final: 54 residues processed: 365 average time/residue: 1.6011 time to fit residues: 677.0606 Evaluate side-chains 329 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 274 time to evaluate : 3.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 774 CYS Chi-restraints excluded: chain A residue 886 HIS Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1036 HIS Chi-restraints excluded: chain A residue 1134 SER Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1259 ASP Chi-restraints excluded: chain A residue 1291 ARG Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain A residue 1317 ILE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 303 ARG Chi-restraints excluded: chain D residue 352 CYS Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 322 PRO Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 129 TRP Chi-restraints excluded: chain G residue 163 ASN Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 180 ASN Chi-restraints excluded: chain G residue 187 TRP Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 379 ILE Chi-restraints excluded: chain G residue 395 ILE Chi-restraints excluded: chain G residue 409 SER Chi-restraints excluded: chain G residue 430 HIS Chi-restraints excluded: chain G residue 440 CYS Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain G residue 517 ASN Chi-restraints excluded: chain c residue 76 THR Chi-restraints excluded: chain c residue 101 THR Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain d residue 84 SER Chi-restraints excluded: chain h residue 44 GLN Chi-restraints excluded: chain h residue 83 ARG Chi-restraints excluded: chain h residue 103 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 0.6980 chunk 224 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 172 optimal weight: 0.2980 chunk 268 optimal weight: 0.3980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 840 ASN A 965 HIS A1150 HIS A1252 HIS ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 GLN ** G 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 541 GLN a 39 HIS a 113 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30408 Z= 0.212 Angle : 0.610 8.479 42550 Z= 0.341 Chirality : 0.038 0.198 4703 Planarity : 0.005 0.083 4180 Dihedral : 26.695 166.536 6888 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.63 % Favored : 93.92 % Rotamer: Outliers : 4.51 % Allowed : 23.06 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.17), residues: 2631 helix: 1.24 (0.14), residues: 1460 sheet: -2.02 (0.43), residues: 124 loop : -1.06 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 236 HIS 0.004 0.001 HIS A 930 PHE 0.020 0.002 PHE E 362 TYR 0.018 0.001 TYR G 506 ARG 0.009 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 313 time to evaluate : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 719 TRP cc_start: 0.8293 (t60) cc_final: 0.8089 (t60) REVERT: A 775 TRP cc_start: 0.6731 (OUTLIER) cc_final: 0.6089 (t-100) REVERT: A 978 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7579 (m-30) REVERT: A 1009 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6776 (mtp180) REVERT: A 1156 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7871 (mp0) REVERT: B 220 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7837 (tm-30) REVERT: B 222 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8021 (mtp180) REVERT: D 77 PHE cc_start: 0.6931 (OUTLIER) cc_final: 0.6120 (m-10) REVERT: D 78 PHE cc_start: 0.8543 (t80) cc_final: 0.7728 (t80) REVERT: D 81 TYR cc_start: 0.7848 (m-80) cc_final: 0.7537 (m-80) REVERT: D 237 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.4558 (mm-30) REVERT: D 310 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6707 (tp) REVERT: D 320 LEU cc_start: 0.7672 (tp) cc_final: 0.6987 (tp) REVERT: D 360 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8264 (mp0) REVERT: D 376 ASP cc_start: 0.7218 (p0) cc_final: 0.6988 (p0) REVERT: E 335 ILE cc_start: 0.7255 (OUTLIER) cc_final: 0.6981 (mp) REVERT: E 373 TYR cc_start: 0.7452 (m-10) cc_final: 0.6962 (m-80) REVERT: F 333 VAL cc_start: 0.7992 (OUTLIER) cc_final: 0.7783 (p) REVERT: G 305 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7772 (mp0) REVERT: G 552 PHE cc_start: 0.8309 (t80) cc_final: 0.7922 (t80) REVERT: G 553 ASP cc_start: 0.9148 (p0) cc_final: 0.8445 (m-30) REVERT: c 64 GLU cc_start: 0.8574 (tp30) cc_final: 0.8314 (tt0) REVERT: d 54 LYS cc_start: 0.8967 (mmmt) cc_final: 0.8729 (mmtt) REVERT: f 92 ARG cc_start: 0.9186 (OUTLIER) cc_final: 0.8869 (ttp80) REVERT: g 90 ASP cc_start: 0.8699 (t0) cc_final: 0.8383 (t0) outliers start: 108 outliers final: 42 residues processed: 394 average time/residue: 1.4996 time to fit residues: 688.1229 Evaluate side-chains 333 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 279 time to evaluate : 2.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 775 TRP Chi-restraints excluded: chain A residue 886 HIS Chi-restraints excluded: chain A residue 966 TRP Chi-restraints excluded: chain A residue 978 ASP Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1009 ARG Chi-restraints excluded: chain A residue 1036 HIS Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1165 ASN Chi-restraints excluded: chain A residue 1216 ASN Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1259 ASP Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain A residue 1317 ILE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 341 ASN Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain D residue 77 PHE Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 236 TRP Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 77 PHE Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain F residue 279 PRO Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 180 ASN Chi-restraints excluded: chain G residue 187 TRP Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 373 SER Chi-restraints excluded: chain G residue 395 ILE Chi-restraints excluded: chain G residue 440 CYS Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain a residue 96 SER Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain c residue 101 THR Chi-restraints excluded: chain d residue 109 SER Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain h residue 103 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 0.3980 chunk 83 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 269 optimal weight: 0.4980 chunk 290 optimal weight: 0.8980 chunk 239 optimal weight: 0.9990 chunk 267 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 216 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 341 ASN D 18 HIS ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30408 Z= 0.196 Angle : 0.589 9.411 42550 Z= 0.328 Chirality : 0.037 0.204 4703 Planarity : 0.004 0.062 4180 Dihedral : 26.613 165.807 6822 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.85 % Favored : 93.73 % Rotamer: Outliers : 4.68 % Allowed : 23.73 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.17), residues: 2631 helix: 1.28 (0.14), residues: 1463 sheet: -1.77 (0.45), residues: 120 loop : -0.95 (0.20), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 236 HIS 0.004 0.001 HIS A1252 PHE 0.023 0.001 PHE A 668 TYR 0.017 0.001 TYR B 347 ARG 0.008 0.000 ARG D 381 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 301 time to evaluate : 2.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 775 TRP cc_start: 0.6728 (OUTLIER) cc_final: 0.6064 (t-100) REVERT: A 805 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8148 (mp0) REVERT: A 845 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8540 (pm20) REVERT: A 1156 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7919 (mp0) REVERT: A 1261 LYS cc_start: 0.7923 (mttt) cc_final: 0.7325 (mtmt) REVERT: B 73 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7414 (tt0) REVERT: B 220 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7784 (tm-30) REVERT: D 18 HIS cc_start: 0.5228 (OUTLIER) cc_final: 0.4867 (m90) REVERT: D 22 MET cc_start: 0.1721 (mmt) cc_final: 0.1352 (mmt) REVERT: D 78 PHE cc_start: 0.8458 (t80) cc_final: 0.8043 (t80) REVERT: D 107 MET cc_start: 0.7793 (ptm) cc_final: 0.7395 (ptm) REVERT: D 237 GLU cc_start: 0.6488 (OUTLIER) cc_final: 0.4536 (mm-30) REVERT: D 310 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6659 (tp) REVERT: D 320 LEU cc_start: 0.7680 (tp) cc_final: 0.7020 (tp) REVERT: D 360 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8246 (mp0) REVERT: D 376 ASP cc_start: 0.7172 (p0) cc_final: 0.6914 (p0) REVERT: E 263 HIS cc_start: 0.7598 (OUTLIER) cc_final: 0.7223 (t-170) REVERT: E 335 ILE cc_start: 0.7296 (OUTLIER) cc_final: 0.7034 (mp) REVERT: E 373 TYR cc_start: 0.7437 (m-10) cc_final: 0.6981 (m-80) REVERT: G 282 PHE cc_start: 0.7845 (m-80) cc_final: 0.7337 (m-80) REVERT: G 305 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7842 (mp0) REVERT: G 552 PHE cc_start: 0.8315 (t80) cc_final: 0.7049 (t80) REVERT: G 555 ILE cc_start: 0.9058 (pp) cc_final: 0.8759 (pp) REVERT: G 556 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.8196 (m-80) REVERT: c 64 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8335 (tt0) REVERT: d 54 LYS cc_start: 0.8983 (mmmt) cc_final: 0.8742 (mmtt) REVERT: f 92 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8876 (ttp80) REVERT: g 90 ASP cc_start: 0.8686 (t0) cc_final: 0.8360 (t0) outliers start: 112 outliers final: 46 residues processed: 384 average time/residue: 1.4684 time to fit residues: 660.3702 Evaluate side-chains 341 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 281 time to evaluate : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 775 TRP Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 886 HIS Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 966 TRP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1036 HIS Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1163 GLN Chi-restraints excluded: chain A residue 1165 ASN Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain A residue 1317 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 341 ASN Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 236 TRP Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain F residue 309 LYS Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 180 ASN Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 187 TRP Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 373 SER Chi-restraints excluded: chain G residue 395 ILE Chi-restraints excluded: chain G residue 427 SER Chi-restraints excluded: chain G residue 440 CYS Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain G residue 517 ASN Chi-restraints excluded: chain G residue 556 TYR Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain c residue 64 GLU Chi-restraints excluded: chain c residue 101 THR Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain h residue 103 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 128 optimal weight: 50.0000 chunk 180 optimal weight: 0.3980 chunk 270 optimal weight: 0.0770 chunk 286 optimal weight: 0.3980 chunk 141 optimal weight: 3.9990 chunk 256 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 341 ASN D 369 HIS ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 502 ASN g 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30408 Z= 0.191 Angle : 0.585 10.225 42550 Z= 0.324 Chirality : 0.036 0.206 4703 Planarity : 0.004 0.059 4180 Dihedral : 26.514 163.900 6818 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.63 % Favored : 93.96 % Rotamer: Outliers : 4.43 % Allowed : 24.14 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.17), residues: 2631 helix: 1.34 (0.14), residues: 1459 sheet: -1.65 (0.46), residues: 118 loop : -0.92 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 236 HIS 0.016 0.001 HIS D 18 PHE 0.030 0.001 PHE A 668 TYR 0.026 0.001 TYR G 372 ARG 0.006 0.000 ARG h 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 300 time to evaluate : 2.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 708 PHE cc_start: 0.8831 (m-80) cc_final: 0.8365 (m-80) REVERT: A 775 TRP cc_start: 0.6710 (OUTLIER) cc_final: 0.6048 (t-100) REVERT: A 805 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8102 (mp0) REVERT: A 978 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7517 (m-30) REVERT: A 1149 ARG cc_start: 0.8619 (mmm-85) cc_final: 0.8418 (mmm-85) REVERT: A 1156 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: B 73 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7504 (tt0) REVERT: B 214 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.6836 (m-80) REVERT: B 220 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7743 (tm-30) REVERT: D 78 PHE cc_start: 0.8580 (t80) cc_final: 0.8212 (t80) REVERT: D 226 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7833 (mm) REVERT: D 237 GLU cc_start: 0.6220 (OUTLIER) cc_final: 0.4296 (mm-30) REVERT: D 310 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6715 (mt) REVERT: D 320 LEU cc_start: 0.7691 (tp) cc_final: 0.7283 (tp) REVERT: D 360 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8264 (mp0) REVERT: E 107 MET cc_start: -0.1515 (tmt) cc_final: -0.1815 (tmm) REVERT: E 223 GLN cc_start: 0.7804 (tp40) cc_final: 0.7521 (tp40) REVERT: E 263 HIS cc_start: 0.7566 (OUTLIER) cc_final: 0.7213 (t-170) REVERT: E 335 ILE cc_start: 0.7363 (OUTLIER) cc_final: 0.7093 (mp) REVERT: E 373 TYR cc_start: 0.7439 (m-10) cc_final: 0.6996 (m-80) REVERT: G 175 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7290 (ptp) REVERT: G 282 PHE cc_start: 0.7796 (m-80) cc_final: 0.7371 (m-80) REVERT: G 305 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7859 (mp0) REVERT: G 552 PHE cc_start: 0.8315 (t80) cc_final: 0.7788 (t80) REVERT: d 54 LYS cc_start: 0.8968 (mmmt) cc_final: 0.8728 (mmtt) REVERT: e 42 ARG cc_start: 0.7592 (mpt180) cc_final: 0.7374 (mpt180) REVERT: f 92 ARG cc_start: 0.9197 (OUTLIER) cc_final: 0.8858 (ttp80) REVERT: g 90 ASP cc_start: 0.8710 (t0) cc_final: 0.8411 (t0) outliers start: 106 outliers final: 51 residues processed: 383 average time/residue: 1.2787 time to fit residues: 574.2345 Evaluate side-chains 339 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 274 time to evaluate : 2.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 775 TRP Chi-restraints excluded: chain A residue 793 SER Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 966 TRP Chi-restraints excluded: chain A residue 978 ASP Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1036 HIS Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1163 GLN Chi-restraints excluded: chain A residue 1165 ASN Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain A residue 1310 LEU Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain A residue 1317 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 341 ASN Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 236 TRP Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain F residue 309 LYS Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 175 MET Chi-restraints excluded: chain G residue 180 ASN Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 187 TRP Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 373 SER Chi-restraints excluded: chain G residue 395 ILE Chi-restraints excluded: chain G residue 427 SER Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 440 CYS Chi-restraints excluded: chain G residue 502 ASN Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain G residue 517 ASN Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain c residue 101 THR Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain d residue 84 SER Chi-restraints excluded: chain d residue 109 SER Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain f residue 50 ILE Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain h residue 103 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 238 optimal weight: 1.9990 chunk 162 optimal weight: 0.0870 chunk 4 optimal weight: 5.9990 chunk 213 optimal weight: 2.9990 chunk 118 optimal weight: 0.0870 chunk 244 optimal weight: 0.6980 chunk 197 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 0.1980 chunk 256 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 341 ASN ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 459 ASN G 502 ASN g 31 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30408 Z= 0.161 Angle : 0.581 15.421 42550 Z= 0.319 Chirality : 0.036 0.204 4703 Planarity : 0.004 0.050 4180 Dihedral : 26.308 162.912 6815 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.36 % Favored : 94.26 % Rotamer: Outliers : 3.97 % Allowed : 24.94 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.17), residues: 2631 helix: 1.43 (0.14), residues: 1459 sheet: -1.56 (0.45), residues: 121 loop : -0.83 (0.20), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 236 HIS 0.004 0.001 HIS E 330 PHE 0.032 0.001 PHE A 668 TYR 0.041 0.001 TYR G 372 ARG 0.008 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 315 time to evaluate : 2.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.7511 (t80) REVERT: A 775 TRP cc_start: 0.6690 (OUTLIER) cc_final: 0.6117 (t-100) REVERT: A 805 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8106 (mp0) REVERT: A 978 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7548 (m-30) REVERT: A 1149 ARG cc_start: 0.8516 (mmm-85) cc_final: 0.8308 (mmm-85) REVERT: A 1156 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: A 1268 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8774 (tt) REVERT: B 73 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: B 214 PHE cc_start: 0.7482 (OUTLIER) cc_final: 0.6693 (m-80) REVERT: D 77 PHE cc_start: 0.6607 (m-80) cc_final: 0.6352 (m-80) REVERT: D 78 PHE cc_start: 0.8623 (t80) cc_final: 0.8224 (t80) REVERT: D 88 TRP cc_start: 0.7525 (m100) cc_final: 0.7180 (m100) REVERT: D 226 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7763 (mm) REVERT: D 237 GLU cc_start: 0.6117 (OUTLIER) cc_final: 0.4065 (mm-30) REVERT: D 310 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6633 (mt) REVERT: D 320 LEU cc_start: 0.7625 (tp) cc_final: 0.7236 (tp) REVERT: D 360 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8267 (mp0) REVERT: D 368 MET cc_start: 0.7211 (tpp) cc_final: 0.6955 (tpt) REVERT: E 22 MET cc_start: 0.1221 (mmt) cc_final: 0.0199 (mmt) REVERT: E 31 TRP cc_start: 0.3295 (t-100) cc_final: 0.2348 (t-100) REVERT: E 37 MET cc_start: 0.6418 (tpp) cc_final: 0.6209 (tpp) REVERT: E 223 GLN cc_start: 0.7780 (tp40) cc_final: 0.7554 (tp40) REVERT: E 263 HIS cc_start: 0.7478 (OUTLIER) cc_final: 0.7131 (t-170) REVERT: E 335 ILE cc_start: 0.7338 (OUTLIER) cc_final: 0.7117 (mp) REVERT: E 358 GLN cc_start: 0.8195 (tp-100) cc_final: 0.7973 (tp-100) REVERT: E 373 TYR cc_start: 0.7494 (m-10) cc_final: 0.7052 (m-80) REVERT: G 175 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7456 (ptp) REVERT: G 282 PHE cc_start: 0.7692 (m-80) cc_final: 0.7338 (m-80) REVERT: G 302 HIS cc_start: 0.8723 (m-70) cc_final: 0.8050 (t-170) REVERT: G 305 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7900 (mp0) REVERT: G 316 MET cc_start: 0.3649 (tpt) cc_final: 0.2870 (ptt) REVERT: G 396 THR cc_start: 0.4144 (OUTLIER) cc_final: 0.3930 (m) REVERT: G 552 PHE cc_start: 0.8242 (t80) cc_final: 0.8023 (t80) REVERT: d 54 LYS cc_start: 0.8985 (mmmt) cc_final: 0.8737 (mmtt) REVERT: f 92 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8838 (ttp80) REVERT: g 90 ASP cc_start: 0.8687 (t0) cc_final: 0.8392 (t0) REVERT: h 31 LYS cc_start: 0.8330 (mptp) cc_final: 0.8085 (mptp) outliers start: 95 outliers final: 35 residues processed: 388 average time/residue: 1.5259 time to fit residues: 690.5413 Evaluate side-chains 321 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 269 time to evaluate : 2.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 775 TRP Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 978 ASP Chi-restraints excluded: chain A residue 1036 HIS Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1163 GLN Chi-restraints excluded: chain A residue 1165 ASN Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1259 ASP Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1317 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 341 ASN Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 236 TRP Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain F residue 309 LYS Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 175 MET Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 187 TRP Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 373 SER Chi-restraints excluded: chain G residue 395 ILE Chi-restraints excluded: chain G residue 396 THR Chi-restraints excluded: chain G residue 427 SER Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 440 CYS Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain c residue 101 THR Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain d residue 109 SER Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain f residue 50 ILE Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain h residue 103 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 9.9990 chunk 257 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 167 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 286 optimal weight: 0.8980 chunk 237 optimal weight: 0.7980 chunk 132 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1315 GLN D 18 HIS ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30408 Z= 0.208 Angle : 0.603 14.850 42550 Z= 0.329 Chirality : 0.037 0.280 4703 Planarity : 0.004 0.049 4180 Dihedral : 26.446 161.927 6809 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.51 % Favored : 94.11 % Rotamer: Outliers : 3.59 % Allowed : 25.77 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.17), residues: 2631 helix: 1.40 (0.14), residues: 1459 sheet: -1.46 (0.46), residues: 121 loop : -0.78 (0.20), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 236 HIS 0.006 0.001 HIS A 886 PHE 0.032 0.001 PHE E 362 TYR 0.050 0.001 TYR G 372 ARG 0.007 0.000 ARG h 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 289 time to evaluate : 3.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 708 PHE cc_start: 0.8750 (m-80) cc_final: 0.8448 (m-80) REVERT: A 723 PHE cc_start: 0.7878 (OUTLIER) cc_final: 0.7668 (t80) REVERT: A 775 TRP cc_start: 0.6834 (OUTLIER) cc_final: 0.6324 (t-100) REVERT: A 805 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7694 (mp0) REVERT: A 978 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7471 (m-30) REVERT: A 1149 ARG cc_start: 0.8588 (mmm-85) cc_final: 0.8373 (mmm-85) REVERT: A 1156 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7883 (mp0) REVERT: A 1268 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8816 (tt) REVERT: A 1315 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.6892 (tm-30) REVERT: B 214 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.6818 (m-80) REVERT: D 18 HIS cc_start: 0.6079 (OUTLIER) cc_final: 0.5811 (m170) REVERT: D 77 PHE cc_start: 0.6631 (m-80) cc_final: 0.6323 (m-10) REVERT: D 78 PHE cc_start: 0.8644 (t80) cc_final: 0.8238 (t80) REVERT: D 226 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7740 (mm) REVERT: D 237 GLU cc_start: 0.6263 (OUTLIER) cc_final: 0.4204 (mm-30) REVERT: D 310 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6706 (mt) REVERT: D 320 LEU cc_start: 0.7735 (tp) cc_final: 0.7334 (tp) REVERT: D 360 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8208 (mp0) REVERT: D 368 MET cc_start: 0.7247 (tpp) cc_final: 0.7021 (tpt) REVERT: E 31 TRP cc_start: 0.3284 (t-100) cc_final: 0.2407 (t-100) REVERT: E 107 MET cc_start: -0.1497 (tmt) cc_final: -0.1797 (tmm) REVERT: E 263 HIS cc_start: 0.7470 (OUTLIER) cc_final: 0.7144 (t-170) REVERT: E 301 LEU cc_start: 0.7504 (tp) cc_final: 0.7277 (mt) REVERT: E 373 TYR cc_start: 0.7503 (m-10) cc_final: 0.7078 (m-80) REVERT: G 282 PHE cc_start: 0.7798 (m-80) cc_final: 0.7410 (m-80) REVERT: G 316 MET cc_start: 0.3822 (tpt) cc_final: 0.3014 (ptt) REVERT: G 396 THR cc_start: 0.4254 (OUTLIER) cc_final: 0.4040 (m) REVERT: G 542 ILE cc_start: 0.8908 (mm) cc_final: 0.8480 (tt) REVERT: G 552 PHE cc_start: 0.8413 (t80) cc_final: 0.8025 (t80) REVERT: G 556 TYR cc_start: 0.8781 (OUTLIER) cc_final: 0.8337 (m-10) REVERT: d 54 LYS cc_start: 0.8971 (mmmt) cc_final: 0.8728 (mmtt) REVERT: f 92 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.8827 (ttp80) REVERT: g 90 ASP cc_start: 0.8719 (t0) cc_final: 0.8436 (t0) outliers start: 86 outliers final: 38 residues processed: 354 average time/residue: 1.4993 time to fit residues: 619.9762 Evaluate side-chains 326 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 272 time to evaluate : 2.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 775 TRP Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 978 ASP Chi-restraints excluded: chain A residue 1036 HIS Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1163 GLN Chi-restraints excluded: chain A residue 1165 ASN Chi-restraints excluded: chain A residue 1259 ASP Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1300 MET Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain A residue 1315 GLN Chi-restraints excluded: chain A residue 1317 ILE Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 341 ASN Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 236 TRP Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain F residue 309 LYS Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 379 ILE Chi-restraints excluded: chain G residue 395 ILE Chi-restraints excluded: chain G residue 396 THR Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 440 CYS Chi-restraints excluded: chain G residue 502 ASN Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain G residue 517 ASN Chi-restraints excluded: chain G residue 556 TYR Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain c residue 101 THR Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain d residue 109 SER Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain f residue 50 ILE Chi-restraints excluded: chain f residue 79 LYS Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain h residue 103 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 276 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 209 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 chunk 241 optimal weight: 0.0980 chunk 159 optimal weight: 0.5980 chunk 285 optimal weight: 0.4980 chunk 178 optimal weight: 0.5980 chunk 173 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 ASN B 341 ASN D 18 HIS ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30408 Z= 0.171 Angle : 0.596 13.731 42550 Z= 0.323 Chirality : 0.036 0.192 4703 Planarity : 0.004 0.047 4180 Dihedral : 26.279 161.254 6803 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.28 % Favored : 94.34 % Rotamer: Outliers : 3.05 % Allowed : 26.36 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.17), residues: 2631 helix: 1.47 (0.14), residues: 1457 sheet: -1.19 (0.45), residues: 130 loop : -0.77 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP G 492 HIS 0.008 0.001 HIS A 886 PHE 0.035 0.001 PHE A 668 TYR 0.037 0.001 TYR G 372 ARG 0.007 0.000 ARG h 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 299 time to evaluate : 3.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 708 PHE cc_start: 0.8705 (m-80) cc_final: 0.8273 (m-80) REVERT: A 775 TRP cc_start: 0.6871 (OUTLIER) cc_final: 0.6426 (t-100) REVERT: A 805 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8115 (mp0) REVERT: A 978 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7506 (m-30) REVERT: A 1156 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7877 (mp0) REVERT: A 1315 GLN cc_start: 0.7147 (OUTLIER) cc_final: 0.6610 (tm-30) REVERT: B 214 PHE cc_start: 0.7421 (OUTLIER) cc_final: 0.6596 (m-80) REVERT: D 18 HIS cc_start: 0.6621 (OUTLIER) cc_final: 0.6258 (m-70) REVERT: D 77 PHE cc_start: 0.6674 (m-80) cc_final: 0.6235 (m-10) REVERT: D 78 PHE cc_start: 0.8637 (t80) cc_final: 0.8213 (t80) REVERT: D 226 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7721 (mm) REVERT: D 237 GLU cc_start: 0.6254 (OUTLIER) cc_final: 0.4396 (mm-30) REVERT: D 310 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6662 (mt) REVERT: D 320 LEU cc_start: 0.7683 (tp) cc_final: 0.7296 (tp) REVERT: D 360 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8249 (mp0) REVERT: D 368 MET cc_start: 0.7203 (tpp) cc_final: 0.6996 (tpt) REVERT: E 22 MET cc_start: 0.1322 (mmt) cc_final: 0.0184 (mmt) REVERT: E 31 TRP cc_start: 0.3340 (t-100) cc_final: 0.2451 (t-100) REVERT: E 107 MET cc_start: -0.1288 (tmt) cc_final: -0.1909 (tmm) REVERT: E 263 HIS cc_start: 0.7477 (OUTLIER) cc_final: 0.7142 (t-170) REVERT: E 301 LEU cc_start: 0.7525 (tp) cc_final: 0.7307 (mt) REVERT: E 358 GLN cc_start: 0.8120 (tp-100) cc_final: 0.7867 (tp-100) REVERT: E 373 TYR cc_start: 0.7500 (m-10) cc_final: 0.7020 (m-80) REVERT: G 282 PHE cc_start: 0.7639 (m-80) cc_final: 0.7368 (m-80) REVERT: G 302 HIS cc_start: 0.8703 (m-70) cc_final: 0.8060 (t70) REVERT: G 316 MET cc_start: 0.3682 (tpt) cc_final: 0.2918 (ptt) REVERT: G 396 THR cc_start: 0.4145 (OUTLIER) cc_final: 0.3900 (m) REVERT: G 542 ILE cc_start: 0.8781 (mm) cc_final: 0.8312 (tt) REVERT: G 552 PHE cc_start: 0.8393 (t80) cc_final: 0.7992 (t80) REVERT: c 118 LYS cc_start: 0.7910 (mmmt) cc_final: 0.7678 (tppt) REVERT: d 54 LYS cc_start: 0.8957 (mmmt) cc_final: 0.8728 (mmtt) REVERT: d 84 SER cc_start: 0.9333 (OUTLIER) cc_final: 0.9072 (p) REVERT: d 120 SER cc_start: 0.8932 (m) cc_final: 0.8715 (p) REVERT: f 92 ARG cc_start: 0.9175 (OUTLIER) cc_final: 0.8828 (ttp80) REVERT: g 90 ASP cc_start: 0.8659 (t0) cc_final: 0.8412 (t0) outliers start: 73 outliers final: 33 residues processed: 356 average time/residue: 1.4696 time to fit residues: 613.6029 Evaluate side-chains 318 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 271 time to evaluate : 2.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 775 TRP Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 886 HIS Chi-restraints excluded: chain A residue 978 ASP Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1036 HIS Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1165 ASN Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1259 ASP Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain A residue 1315 GLN Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 236 TRP Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain F residue 309 LYS Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 373 SER Chi-restraints excluded: chain G residue 395 ILE Chi-restraints excluded: chain G residue 396 THR Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 502 ASN Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain c residue 101 THR Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain d residue 84 SER Chi-restraints excluded: chain d residue 109 SER Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain f residue 50 ILE Chi-restraints excluded: chain f residue 92 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 176 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 170 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 181 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 224 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 18 HIS ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 30408 Z= 0.206 Angle : 0.619 15.043 42550 Z= 0.333 Chirality : 0.037 0.205 4703 Planarity : 0.004 0.049 4180 Dihedral : 26.368 160.895 6798 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.47 % Favored : 94.18 % Rotamer: Outliers : 2.76 % Allowed : 26.94 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.17), residues: 2631 helix: 1.43 (0.14), residues: 1460 sheet: -1.02 (0.44), residues: 137 loop : -0.74 (0.20), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP G 492 HIS 0.011 0.001 HIS D 18 PHE 0.038 0.001 PHE E 362 TYR 0.040 0.001 TYR G 372 ARG 0.007 0.000 ARG h 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 279 time to evaluate : 2.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 708 PHE cc_start: 0.8748 (m-80) cc_final: 0.8514 (m-80) REVERT: A 775 TRP cc_start: 0.6820 (OUTLIER) cc_final: 0.6384 (t-100) REVERT: A 805 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: A 978 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7471 (m-30) REVERT: A 1156 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: B 214 PHE cc_start: 0.7391 (OUTLIER) cc_final: 0.6654 (m-80) REVERT: D 18 HIS cc_start: 0.6828 (OUTLIER) cc_final: 0.6559 (m-70) REVERT: D 77 PHE cc_start: 0.6741 (m-80) cc_final: 0.6267 (m-80) REVERT: D 78 PHE cc_start: 0.8643 (t80) cc_final: 0.8218 (t80) REVERT: D 226 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7727 (mm) REVERT: D 237 GLU cc_start: 0.6403 (OUTLIER) cc_final: 0.4342 (mm-30) REVERT: D 310 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6579 (mt) REVERT: D 320 LEU cc_start: 0.7753 (tp) cc_final: 0.7088 (tp) REVERT: D 360 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8195 (mp0) REVERT: E 31 TRP cc_start: 0.3166 (t-100) cc_final: 0.2349 (t-100) REVERT: E 263 HIS cc_start: 0.7465 (OUTLIER) cc_final: 0.7160 (t-170) REVERT: E 373 TYR cc_start: 0.7473 (m-10) cc_final: 0.7019 (m-80) REVERT: G 282 PHE cc_start: 0.7728 (m-80) cc_final: 0.7383 (m-80) REVERT: G 302 HIS cc_start: 0.8719 (m-70) cc_final: 0.8019 (t70) REVERT: G 316 MET cc_start: 0.3992 (tpt) cc_final: 0.3185 (ptt) REVERT: G 396 THR cc_start: 0.4203 (OUTLIER) cc_final: 0.3959 (m) REVERT: d 54 LYS cc_start: 0.8982 (mmmt) cc_final: 0.8745 (mmtt) REVERT: d 120 SER cc_start: 0.8949 (m) cc_final: 0.8735 (p) REVERT: f 92 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.8835 (ttp80) REVERT: g 90 ASP cc_start: 0.8669 (t0) cc_final: 0.8419 (t0) outliers start: 66 outliers final: 39 residues processed: 331 average time/residue: 1.5002 time to fit residues: 584.0852 Evaluate side-chains 316 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 265 time to evaluate : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 775 TRP Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 978 ASP Chi-restraints excluded: chain A residue 1036 HIS Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1165 ASN Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1259 ASP Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1310 LEU Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 236 TRP Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 373 SER Chi-restraints excluded: chain G residue 379 ILE Chi-restraints excluded: chain G residue 395 ILE Chi-restraints excluded: chain G residue 396 THR Chi-restraints excluded: chain G residue 427 SER Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 502 ASN Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain G residue 517 ASN Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain c residue 76 THR Chi-restraints excluded: chain c residue 101 THR Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain d residue 84 SER Chi-restraints excluded: chain d residue 109 SER Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain f residue 50 ILE Chi-restraints excluded: chain f residue 92 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 0.7980 chunk 273 optimal weight: 0.5980 chunk 249 optimal weight: 0.5980 chunk 265 optimal weight: 0.8980 chunk 160 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 240 optimal weight: 0.8980 chunk 251 optimal weight: 0.2980 chunk 264 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1315 GLN D 18 HIS ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30408 Z= 0.186 Angle : 0.618 12.969 42550 Z= 0.331 Chirality : 0.036 0.160 4703 Planarity : 0.004 0.046 4180 Dihedral : 26.310 160.530 6798 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.51 % Favored : 94.18 % Rotamer: Outliers : 2.59 % Allowed : 27.23 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.17), residues: 2631 helix: 1.44 (0.14), residues: 1462 sheet: -1.14 (0.45), residues: 128 loop : -0.72 (0.20), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP G 492 HIS 0.015 0.001 HIS D 18 PHE 0.037 0.001 PHE A 668 TYR 0.035 0.001 TYR G 372 ARG 0.007 0.000 ARG h 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 282 time to evaluate : 2.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 708 PHE cc_start: 0.8738 (m-80) cc_final: 0.8524 (m-80) REVERT: A 775 TRP cc_start: 0.6808 (OUTLIER) cc_final: 0.6378 (t-100) REVERT: A 796 ILE cc_start: 0.7369 (pp) cc_final: 0.7038 (pt) REVERT: A 805 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8066 (mp0) REVERT: A 978 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7486 (m-30) REVERT: A 1156 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: A 1315 GLN cc_start: 0.7191 (OUTLIER) cc_final: 0.6809 (tm-30) REVERT: B 214 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.6546 (m-80) REVERT: D 18 HIS cc_start: 0.6631 (OUTLIER) cc_final: 0.6223 (m-70) REVERT: D 77 PHE cc_start: 0.6855 (m-80) cc_final: 0.6344 (m-80) REVERT: D 78 PHE cc_start: 0.8616 (t80) cc_final: 0.8210 (t80) REVERT: D 226 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7724 (mm) REVERT: D 237 GLU cc_start: 0.6418 (OUTLIER) cc_final: 0.4455 (mm-30) REVERT: D 310 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6579 (mt) REVERT: D 320 LEU cc_start: 0.7720 (tp) cc_final: 0.7078 (tp) REVERT: D 360 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8252 (mp0) REVERT: E 22 MET cc_start: 0.1182 (mmt) cc_final: 0.0198 (mmt) REVERT: E 31 TRP cc_start: 0.3110 (t-100) cc_final: 0.2322 (t-100) REVERT: E 107 MET cc_start: -0.2250 (tmm) cc_final: -0.2459 (tmm) REVERT: E 263 HIS cc_start: 0.7399 (OUTLIER) cc_final: 0.7135 (t-170) REVERT: E 373 TYR cc_start: 0.7479 (m-10) cc_final: 0.7031 (m-80) REVERT: G 282 PHE cc_start: 0.7686 (m-80) cc_final: 0.7352 (m-80) REVERT: G 302 HIS cc_start: 0.8764 (m-70) cc_final: 0.8115 (t70) REVERT: G 316 MET cc_start: 0.4004 (tpt) cc_final: 0.3229 (ptt) REVERT: G 396 THR cc_start: 0.4138 (OUTLIER) cc_final: 0.3861 (m) REVERT: G 542 ILE cc_start: 0.8778 (mm) cc_final: 0.8429 (tt) REVERT: G 550 ASP cc_start: 0.8930 (t0) cc_final: 0.8697 (t0) REVERT: G 552 PHE cc_start: 0.8375 (t80) cc_final: 0.7881 (t80) REVERT: d 54 LYS cc_start: 0.8964 (mmmt) cc_final: 0.8732 (mmtt) REVERT: d 120 SER cc_start: 0.8947 (m) cc_final: 0.8746 (p) REVERT: f 92 ARG cc_start: 0.9197 (OUTLIER) cc_final: 0.8815 (ttp80) REVERT: g 90 ASP cc_start: 0.8659 (t0) cc_final: 0.8412 (t0) REVERT: h 31 LYS cc_start: 0.8437 (mptt) cc_final: 0.8217 (mmtt) outliers start: 62 outliers final: 35 residues processed: 333 average time/residue: 1.4566 time to fit residues: 567.9656 Evaluate side-chains 316 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 268 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 775 TRP Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 978 ASP Chi-restraints excluded: chain A residue 1036 HIS Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1165 ASN Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1259 ASP Chi-restraints excluded: chain A residue 1310 LEU Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain A residue 1315 GLN Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 236 TRP Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 373 SER Chi-restraints excluded: chain G residue 379 ILE Chi-restraints excluded: chain G residue 395 ILE Chi-restraints excluded: chain G residue 396 THR Chi-restraints excluded: chain G residue 427 SER Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 440 CYS Chi-restraints excluded: chain G residue 502 ASN Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain c residue 101 THR Chi-restraints excluded: chain d residue 84 SER Chi-restraints excluded: chain d residue 109 SER Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain f residue 50 ILE Chi-restraints excluded: chain f residue 92 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 5.9990 chunk 281 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 195 optimal weight: 2.9990 chunk 294 optimal weight: 0.9980 chunk 271 optimal weight: 0.9990 chunk 234 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 974 GLN A1315 GLN ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 304 ASN a 76 GLN b 75 HIS f 75 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 30408 Z= 0.270 Angle : 0.660 12.913 42550 Z= 0.354 Chirality : 0.039 0.211 4703 Planarity : 0.004 0.048 4180 Dihedral : 26.675 160.202 6798 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.70 % Favored : 93.99 % Rotamer: Outliers : 2.42 % Allowed : 27.32 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.17), residues: 2631 helix: 1.36 (0.14), residues: 1451 sheet: -1.07 (0.45), residues: 138 loop : -0.79 (0.20), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP G 492 HIS 0.012 0.001 HIS D 18 PHE 0.044 0.002 PHE E 362 TYR 0.054 0.002 TYR G 372 ARG 0.007 0.000 ARG h 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 272 time to evaluate : 2.795 Fit side-chains revert: symmetry clash REVERT: A 708 PHE cc_start: 0.8828 (m-80) cc_final: 0.8379 (m-80) REVERT: A 775 TRP cc_start: 0.6853 (OUTLIER) cc_final: 0.6384 (t-100) REVERT: A 796 ILE cc_start: 0.7688 (pp) cc_final: 0.7354 (pt) REVERT: A 805 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8108 (mp0) REVERT: A 1156 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: A 1315 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.6786 (tm-30) REVERT: B 214 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.6711 (m-80) REVERT: D 77 PHE cc_start: 0.6889 (m-80) cc_final: 0.6337 (m-80) REVERT: D 78 PHE cc_start: 0.8613 (t80) cc_final: 0.8223 (t80) REVERT: D 226 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7711 (mm) REVERT: D 237 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.4560 (mm-30) REVERT: D 310 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6675 (mt) REVERT: D 320 LEU cc_start: 0.7832 (tp) cc_final: 0.7151 (tp) REVERT: E 22 MET cc_start: 0.1272 (mmt) cc_final: 0.0299 (mmt) REVERT: E 31 TRP cc_start: 0.3133 (t-100) cc_final: 0.2368 (t-100) REVERT: E 263 HIS cc_start: 0.7479 (OUTLIER) cc_final: 0.7258 (t-170) REVERT: E 373 TYR cc_start: 0.7494 (m-10) cc_final: 0.7002 (m-10) REVERT: G 396 THR cc_start: 0.4390 (OUTLIER) cc_final: 0.4156 (m) REVERT: G 475 TYR cc_start: 0.7773 (m-80) cc_final: 0.7556 (m-80) REVERT: G 542 ILE cc_start: 0.8792 (mm) cc_final: 0.8482 (tt) REVERT: f 92 ARG cc_start: 0.9278 (OUTLIER) cc_final: 0.8831 (ttp80) REVERT: g 90 ASP cc_start: 0.8690 (t0) cc_final: 0.8433 (t0) REVERT: h 31 LYS cc_start: 0.8452 (mptt) cc_final: 0.8177 (mmtt) outliers start: 58 outliers final: 38 residues processed: 318 average time/residue: 1.4869 time to fit residues: 554.6096 Evaluate side-chains 311 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 262 time to evaluate : 2.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 775 TRP Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 1036 HIS Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1165 ASN Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1259 ASP Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1310 LEU Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain A residue 1315 GLN Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 236 TRP Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 336 PHE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 373 SER Chi-restraints excluded: chain G residue 379 ILE Chi-restraints excluded: chain G residue 395 ILE Chi-restraints excluded: chain G residue 396 THR Chi-restraints excluded: chain G residue 427 SER Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 440 CYS Chi-restraints excluded: chain G residue 502 ASN Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain c residue 76 THR Chi-restraints excluded: chain c residue 101 THR Chi-restraints excluded: chain d residue 84 SER Chi-restraints excluded: chain d residue 109 SER Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain f residue 92 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 186 optimal weight: 5.9990 chunk 250 optimal weight: 0.0770 chunk 71 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 235 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 241 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 0.0670 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1315 GLN ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.126866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.085083 restraints weight = 59647.502| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.50 r_work: 0.3187 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30408 Z= 0.178 Angle : 0.627 12.471 42550 Z= 0.336 Chirality : 0.036 0.246 4703 Planarity : 0.004 0.049 4180 Dihedral : 26.371 166.029 6798 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.59 % Favored : 94.15 % Rotamer: Outliers : 2.05 % Allowed : 27.82 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.17), residues: 2631 helix: 1.41 (0.14), residues: 1457 sheet: -0.96 (0.45), residues: 137 loop : -0.70 (0.20), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP G 492 HIS 0.008 0.001 HIS D 18 PHE 0.040 0.001 PHE A 668 TYR 0.034 0.001 TYR G 372 ARG 0.006 0.000 ARG h 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10785.75 seconds wall clock time: 197 minutes 57.69 seconds (11877.69 seconds total)