Starting phenix.real_space_refine on Thu Jul 25 07:43:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tof_41449/07_2024/8tof_41449_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tof_41449/07_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_41449/07_2024/8tof_41449.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tof_41449/07_2024/8tof_41449.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tof_41449/07_2024/8tof_41449_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tof_41449/07_2024/8tof_41449_neut.cif" } 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 17.04, per 1000 atoms: 0.59 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: 13.86 Conformation dependent library (CDL) restraints added in 4.5 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... Secondary structure from input PDB file: 115 helices and 21 sheets defined 59.2% alpha, 5.8% beta 169 base pairs and 303 stacking pairs defined. Time for finding SS restraints: 12.48 Creating SS restraints... Processing helix chain 'A' and resid 664 through 676 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 678 through 692 removed outlier: 3.547A pdb=" N TYR A 692 " --> pdb=" O ILE A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 710 removed outlier: 3.527A pdb=" N PHE A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 725 Processing helix chain 'A' and resid 771 through 778 removed outlier: 3.664A pdb=" N LEU A 778 " --> pdb=" O CYS A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 791 removed outlier: 3.608A pdb=" N SER A 790 " --> pdb=" O VAL A 787 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU A 791 " --> pdb=" O TRP A 788 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 787 through 791' Processing helix chain 'A' and resid 801 through 840 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 842 through 849 Processing helix chain 'A' and resid 852 through 857 removed outlier: 4.171A pdb=" N GLY A 856 " --> pdb=" O PRO A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 872 through 885 removed outlier: 3.596A pdb=" N HIS A 884 " --> pdb=" O ILE A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 928 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 929 through 934 removed outlier: 3.532A pdb=" N LEU A 933 " --> pdb=" O ASP A 929 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR A 934 " --> pdb=" O HIS A 930 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 929 through 934' Processing helix chain 'A' and resid 937 through 943 Processing helix chain 'A' and resid 944 through 965 removed outlier: 3.598A pdb=" N ILE A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 999 Processing helix chain 'A' and resid 1003 through 1022 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 1039 removed outlier: 3.752A pdb=" N ASN A1039 " --> pdb=" O SER A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1173 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) Processing helix chain 'A' and resid 1179 through 1184 removed outlier: 4.053A pdb=" N ASP A1183 " --> pdb=" O THR A1179 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1194 removed outlier: 3.573A pdb=" N MET A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1216 Processing helix chain 'A' and resid 1220 through 1230 removed outlier: 3.730A pdb=" N GLU A1225 " --> pdb=" O HIS A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1240 Processing helix chain 'A' and resid 1242 through 1258 Processing helix chain 'A' and resid 1260 through 1274 Processing helix chain 'A' and resid 1279 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 55 removed outlier: 3.939A pdb=" N ARG B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 79 through 87 Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 97 through 105 Processing helix chain 'B' and resid 115 through 136 Processing helix chain 'B' and resid 164 through 175 removed outlier: 3.563A pdb=" N LEU B 168 " --> pdb=" O ASN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 243 through 262 Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 272 through 276 removed outlier: 3.726A pdb=" N SER B 275 " --> pdb=" O GLY B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 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 316 through 330 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) removed outlier: 3.618A pdb=" N ASN B 330 " --> pdb=" O THR B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 381 Processing helix chain 'D' and resid 68 through 73 removed outlier: 4.245A pdb=" N ASN D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.594A pdb=" N TRP D 88 " --> pdb=" O LYS D 85 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP D 89 " --> pdb=" O SER D 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 85 through 89' Processing helix chain 'D' and resid 101 through 131 Processing helix chain 'D' and resid 225 through 240 removed outlier: 3.776A pdb=" N THR D 240 " --> pdb=" O TRP D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 266 Processing helix chain 'D' and resid 270 through 297 removed outlier: 3.997A pdb=" N SER D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) 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 317 removed outlier: 4.463A pdb=" N GLN D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP D 307 " --> pdb=" O ARG D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 327 through 344 removed outlier: 3.666A pdb=" N LEU D 331 " --> pdb=" O GLY D 327 " (cutoff:3.500A) Proline residue: D 339 - end of helix Processing helix chain 'D' and resid 348 through 369 Processing helix chain 'D' and resid 391 through 399 removed outlier: 3.727A pdb=" N VAL D 397 " --> pdb=" O GLN D 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 73 removed outlier: 4.153A pdb=" N ASN E 73 " --> pdb=" O GLU E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 89 Processing helix chain 'E' and resid 101 through 131 Processing helix chain 'E' and resid 225 through 241 Processing helix chain 'E' and resid 253 through 266 removed outlier: 3.559A pdb=" N SER E 266 " --> pdb=" O GLU E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 297 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 317 removed outlier: 4.319A pdb=" N GLN E 305 " --> pdb=" O LEU E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 325 Processing helix chain 'E' and resid 327 through 344 removed outlier: 3.554A pdb=" N LEU E 331 " --> pdb=" O GLY E 327 " (cutoff:3.500A) Proline residue: E 339 - end of helix Processing helix chain 'E' and resid 348 through 369 Processing helix chain 'E' and resid 369 through 375 Processing helix chain 'F' and resid 303 through 313 Processing helix chain 'F' and resid 315 through 330 Processing helix chain 'F' and resid 333 through 335 No H-bonds generated for 'chain 'F' and resid 333 through 335' Processing helix chain 'F' and resid 336 through 346 Processing helix chain 'G' and resid 120 through 128 Processing helix chain 'G' and resid 163 through 167 Processing helix chain 'G' and resid 292 through 296 removed outlier: 4.093A pdb=" N LEU G 296 " --> pdb=" O PRO G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 313 Processing helix chain 'G' and resid 315 through 330 removed outlier: 3.618A pdb=" N LEU G 319 " --> pdb=" O SER G 315 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN G 325 " --> pdb=" O LYS G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 331 through 335 removed outlier: 5.618A pdb=" N ILE G 335 " --> pdb=" O ASN G 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 344 removed outlier: 3.645A pdb=" N ILE G 343 " --> pdb=" O LEU G 339 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASP G 344 " --> pdb=" O LEU G 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 354 through 359 removed outlier: 3.723A pdb=" N LYS G 358 " --> pdb=" O PRO G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 382 through 387 Processing helix chain 'G' and resid 393 through 397 removed outlier: 3.597A pdb=" N THR G 396 " --> pdb=" O GLN G 393 " (cutoff:3.500A) Processing helix chain 'G' and resid 430 through 434 Processing helix chain 'G' and resid 544 through 565 removed outlier: 3.611A pdb=" N LYS G 548 " --> pdb=" O GLU G 544 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 57 Processing helix chain 'a' and resid 63 through 76 Processing helix chain 'a' and resid 85 through 114 Processing helix chain 'a' and resid 120 through 132 Processing helix chain 'b' and resid 25 through 29 Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 49 through 76 removed outlier: 3.569A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP b 68 " --> pdb=" O ASN b 64 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 94 Processing helix chain 'c' and resid 17 through 21 Processing helix chain 'c' and resid 26 through 37 Processing helix chain 'c' and resid 45 through 73 removed outlier: 4.428A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 90 Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'c' and resid 112 through 116 Processing helix chain 'd' and resid 34 through 46 Processing helix chain 'd' and resid 52 through 81 Processing helix chain 'd' and resid 87 through 99 Processing helix chain 'd' and resid 100 through 121 removed outlier: 3.509A pdb=" N ALA d 121 " --> pdb=" O LYS d 117 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 57 Processing helix chain 'e' and resid 63 through 79 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 85 through 114 Processing helix chain 'e' and resid 120 through 132 Processing helix chain 'f' and resid 25 through 29 Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 49 through 76 Processing helix chain 'f' and resid 82 through 93 Processing helix chain 'g' and resid 16 through 22 Processing helix chain 'g' and resid 26 through 36 Processing helix chain 'g' and resid 45 through 73 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 79 through 90 Processing helix chain 'g' and resid 90 through 97 Processing helix chain 'g' and resid 112 through 116 Processing helix chain 'h' and resid 34 through 46 Processing helix chain 'h' and resid 52 through 81 Processing helix chain 'h' and resid 87 through 99 Processing helix chain 'h' and resid 100 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 756 through 757 Processing sheet with id=AA2, first strand: chain 'A' and resid 977 through 978 removed outlier: 3.796A pdb=" N HIS A1311 " --> pdb=" O ASP A1306 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 233 through 237 removed outlier: 7.681A pdb=" N VAL B 234 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N THR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL B 236 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N SER B 207 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL B 180 " --> pdb=" O MET B 204 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N CYS B 206 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N TYR B 182 " --> pdb=" O CYS B 206 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N PHE B 208 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP B 184 " --> pdb=" O PHE B 208 " (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) removed outlier: 6.310A pdb=" N ALA B 142 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE B 63 " --> pdb=" O GLU G 177 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N SER G 179 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ARG B 65 " --> pdb=" O SER G 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 37 through 39 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=AA5, first strand: chain 'D' and resid 37 through 39 removed outlier: 3.670A pdb=" N LEU D 21 " --> pdb=" O HIS D 18 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N HIS D 18 " --> pdb=" O LEU D 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR D 23 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 244 through 246 Processing sheet with id=AA7, first strand: chain 'E' and resid 37 through 39 removed outlier: 6.469A pdb=" N PHE E 78 " --> pdb=" O LEU E 28 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 37 through 39 Processing sheet with id=AA9, first strand: chain 'F' and resid 272 through 274 Processing sheet with id=AB1, first strand: chain 'G' and resid 437 through 439 Processing sheet with id=AB2, first strand: chain 'G' and resid 476 through 477 Processing sheet with id=AB3, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.814A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'a' and resid 118 through 119 Processing sheet with id=AB5, first strand: chain 'b' and resid 96 through 98 Processing sheet with id=AB6, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.248A pdb=" N ARG c 42 " --> pdb=" O ILE d 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AB8, first strand: chain 'c' and resid 100 through 102 Processing sheet with id=AB9, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.939A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AC2, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.299A pdb=" N ARG g 42 " --> pdb=" O ILE h 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'g' and resid 77 through 78 1141 hydrogen bonds defined for protein. 3300 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: 17.45 Time building geometry restraints manager: 14.86 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: 160 2.44 - 3.06: 19267 3.06 - 3.67: 48621 3.67 - 4.29: 73673 4.29 - 4.90: 112402 Nonbonded interactions: 254123 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 254118 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 15.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.140 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 99.900 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.620 ------------------------------------------------------------------------------- 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= 0.512 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 : 2.821 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: 1.4818 time to fit residues: 627.8499 Evaluate side-chains 329 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 274 time to evaluate : 2.785 ------------------------------------------------------------------------------- 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: 0.7980 chunk 224 optimal weight: 0.8980 chunk 124 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 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: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 HIS A1150 HIS A1252 HIS B 43 HIS D 369 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 b 75 HIS d 81 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30408 Z= 0.204 Angle : 0.613 8.079 42550 Z= 0.342 Chirality : 0.038 0.193 4703 Planarity : 0.004 0.084 4180 Dihedral : 26.646 167.051 6888 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.85 % Favored : 93.69 % Rotamer: Outliers : 4.55 % Allowed : 23.27 % Favored : 72.18 % 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: 0.61 (0.17), residues: 2631 helix: 1.66 (0.14), residues: 1452 sheet: -2.25 (0.45), residues: 109 loop : -1.06 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 236 HIS 0.006 0.001 HIS B 49 PHE 0.020 0.002 PHE E 362 TYR 0.018 0.001 TYR G 506 ARG 0.008 0.000 ARG D 381 *********************** 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 424 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 315 time to evaluate : 2.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 719 TRP cc_start: 0.8304 (t60) cc_final: 0.8055 (t60) REVERT: A 775 TRP cc_start: 0.6778 (OUTLIER) cc_final: 0.6139 (t-100) REVERT: A 978 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7566 (m-30) REVERT: A 1156 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7874 (mp0) REVERT: B 220 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7829 (tm-30) REVERT: B 222 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7960 (mtp180) REVERT: D 77 PHE cc_start: 0.6861 (OUTLIER) cc_final: 0.6080 (m-10) REVERT: D 78 PHE cc_start: 0.8531 (t80) cc_final: 0.7722 (t80) REVERT: D 81 TYR cc_start: 0.7830 (m-80) cc_final: 0.7514 (m-80) REVERT: D 237 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.4485 (mm-30) REVERT: D 310 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6894 (tp) REVERT: D 320 LEU cc_start: 0.7675 (tp) cc_final: 0.6996 (tp) REVERT: D 360 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8267 (mp0) REVERT: D 376 ASP cc_start: 0.7332 (p0) cc_final: 0.7099 (p0) REVERT: E 335 ILE cc_start: 0.7240 (OUTLIER) cc_final: 0.6977 (mp) REVERT: E 373 TYR cc_start: 0.7383 (m-10) cc_final: 0.6847 (m-80) REVERT: G 282 PHE cc_start: 0.7869 (m-80) cc_final: 0.7364 (m-80) REVERT: G 552 PHE cc_start: 0.8285 (t80) cc_final: 0.7952 (t80) REVERT: G 553 ASP cc_start: 0.9129 (p0) cc_final: 0.8331 (m-30) REVERT: c 64 GLU cc_start: 0.8555 (tp30) cc_final: 0.8300 (tt0) REVERT: d 54 LYS cc_start: 0.8954 (mmmt) cc_final: 0.8716 (mmtt) outliers start: 109 outliers final: 41 residues processed: 397 average time/residue: 1.3894 time to fit residues: 647.6552 Evaluate side-chains 326 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 277 time to evaluate : 2.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 1317 ILE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 101 SER 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 292 CYS Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 355 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 309 LYS Chi-restraints excluded: chain F residue 316 MET 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 364 VAL 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 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 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: 2.9990 chunk 83 optimal weight: 2.9990 chunk 223 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 chunk 290 optimal weight: 0.9980 chunk 239 optimal weight: 1.9990 chunk 267 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 216 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: B 341 ASN D 18 HIS D 369 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** g 104 GLN h 46 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 30408 Z= 0.265 Angle : 0.619 9.281 42550 Z= 0.344 Chirality : 0.038 0.208 4703 Planarity : 0.004 0.068 4180 Dihedral : 26.840 165.420 6823 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.08 % Favored : 93.50 % Rotamer: Outliers : 4.64 % Allowed : 23.22 % Favored : 72.14 % 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: 0.70 (0.17), residues: 2631 helix: 1.68 (0.14), residues: 1465 sheet: -1.92 (0.44), residues: 120 loop : -1.00 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 236 HIS 0.005 0.001 HIS B 78 PHE 0.024 0.002 PHE A 668 TYR 0.022 0.001 TYR B 347 ARG 0.008 0.000 ARG B 46 *********************** 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 402 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 291 time to evaluate : 2.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 719 TRP cc_start: 0.8407 (t60) cc_final: 0.8149 (t60) REVERT: A 775 TRP cc_start: 0.6820 (OUTLIER) cc_final: 0.6148 (t-100) REVERT: A 805 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: A 845 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8439 (pm20) REVERT: A 978 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7530 (m-30) REVERT: A 1156 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7886 (mp0) REVERT: B 73 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7421 (tt0) REVERT: B 220 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7798 (tm-30) REVERT: B 222 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7983 (mtp180) REVERT: D 18 HIS cc_start: 0.5399 (OUTLIER) cc_final: 0.5086 (m90) REVERT: D 77 PHE cc_start: 0.6897 (OUTLIER) cc_final: 0.6197 (m-10) REVERT: D 78 PHE cc_start: 0.8480 (t80) cc_final: 0.8186 (t80) REVERT: D 237 GLU cc_start: 0.6666 (OUTLIER) cc_final: 0.4518 (mm-30) REVERT: D 310 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.6924 (tp) REVERT: D 320 LEU cc_start: 0.7761 (tp) cc_final: 0.7020 (tp) REVERT: E 263 HIS cc_start: 0.7674 (OUTLIER) cc_final: 0.7317 (t-170) REVERT: E 335 ILE cc_start: 0.7317 (OUTLIER) cc_final: 0.6998 (mp) REVERT: G 175 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7407 (ptp) REVERT: G 302 HIS cc_start: 0.8975 (m90) cc_final: 0.8763 (m-70) REVERT: G 552 PHE cc_start: 0.8318 (t80) cc_final: 0.7899 (t80) REVERT: c 64 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8338 (tt0) outliers start: 111 outliers final: 48 residues processed: 375 average time/residue: 1.4320 time to fit residues: 627.8674 Evaluate side-chains 339 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 276 time to evaluate : 2.660 ------------------------------------------------------------------------------- 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 845 GLU Chi-restraints excluded: chain A residue 886 HIS Chi-restraints excluded: chain A residue 934 THR 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 978 ASP Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1033 LEU 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 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 222 ARG Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 77 PHE 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 242 ASP Chi-restraints excluded: chain E residue 263 HIS 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 169 THR 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 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 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 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 64 GLU 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 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: 2.9990 chunk 202 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 128 optimal weight: 40.0000 chunk 180 optimal weight: 4.9990 chunk 270 optimal weight: 0.9980 chunk 286 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 256 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 HIS D 369 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 502 ASN ** G 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30408 Z= 0.242 Angle : 0.613 11.992 42550 Z= 0.338 Chirality : 0.038 0.211 4703 Planarity : 0.004 0.059 4180 Dihedral : 26.728 166.125 6815 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.01 % Favored : 93.58 % Rotamer: Outliers : 4.97 % Allowed : 23.43 % 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: 0.82 (0.17), residues: 2631 helix: 1.75 (0.14), residues: 1465 sheet: -1.79 (0.45), residues: 118 loop : -0.91 (0.20), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 236 HIS 0.018 0.001 HIS D 18 PHE 0.030 0.002 PHE A 668 TYR 0.021 0.001 TYR B 347 ARG 0.010 0.000 ARG D 381 *********************** 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 422 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 303 time to evaluate : 3.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 708 PHE cc_start: 0.8861 (m-80) cc_final: 0.8538 (m-80) REVERT: A 719 TRP cc_start: 0.8488 (t60) cc_final: 0.8201 (t60) REVERT: A 775 TRP cc_start: 0.6792 (OUTLIER) cc_final: 0.6137 (t-100) REVERT: A 978 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7516 (m-30) REVERT: A 1138 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8516 (tp) REVERT: A 1156 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: B 73 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7372 (tt0) REVERT: B 214 PHE cc_start: 0.7492 (OUTLIER) cc_final: 0.7089 (m-80) REVERT: B 220 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7791 (tm-30) REVERT: B 283 CYS cc_start: 0.8385 (p) cc_final: 0.8154 (p) REVERT: D 77 PHE cc_start: 0.6929 (m-80) cc_final: 0.6249 (m-10) REVERT: D 78 PHE cc_start: 0.8562 (t80) cc_final: 0.8204 (t80) REVERT: D 107 MET cc_start: 0.7793 (ppp) cc_final: 0.7360 (ppp) REVERT: D 237 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.4468 (mm-30) REVERT: D 310 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.6940 (tp) REVERT: D 320 LEU cc_start: 0.7753 (tp) cc_final: 0.6948 (tp) REVERT: D 368 MET cc_start: 0.7130 (tpp) cc_final: 0.6894 (tpt) REVERT: D 376 ASP cc_start: 0.7311 (p0) cc_final: 0.7088 (p0) REVERT: E 107 MET cc_start: -0.1615 (tmt) cc_final: -0.1840 (tmm) REVERT: E 263 HIS cc_start: 0.7660 (OUTLIER) cc_final: 0.7313 (t-170) REVERT: E 335 ILE cc_start: 0.7308 (OUTLIER) cc_final: 0.7005 (mp) REVERT: E 373 TYR cc_start: 0.7289 (m-10) cc_final: 0.6721 (m-10) REVERT: G 164 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6874 (mpt-90) REVERT: G 302 HIS cc_start: 0.8981 (m90) cc_final: 0.8763 (m-70) REVERT: G 316 MET cc_start: 0.3718 (tpt) cc_final: 0.2896 (ptt) REVERT: G 552 PHE cc_start: 0.8424 (t80) cc_final: 0.7854 (t80) REVERT: G 556 TYR cc_start: 0.8739 (OUTLIER) cc_final: 0.8508 (m-10) REVERT: c 64 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8339 (tt0) REVERT: d 54 LYS cc_start: 0.8979 (mmmt) cc_final: 0.8679 (mmtt) REVERT: g 92 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7602 (mm-30) REVERT: h 31 LYS cc_start: 0.8403 (mptp) cc_final: 0.8153 (mptp) outliers start: 119 outliers final: 51 residues processed: 392 average time/residue: 1.4553 time to fit residues: 669.2103 Evaluate side-chains 347 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 282 time to evaluate : 2.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 775 TRP Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 934 THR 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 1033 LEU Chi-restraints excluded: chain A residue 1036 HIS Chi-restraints excluded: chain A residue 1138 LEU 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 1300 MET 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 75 CYS 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 236 TRP Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 292 CYS 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 D residue 367 LEU Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 164 ARG 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 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 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 64 GLU 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 e residue 87 SER Chi-restraints excluded: chain g residue 92 GLU 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: 2.9990 chunk 162 optimal weight: 0.0040 chunk 4 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 244 optimal weight: 0.5980 chunk 197 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 30.0000 chunk 256 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1315 GLN ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 502 ASN ** G 510 GLN ** 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: 0.6889 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 30408 Z= 0.285 Angle : 0.635 16.952 42550 Z= 0.348 Chirality : 0.039 0.209 4703 Planarity : 0.004 0.051 4180 Dihedral : 26.883 179.626 6810 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.12 % Favored : 93.50 % Rotamer: Outliers : 5.05 % Allowed : 24.10 % Favored : 70.84 % 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: 0.76 (0.17), residues: 2631 helix: 1.66 (0.14), residues: 1472 sheet: -1.88 (0.44), residues: 124 loop : -0.87 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 236 HIS 0.005 0.001 HIS e 39 PHE 0.029 0.002 PHE A 668 TYR 0.022 0.002 TYR B 347 ARG 0.007 0.000 ARG D 381 *********************** 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 425 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 304 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 708 PHE cc_start: 0.8920 (m-80) cc_final: 0.8594 (m-80) REVERT: A 719 TRP cc_start: 0.8540 (t60) cc_final: 0.8271 (t60) REVERT: A 775 TRP cc_start: 0.6861 (OUTLIER) cc_final: 0.6206 (t-100) REVERT: A 885 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7772 (mt-10) REVERT: A 978 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7486 (m-30) REVERT: A 1138 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8460 (tp) REVERT: A 1156 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: A 1315 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.7151 (tm-30) REVERT: B 73 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7678 (tt0) REVERT: B 109 ASP cc_start: 0.8565 (p0) cc_final: 0.8341 (p0) REVERT: B 214 PHE cc_start: 0.7549 (OUTLIER) cc_final: 0.7093 (m-80) REVERT: B 220 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7796 (tm-30) REVERT: B 283 CYS cc_start: 0.8363 (p) cc_final: 0.7778 (p) REVERT: D 22 MET cc_start: 0.1674 (mmp) cc_final: 0.1204 (mmp) REVERT: D 77 PHE cc_start: 0.6967 (m-80) cc_final: 0.6231 (m-10) REVERT: D 78 PHE cc_start: 0.8607 (t80) cc_final: 0.8235 (t80) REVERT: D 98 ARG cc_start: 0.3876 (mtt90) cc_final: 0.3260 (ptp-170) REVERT: D 107 MET cc_start: 0.7859 (ppp) cc_final: 0.7321 (ppp) REVERT: D 237 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.4443 (mm-30) REVERT: D 310 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.6941 (tp) REVERT: D 320 LEU cc_start: 0.7831 (tp) cc_final: 0.6993 (tp) REVERT: D 368 MET cc_start: 0.7206 (tpp) cc_final: 0.6916 (tpt) REVERT: D 376 ASP cc_start: 0.7260 (p0) cc_final: 0.7033 (p0) REVERT: E 22 MET cc_start: 0.1265 (mmt) cc_final: 0.0207 (mmt) REVERT: E 31 TRP cc_start: 0.3574 (t-100) cc_final: 0.2747 (t-100) REVERT: E 37 MET cc_start: 0.6154 (tpp) cc_final: 0.5894 (tpp) REVERT: E 263 HIS cc_start: 0.7616 (OUTLIER) cc_final: 0.7310 (t-170) REVERT: E 335 ILE cc_start: 0.7422 (OUTLIER) cc_final: 0.7200 (mp) REVERT: G 302 HIS cc_start: 0.9018 (m90) cc_final: 0.8779 (m-70) REVERT: G 552 PHE cc_start: 0.8426 (t80) cc_final: 0.7796 (t80) REVERT: a 56 LYS cc_start: 0.9147 (ttpp) cc_final: 0.8889 (ttmm) REVERT: c 64 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: d 54 LYS cc_start: 0.8991 (mmmt) cc_final: 0.8710 (mmtt) REVERT: h 31 LYS cc_start: 0.8468 (mptp) cc_final: 0.8261 (mptp) outliers start: 121 outliers final: 51 residues processed: 399 average time/residue: 1.4276 time to fit residues: 664.7937 Evaluate side-chains 340 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 277 time to evaluate : 2.631 ------------------------------------------------------------------------------- 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 813 GLU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 978 ASP Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1036 HIS Chi-restraints excluded: chain A residue 1138 LEU 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 1228 LEU Chi-restraints excluded: chain A residue 1268 LEU 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 1315 GLN 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 133 ARG Chi-restraints excluded: chain B residue 214 PHE 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 236 TRP Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 292 CYS 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 D residue 367 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain F residue 262 PHE 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 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 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 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 d residue 109 SER Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 1.9990 chunk 257 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 167 optimal weight: 6.9990 chunk 70 optimal weight: 0.0770 chunk 286 optimal weight: 1.9990 chunk 237 optimal weight: 0.7980 chunk 132 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 150 optimal weight: 1.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1315 GLN ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 502 ASN ** G 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 30408 Z= 0.212 Angle : 0.617 13.091 42550 Z= 0.338 Chirality : 0.037 0.202 4703 Planarity : 0.004 0.052 4180 Dihedral : 26.684 178.857 6807 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.70 % Favored : 93.92 % Rotamer: Outliers : 3.72 % Allowed : 25.52 % Favored : 70.76 % 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: 0.90 (0.17), residues: 2631 helix: 1.75 (0.14), residues: 1480 sheet: -1.80 (0.44), residues: 124 loop : -0.79 (0.20), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 236 HIS 0.009 0.001 HIS A 886 PHE 0.032 0.002 PHE E 362 TYR 0.018 0.001 TYR B 347 ARG 0.008 0.000 ARG B 46 *********************** 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 394 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 305 time to evaluate : 2.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 719 TRP cc_start: 0.8540 (t60) cc_final: 0.8255 (t60) REVERT: A 775 TRP cc_start: 0.6842 (OUTLIER) cc_final: 0.6210 (t-100) REVERT: A 978 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7505 (m-30) REVERT: A 1033 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5939 (tm) REVERT: A 1156 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7901 (mp0) REVERT: A 1315 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7265 (tm-30) REVERT: B 73 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7715 (tt0) REVERT: B 214 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.6793 (m-80) REVERT: B 220 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7764 (tm-30) REVERT: D 22 MET cc_start: 0.2074 (mmp) cc_final: 0.1745 (mmp) REVERT: D 78 PHE cc_start: 0.8618 (t80) cc_final: 0.8229 (t80) REVERT: D 98 ARG cc_start: 0.3995 (mtt90) cc_final: 0.3307 (ptp-170) REVERT: D 107 MET cc_start: 0.7802 (ppp) cc_final: 0.7269 (ppp) REVERT: D 237 GLU cc_start: 0.6378 (OUTLIER) cc_final: 0.4216 (mm-30) REVERT: D 310 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.6939 (tp) REVERT: D 320 LEU cc_start: 0.7774 (tp) cc_final: 0.6943 (tp) REVERT: D 368 MET cc_start: 0.7153 (tpp) cc_final: 0.6916 (tpt) REVERT: D 376 ASP cc_start: 0.7172 (p0) cc_final: 0.6960 (p0) REVERT: E 31 TRP cc_start: 0.3363 (t-100) cc_final: 0.2556 (t-100) REVERT: E 37 MET cc_start: 0.6368 (tpp) cc_final: 0.6157 (tpp) REVERT: E 107 MET cc_start: -0.1672 (tmt) cc_final: -0.1930 (tmm) REVERT: E 263 HIS cc_start: 0.7554 (OUTLIER) cc_final: 0.7291 (t-170) REVERT: E 373 TYR cc_start: 0.7213 (m-10) cc_final: 0.6569 (m-80) REVERT: G 302 HIS cc_start: 0.9017 (m90) cc_final: 0.8793 (m-70) REVERT: G 316 MET cc_start: 0.3850 (tpt) cc_final: 0.3034 (ptt) REVERT: a 56 LYS cc_start: 0.9174 (ttpp) cc_final: 0.8926 (ttmm) REVERT: c 64 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8346 (tt0) REVERT: c 118 LYS cc_start: 0.7916 (mmmt) cc_final: 0.7654 (tppt) REVERT: d 54 LYS cc_start: 0.8978 (mmmt) cc_final: 0.8714 (mmtt) outliers start: 89 outliers final: 47 residues processed: 369 average time/residue: 1.3936 time to fit residues: 602.4558 Evaluate side-chains 335 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 277 time to evaluate : 2.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 775 TRP Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 978 ASP Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1033 LEU 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 1228 LEU 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 1315 GLN Chi-restraints excluded: chain A residue 1317 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 341 ASN Chi-restraints excluded: chain B residue 380 LEU 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 323 ILE Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain F residue 309 LYS Chi-restraints excluded: chain F residue 336 PHE 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 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 427 SER 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 64 GLU 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 e residue 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 276 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 163 optimal weight: 4.9990 chunk 209 optimal weight: 3.9990 chunk 162 optimal weight: 0.0980 chunk 241 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 285 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 173 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 GLN ** G 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30408 Z= 0.193 Angle : 0.603 11.986 42550 Z= 0.330 Chirality : 0.037 0.190 4703 Planarity : 0.004 0.055 4180 Dihedral : 26.532 179.596 6806 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.85 % Favored : 93.77 % Rotamer: Outliers : 3.47 % Allowed : 25.86 % Favored : 70.68 % 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: 1.04 (0.17), residues: 2631 helix: 1.84 (0.14), residues: 1482 sheet: -1.55 (0.43), residues: 133 loop : -0.72 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP G 492 HIS 0.006 0.001 HIS A 886 PHE 0.027 0.001 PHE A 668 TYR 0.017 0.001 TYR B 347 ARG 0.006 0.000 ARG c 71 *********************** 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 391 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 308 time to evaluate : 2.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 719 TRP cc_start: 0.8551 (t60) cc_final: 0.8258 (t60) REVERT: A 775 TRP cc_start: 0.6859 (OUTLIER) cc_final: 0.6318 (t-100) REVERT: A 796 ILE cc_start: 0.7334 (pp) cc_final: 0.6991 (pt) REVERT: A 978 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7514 (m-30) REVERT: A 1156 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7883 (mp0) REVERT: B 73 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7720 (tt0) REVERT: B 214 PHE cc_start: 0.7402 (OUTLIER) cc_final: 0.6702 (m-80) REVERT: D 22 MET cc_start: 0.2279 (mmp) cc_final: 0.1842 (mmp) REVERT: D 78 PHE cc_start: 0.8690 (t80) cc_final: 0.8330 (t80) REVERT: D 98 ARG cc_start: 0.3940 (mtt90) cc_final: 0.3291 (ptp-110) REVERT: D 107 MET cc_start: 0.7787 (ppp) cc_final: 0.7205 (ppp) REVERT: D 237 GLU cc_start: 0.6416 (OUTLIER) cc_final: 0.4214 (mm-30) REVERT: D 310 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.6939 (tp) REVERT: D 320 LEU cc_start: 0.7786 (tp) cc_final: 0.6945 (tp) REVERT: D 376 ASP cc_start: 0.7310 (p0) cc_final: 0.7103 (p0) REVERT: E 22 MET cc_start: 0.1459 (mmt) cc_final: 0.0246 (mmt) REVERT: E 31 TRP cc_start: 0.3339 (t-100) cc_final: 0.2566 (t-100) REVERT: E 107 MET cc_start: -0.1311 (tmt) cc_final: -0.1912 (tmm) REVERT: E 263 HIS cc_start: 0.7487 (OUTLIER) cc_final: 0.7222 (t-170) REVERT: E 373 TYR cc_start: 0.7205 (m-10) cc_final: 0.6566 (m-80) REVERT: G 302 HIS cc_start: 0.9009 (m90) cc_final: 0.8786 (m-70) REVERT: G 316 MET cc_start: 0.3807 (tpt) cc_final: 0.3019 (ptt) REVERT: G 497 LEU cc_start: 0.8129 (tp) cc_final: 0.7863 (pt) REVERT: G 502 ASN cc_start: 0.7580 (OUTLIER) cc_final: 0.7349 (m110) REVERT: G 552 PHE cc_start: 0.8384 (t80) cc_final: 0.7972 (t80) REVERT: a 56 LYS cc_start: 0.9145 (ttpp) cc_final: 0.8917 (ttmm) REVERT: d 54 LYS cc_start: 0.8975 (mmmt) cc_final: 0.8716 (mmtt) REVERT: f 53 GLU cc_start: 0.8515 (tp30) cc_final: 0.8179 (tp30) outliers start: 83 outliers final: 43 residues processed: 364 average time/residue: 1.3391 time to fit residues: 573.9659 Evaluate side-chains 328 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 276 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 775 TRP Chi-restraints excluded: chain A residue 793 SER Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 978 ASP Chi-restraints excluded: chain A residue 1006 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 1163 GLN Chi-restraints excluded: chain A residue 1165 ASN Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1268 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 114 ASP Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 341 ASN 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 D residue 367 LEU Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain F residue 336 PHE 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 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 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 e residue 80 THR Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain f residue 49 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 176 optimal weight: 0.0020 chunk 113 optimal weight: 0.7980 chunk 170 optimal weight: 0.4980 chunk 85 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 224 optimal weight: 0.7980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 502 ASN a 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30408 Z= 0.189 Angle : 0.620 15.512 42550 Z= 0.334 Chirality : 0.036 0.182 4703 Planarity : 0.004 0.057 4180 Dihedral : 26.470 178.822 6805 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.55 % Favored : 94.07 % Rotamer: Outliers : 2.92 % Allowed : 26.65 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.17), residues: 2631 helix: 1.91 (0.14), residues: 1472 sheet: -1.41 (0.43), residues: 133 loop : -0.68 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP G 492 HIS 0.006 0.001 HIS A 886 PHE 0.042 0.001 PHE E 362 TYR 0.036 0.001 TYR G 372 ARG 0.007 0.000 ARG a 42 *********************** 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 372 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 302 time to evaluate : 3.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 719 TRP cc_start: 0.8351 (t60) cc_final: 0.8136 (t60) REVERT: A 775 TRP cc_start: 0.6866 (OUTLIER) cc_final: 0.6314 (t-100) REVERT: A 796 ILE cc_start: 0.7289 (pp) cc_final: 0.6955 (pt) REVERT: A 1149 ARG cc_start: 0.8575 (mmm-85) cc_final: 0.8360 (mmm-85) REVERT: A 1156 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7873 (mp0) REVERT: B 214 PHE cc_start: 0.7384 (OUTLIER) cc_final: 0.6686 (m-80) REVERT: D 22 MET cc_start: 0.2217 (mmp) cc_final: 0.1805 (mmp) REVERT: D 78 PHE cc_start: 0.8643 (t80) cc_final: 0.8255 (t80) REVERT: D 98 ARG cc_start: 0.4135 (mtt90) cc_final: 0.3393 (ptp-110) REVERT: D 107 MET cc_start: 0.7800 (ppp) cc_final: 0.7185 (ppp) REVERT: D 237 GLU cc_start: 0.6284 (OUTLIER) cc_final: 0.4100 (mm-30) REVERT: D 310 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7088 (tp) REVERT: D 320 LEU cc_start: 0.7805 (tp) cc_final: 0.6951 (tp) REVERT: D 360 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8167 (mp0) REVERT: D 376 ASP cc_start: 0.7182 (p0) cc_final: 0.6982 (p0) REVERT: E 22 MET cc_start: 0.1586 (mmt) cc_final: 0.0387 (mmt) REVERT: E 31 TRP cc_start: 0.3333 (t-100) cc_final: 0.2626 (t-100) REVERT: E 107 MET cc_start: -0.1339 (tmt) cc_final: -0.2004 (tmm) REVERT: E 263 HIS cc_start: 0.7472 (OUTLIER) cc_final: 0.7230 (t-170) REVERT: E 373 TYR cc_start: 0.7229 (m-10) cc_final: 0.6588 (m-80) REVERT: G 282 PHE cc_start: 0.7771 (m-80) cc_final: 0.7344 (m-80) REVERT: G 302 HIS cc_start: 0.8970 (m90) cc_final: 0.8764 (m-70) REVERT: G 316 MET cc_start: 0.3839 (tpt) cc_final: 0.3145 (ptt) REVERT: G 552 PHE cc_start: 0.8151 (t80) cc_final: 0.7942 (t80) REVERT: d 54 LYS cc_start: 0.8981 (mmmt) cc_final: 0.8730 (mmtt) REVERT: f 53 GLU cc_start: 0.8482 (tp30) cc_final: 0.8173 (tp30) outliers start: 70 outliers final: 43 residues processed: 354 average time/residue: 1.4216 time to fit residues: 589.1366 Evaluate side-chains 334 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 285 time to evaluate : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 775 TRP Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 1006 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 1268 LEU Chi-restraints excluded: chain A residue 1317 ILE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 341 ASN 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 D residue 367 LEU Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain F residue 336 PHE 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 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 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 b residue 50 ILE 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 109 SER Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain f residue 49 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 0.8980 chunk 273 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 chunk 265 optimal weight: 0.6980 chunk 160 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 208 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 240 optimal weight: 1.9990 chunk 251 optimal weight: 0.0000 chunk 264 optimal weight: 0.8980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1143 ASN B 76 GLN ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 GLN ** G 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 502 ASN a 76 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30408 Z= 0.199 Angle : 0.629 17.507 42550 Z= 0.337 Chirality : 0.037 0.215 4703 Planarity : 0.004 0.054 4180 Dihedral : 26.484 178.736 6803 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.66 % Favored : 93.99 % Rotamer: Outliers : 2.72 % Allowed : 27.53 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.17), residues: 2631 helix: 1.94 (0.14), residues: 1473 sheet: -1.31 (0.43), residues: 133 loop : -0.67 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP G 492 HIS 0.004 0.001 HIS B 49 PHE 0.036 0.001 PHE F 326 TYR 0.045 0.001 TYR G 372 ARG 0.005 0.000 ARG c 71 *********************** 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 356 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 291 time to evaluate : 3.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 775 TRP cc_start: 0.6855 (OUTLIER) cc_final: 0.6339 (t-100) REVERT: A 796 ILE cc_start: 0.7306 (pp) cc_final: 0.6968 (pt) REVERT: A 1156 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7860 (mp0) REVERT: B 214 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.6577 (m-80) REVERT: D 22 MET cc_start: 0.2434 (mmp) cc_final: 0.1946 (mmp) REVERT: D 78 PHE cc_start: 0.8629 (t80) cc_final: 0.8284 (t80) REVERT: D 98 ARG cc_start: 0.3960 (mtt90) cc_final: 0.3592 (ptp-170) REVERT: D 237 GLU cc_start: 0.6213 (OUTLIER) cc_final: 0.4155 (mm-30) REVERT: D 310 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7082 (tp) REVERT: D 320 LEU cc_start: 0.7803 (tp) cc_final: 0.7005 (tp) REVERT: D 360 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8166 (mp0) REVERT: D 376 ASP cc_start: 0.7296 (p0) cc_final: 0.7076 (p0) REVERT: E 22 MET cc_start: 0.1594 (mmt) cc_final: 0.0421 (mmt) REVERT: E 107 MET cc_start: -0.1181 (tmt) cc_final: -0.1787 (tmm) REVERT: E 263 HIS cc_start: 0.7410 (OUTLIER) cc_final: 0.7097 (t-90) REVERT: E 373 TYR cc_start: 0.7268 (m-10) cc_final: 0.6624 (m-80) REVERT: G 282 PHE cc_start: 0.7709 (m-80) cc_final: 0.7316 (m-80) REVERT: G 316 MET cc_start: 0.3948 (tpt) cc_final: 0.3262 (ptt) REVERT: G 542 ILE cc_start: 0.8501 (mm) cc_final: 0.8284 (tt) REVERT: d 54 LYS cc_start: 0.8994 (mmmt) cc_final: 0.8738 (mmtt) REVERT: f 53 GLU cc_start: 0.8489 (tp30) cc_final: 0.8180 (tp30) outliers start: 65 outliers final: 40 residues processed: 337 average time/residue: 1.4051 time to fit residues: 555.9019 Evaluate side-chains 318 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 272 time to evaluate : 2.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 775 TRP Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 1006 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 1268 LEU Chi-restraints excluded: chain A residue 1300 MET Chi-restraints excluded: chain A residue 1317 ILE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 341 ASN 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 D residue 367 LEU Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 349 LEU 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 169 THR Chi-restraints excluded: chain G residue 180 ASN Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 364 VAL 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 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 109 SER Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain f residue 49 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 1.9990 chunk 281 optimal weight: 0.8980 chunk 171 optimal weight: 0.0370 chunk 133 optimal weight: 7.9990 chunk 195 optimal weight: 2.9990 chunk 294 optimal weight: 0.1980 chunk 271 optimal weight: 1.9990 chunk 234 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 overall best weight: 1.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1143 ASN ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 304 ASN ** G 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 30408 Z= 0.231 Angle : 0.642 17.170 42550 Z= 0.344 Chirality : 0.037 0.199 4703 Planarity : 0.004 0.052 4180 Dihedral : 26.557 179.178 6801 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.78 % Favored : 93.88 % Rotamer: Outliers : 2.21 % Allowed : 28.40 % Favored : 69.38 % 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: 1.12 (0.17), residues: 2631 helix: 1.91 (0.14), residues: 1470 sheet: -1.11 (0.44), residues: 140 loop : -0.71 (0.20), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP G 492 HIS 0.004 0.001 HIS B 49 PHE 0.048 0.002 PHE E 362 TYR 0.022 0.001 TYR b 88 ARG 0.005 0.000 ARG c 71 ********************** 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 331 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 278 time to evaluate : 2.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 775 TRP cc_start: 0.6846 (OUTLIER) cc_final: 0.6328 (t-100) REVERT: A 796 ILE cc_start: 0.7516 (pp) cc_final: 0.7174 (pt) REVERT: A 805 GLU cc_start: 0.8177 (mp0) cc_final: 0.7662 (mp0) REVERT: A 978 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7507 (m-30) REVERT: A 1156 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7965 (mp0) REVERT: B 214 PHE cc_start: 0.7348 (OUTLIER) cc_final: 0.6627 (m-80) REVERT: D 22 MET cc_start: 0.2434 (mmp) cc_final: 0.2095 (mmp) REVERT: D 77 PHE cc_start: 0.6713 (m-80) cc_final: 0.6376 (m-10) REVERT: D 78 PHE cc_start: 0.8658 (t80) cc_final: 0.8270 (t80) REVERT: D 98 ARG cc_start: 0.3700 (mtt90) cc_final: 0.3195 (ptp-170) REVERT: D 107 MET cc_start: 0.7765 (ppp) cc_final: 0.6951 (ppp) REVERT: D 237 GLU cc_start: 0.6149 (OUTLIER) cc_final: 0.4049 (mm-30) REVERT: D 310 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7082 (tp) REVERT: D 320 LEU cc_start: 0.7840 (tp) cc_final: 0.7072 (tp) REVERT: D 376 ASP cc_start: 0.7340 (p0) cc_final: 0.7094 (p0) REVERT: E 22 MET cc_start: 0.1543 (mmt) cc_final: 0.0706 (mmt) REVERT: E 263 HIS cc_start: 0.7409 (OUTLIER) cc_final: 0.7092 (t-90) REVERT: E 347 MET cc_start: 0.5456 (pmm) cc_final: 0.4967 (pmt) REVERT: E 373 TYR cc_start: 0.7331 (m-10) cc_final: 0.6662 (m-80) REVERT: G 316 MET cc_start: 0.4060 (tpt) cc_final: 0.3327 (ptt) REVERT: G 542 ILE cc_start: 0.8472 (mm) cc_final: 0.8257 (tt) REVERT: G 552 PHE cc_start: 0.8451 (t80) cc_final: 0.7754 (t80) REVERT: d 54 LYS cc_start: 0.8999 (mmmt) cc_final: 0.8736 (mmtt) REVERT: f 53 GLU cc_start: 0.8524 (tp30) cc_final: 0.8196 (tp30) outliers start: 53 outliers final: 41 residues processed: 319 average time/residue: 1.4312 time to fit residues: 533.3908 Evaluate side-chains 316 residues out of total 2394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 268 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 775 TRP Chi-restraints excluded: chain A residue 793 SER Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 978 ASP Chi-restraints excluded: chain A residue 1006 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 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 123 SER Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 341 ASN 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 D residue 367 LEU Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain F residue 336 PHE 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 364 VAL Chi-restraints excluded: chain G residue 395 ILE 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 76 THR 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 49 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 186 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 235 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 241 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1143 ASN ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** a 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.123291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.081235 restraints weight = 59037.927| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.43 r_work: 0.3098 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 30408 Z= 0.295 Angle : 0.669 16.756 42550 Z= 0.360 Chirality : 0.039 0.278 4703 Planarity : 0.004 0.049 4180 Dihedral : 26.858 179.739 6801 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.23 % Favored : 93.42 % Rotamer: Outliers : 2.46 % Allowed : 28.28 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.04 % 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: 0.97 (0.17), residues: 2631 helix: 1.76 (0.14), residues: 1474 sheet: -1.11 (0.44), residues: 140 loop : -0.76 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP G 492 HIS 0.005 0.001 HIS e 39 PHE 0.029 0.002 PHE A 708 TYR 0.027 0.002 TYR b 88 ARG 0.005 0.000 ARG A1149 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10699.85 seconds wall clock time: 188 minutes 34.99 seconds (11314.99 seconds total)