Starting phenix.real_space_refine on Mon Aug 25 04:17:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yi5_33852/08_2025/7yi5_33852.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yi5_33852/08_2025/7yi5_33852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yi5_33852/08_2025/7yi5_33852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yi5_33852/08_2025/7yi5_33852.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yi5_33852/08_2025/7yi5_33852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yi5_33852/08_2025/7yi5_33852.map" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 302 5.49 5 S 87 5.16 5 C 15166 2.51 5 N 4501 2.21 5 O 5328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25389 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 4258 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 7, 'TRANS': 498} Chain breaks: 5 Chain: "B" Number of atoms: 2923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2923 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 15, 'TRANS': 352} Chain: "C" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2326 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 273} Chain breaks: 2 Chain: "D" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2626 Classifications: {'peptide': 321} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 302} Chain breaks: 5 Chain: "F" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 178 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "H" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "I" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "J" 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: "L" 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: "M" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "N" 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: "O" Number of atoms: 3076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3076 Classifications: {'DNA': 151} Link IDs: {'rna3p': 150} Chain: "P" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3115 Classifications: {'DNA': 151} Link IDs: {'rna3p': 150} Chain: "E" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 853 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain breaks: 1 Chain: "G" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 830 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 822 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 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: "D" 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 9999 SG CYS D 263 106.230 97.946 71.560 1.00573.15 S ATOM 10016 SG CYS D 266 107.679 94.534 71.575 1.00560.27 S ATOM 10169 SG CYS D 286 109.562 97.207 73.325 1.00571.47 S ATOM 10080 SG CYS D 275 96.808 107.153 70.789 1.00661.37 S ATOM 10101 SG CYS D 278 98.603 107.038 67.692 1.00670.73 S ATOM 10327 SG CYS D 306 98.591 109.037 67.325 1.00705.46 S ATOM 11248 SG CYS D 440 128.858 65.635 63.691 1.00512.16 S ATOM 11274 SG CYS D 443 131.568 65.262 60.865 1.00521.23 S ATOM 11463 SG CYS D 466 132.509 64.378 64.355 1.00538.59 S ATOM 11060 SG CYS D 417 131.450 55.114 67.441 1.00536.70 S ATOM 11087 SG CYS D 420 131.195 51.337 67.907 1.00531.82 S ATOM 11343 SG CYS D 451 132.166 53.556 70.821 1.00493.39 S Time building chain proxies: 5.62, per 1000 atoms: 0.22 Number of scatterers: 25389 At special positions: 0 Unit cell: (186.19, 154.798, 137.477, 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 87 16.00 P 302 15.00 O 5328 8.00 N 4501 7.00 C 15166 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 829.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 188 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" ND1 HIS D 283 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 266 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 286 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 263 " pdb=" ZN D 702 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 306 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 278 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 275 " pdb=" ZN D 703 " pdb="ZN ZN D 703 " - pdb=" NE2 HIS D 469 " pdb="ZN ZN D 703 " - pdb=" SG CYS D 466 " pdb="ZN ZN D 703 " - pdb=" SG CYS D 443 " pdb="ZN ZN D 703 " - pdb=" SG CYS D 440 " pdb=" ZN D 704 " pdb="ZN ZN D 704 " - pdb=" ND1 HIS D 448 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 417 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 451 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 420 " Number of angles added : 9 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4474 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 20 sheets defined 59.0% alpha, 7.0% beta 148 base pairs and 248 stacking pairs defined. Time for finding SS restraints: 3.63 Creating SS restraints... Processing helix chain 'A' and resid 667 through 677 Processing helix chain 'A' and resid 678 through 694 Processing helix chain 'A' and resid 698 through 711 removed outlier: 3.543A pdb=" N LEU A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 725 Processing helix chain 'A' and resid 759 through 764 removed outlier: 3.869A pdb=" N PHE A 764 " --> pdb=" O SER A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 778 Processing helix chain 'A' and resid 785 through 790 removed outlier: 3.622A pdb=" N ALA A 789 " --> pdb=" O HIS A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 839 removed outlier: 3.754A pdb=" N LYS A 837 " --> pdb=" O THR A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 875 through 885 removed outlier: 3.681A pdb=" N ASP A 881 " --> pdb=" O PHE A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 928 removed outlier: 4.331A pdb=" N LYS A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N PHE A 925 " --> pdb=" O GLN A 921 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS A 926 " --> pdb=" O LYS A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 935 removed outlier: 3.797A pdb=" N LEU A 933 " --> pdb=" O ASP A 929 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 934 " --> pdb=" O HIS A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 943 removed outlier: 3.911A pdb=" N LYS A 941 " --> pdb=" O GLN A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 960 Processing helix chain 'A' and resid 982 through 999 removed outlier: 3.810A pdb=" N TYR A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1022 removed outlier: 3.961A pdb=" N GLU A1008 " --> pdb=" O ASN A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1031 Processing helix chain 'A' and resid 1141 through 1164 removed outlier: 3.910A pdb=" N MET A1164 " --> pdb=" O GLU A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1174 Processing helix chain 'A' and resid 1190 through 1195 removed outlier: 3.896A pdb=" N MET A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY A1195 " --> pdb=" O LEU A1191 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1190 through 1195' Processing helix chain 'A' and resid 1202 through 1217 Processing helix chain 'A' and resid 1220 through 1233 Processing helix chain 'A' and resid 1236 through 1240 Processing helix chain 'A' and resid 1241 through 1258 Processing helix chain 'A' and resid 1259 through 1276 removed outlier: 3.563A pdb=" N SER A1276 " --> pdb=" O ASP A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1294 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.509A pdb=" N ASN B 31 " --> pdb=" O ASP B 28 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR B 32 " --> pdb=" O VAL B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 32' Processing helix chain 'B' and resid 42 through 55 removed outlier: 3.619A pdb=" N ARG B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 59 removed outlier: 3.662A pdb=" N LYS B 59 " --> pdb=" O GLY B 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 59' Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 79 through 89 Processing helix chain 'B' and resid 98 through 104 Processing helix chain 'B' and resid 115 through 137 Processing helix chain 'B' and resid 164 through 175 removed outlier: 3.859A 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 removed outlier: 3.774A pdb=" N SER B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 272 through 276 removed outlier: 4.246A pdb=" N SER B 275 " --> pdb=" O GLY B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 300 removed outlier: 3.966A pdb=" N CYS B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 330 removed outlier: 3.872A pdb=" N ARG B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN B 330 " --> pdb=" O THR B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 348 removed outlier: 4.094A pdb=" N GLY B 348 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 381 Processing helix chain 'C' and resid 68 through 73 removed outlier: 3.940A pdb=" N ASN C 73 " --> pdb=" O GLU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 89 removed outlier: 3.543A pdb=" N ASP C 89 " --> pdb=" O SER C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 124 Processing helix chain 'C' and resid 225 through 241 Processing helix chain 'C' and resid 253 through 267 Processing helix chain 'C' and resid 271 through 297 removed outlier: 4.984A pdb=" N GLY C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ASN C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 315 removed outlier: 4.205A pdb=" N LEU C 304 " --> pdb=" O ARG C 300 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLN C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 325 Processing helix chain 'C' and resid 329 through 335 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 369 Processing helix chain 'C' and resid 391 through 401 Processing helix chain 'D' and resid 120 through 127 Processing helix chain 'D' and resid 168 through 170 No H-bonds generated for 'chain 'D' and resid 168 through 170' Processing helix chain 'D' and resid 171 through 176 removed outlier: 3.667A pdb=" N MET D 175 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR D 176 " --> pdb=" O THR D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 171 through 176' Processing helix chain 'D' and resid 303 through 312 Processing helix chain 'D' and resid 316 through 328 removed outlier: 4.143A pdb=" N LYS D 320 " --> pdb=" O MET D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 344 through 346 No H-bonds generated for 'chain 'D' and resid 344 through 346' Processing helix chain 'D' and resid 402 through 407 removed outlier: 3.639A pdb=" N THR D 405 " --> pdb=" O ASN D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 434 removed outlier: 3.642A pdb=" N ASN D 433 " --> pdb=" O HIS D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 564 removed outlier: 4.189A pdb=" N GLN D 562 " --> pdb=" O SER D 558 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 563 Processing helix chain 'H' and resid 24 through 28 Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 49 through 76 removed outlier: 3.797A pdb=" N GLU H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 93 Processing helix chain 'I' and resid 16 through 22 Processing helix chain 'I' and resid 26 through 37 Processing helix chain 'I' and resid 46 through 73 Processing helix chain 'I' and resid 79 through 90 Processing helix chain 'I' and resid 90 through 97 Processing helix chain 'I' and resid 112 through 116 Processing helix chain 'J' and resid 34 through 46 Processing helix chain 'J' and resid 52 through 81 Processing helix chain 'J' and resid 87 through 99 Processing helix chain 'J' and resid 100 through 121 removed outlier: 3.613A pdb=" N ALA J 104 " --> pdb=" O PRO J 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 50 through 76 removed outlier: 3.798A pdb=" N ASP L 68 " --> pdb=" O ASN L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 93 Processing helix chain 'M' and resid 16 through 22 Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 46 through 73 Processing helix chain 'M' and resid 79 through 90 Processing helix chain 'M' and resid 90 through 97 Processing helix chain 'M' and resid 112 through 116 Processing helix chain 'N' and resid 34 through 46 Processing helix chain 'N' and resid 52 through 81 Processing helix chain 'N' and resid 87 through 99 removed outlier: 3.525A pdb=" N ILE N 91 " --> pdb=" O THR N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 121 removed outlier: 3.663A pdb=" N ALA N 104 " --> pdb=" O PRO N 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 73 removed outlier: 4.231A pdb=" N ASN E 73 " --> pdb=" O GLU E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.939A pdb=" N ASP E 89 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 124 Processing helix chain 'G' and resid 44 through 55 Processing helix chain 'G' and resid 63 through 75 Processing helix chain 'G' and resid 85 through 114 Processing helix chain 'G' and resid 120 through 131 removed outlier: 3.725A pdb=" N ILE G 124 " --> pdb=" O MET G 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 55 Processing helix chain 'K' and resid 63 through 77 removed outlier: 3.502A pdb=" N PHE K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 132 removed outlier: 3.501A pdb=" N ILE K 124 " --> pdb=" O MET K 120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 975 through 978 removed outlier: 4.039A pdb=" N HIS A1311 " --> pdb=" O ASP A1306 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP A1306 " --> pdb=" O HIS A1311 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 61 through 64 removed outlier: 3.781A pdb=" N VAL B 143 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE B 24 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N VAL B 267 " --> pdb=" O MET B 306 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N VAL B 308 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU B 269 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU B 181 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N GLN B 270 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ILE B 183 " --> pdb=" O GLN B 270 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL B 180 " --> pdb=" O MET B 204 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N CYS B 206 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TYR B 182 " --> pdb=" O CYS B 206 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N PHE B 208 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASP B 184 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N LYS B 210 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL B 234 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N THR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL B 236 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER B 207 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LEU B 238 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N HIS B 209 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 13 through 18 Processing sheet with id=AA4, first strand: chain 'C' and resid 13 through 18 removed outlier: 6.479A pdb=" N PHE C 78 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 245 through 246 Processing sheet with id=AA6, first strand: chain 'D' and resid 364 through 366 Processing sheet with id=AA7, first strand: chain 'D' and resid 473 through 476 Processing sheet with id=AA8, first strand: chain 'D' and resid 520 through 521 Processing sheet with id=AA9, first strand: chain 'H' and resid 45 through 46 removed outlier: 7.578A pdb=" N ARG H 45 " --> pdb=" O ILE G 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 80 through 81 Processing sheet with id=AB2, first strand: chain 'H' and resid 96 through 97 removed outlier: 6.574A pdb=" N THR H 96 " --> pdb=" O THR M 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'I' and resid 42 through 43 removed outlier: 7.665A pdb=" N ARG I 42 " --> pdb=" O ILE J 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'I' and resid 77 through 78 Processing sheet with id=AB5, first strand: chain 'I' and resid 100 through 102 Processing sheet with id=AB6, first strand: chain 'L' and resid 45 through 46 removed outlier: 8.009A pdb=" N ARG L 45 " --> pdb=" O ILE K 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'L' and resid 80 through 81 Processing sheet with id=AB8, first strand: chain 'M' and resid 42 through 43 removed outlier: 7.509A pdb=" N ARG M 42 " --> pdb=" O ILE N 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'M' and resid 77 through 78 Processing sheet with id=AC1, first strand: chain 'E' and resid 37 through 39 removed outlier: 6.220A pdb=" N PHE E 78 " --> pdb=" O LEU E 28 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 37 through 39 removed outlier: 4.130A pdb=" N LEU E 15 " --> pdb=" O ARG E 98 " (cutoff:3.500A) 1021 hydrogen bonds defined for protein. 2943 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 377 hydrogen bonds 738 hydrogen bond angles 0 basepair planarities 148 basepair parallelities 248 stacking parallelities Total time for adding SS restraints: 7.56 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7224 1.34 - 1.46: 7558 1.46 - 1.58: 10993 1.58 - 1.71: 602 1.71 - 1.83: 137 Bond restraints: 26514 Sorted by residual: bond pdb=" C LYS D 107 " pdb=" N VAL D 108 " ideal model delta sigma weight residual 1.332 1.351 -0.019 5.60e-03 3.19e+04 1.15e+01 bond pdb=" CA MET A 765 " pdb=" CB MET A 765 " ideal model delta sigma weight residual 1.526 1.552 -0.026 1.20e-02 6.94e+03 4.57e+00 bond pdb=" C SER K 86 " pdb=" N SER K 87 " ideal model delta sigma weight residual 1.335 1.315 0.020 1.32e-02 5.74e+03 2.37e+00 bond pdb=" C CYS D 451 " pdb=" N VAL D 452 " ideal model delta sigma weight residual 1.324 1.336 -0.012 8.60e-03 1.35e+04 1.96e+00 bond pdb=" SD MET B 47 " pdb=" CE MET B 47 " ideal model delta sigma weight residual 1.791 1.756 0.035 2.50e-02 1.60e+03 1.93e+00 ... (remaining 26509 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 36854 2.98 - 5.96: 184 5.96 - 8.94: 18 8.94 - 11.92: 4 11.92 - 14.90: 2 Bond angle restraints: 37062 Sorted by residual: angle pdb=" C LEU N 98 " pdb=" N LEU N 99 " pdb=" CA LEU N 99 " ideal model delta sigma weight residual 122.15 107.25 14.90 3.47e+00 8.31e-02 1.84e+01 angle pdb=" N MET B 47 " pdb=" CA MET B 47 " pdb=" CB MET B 47 " ideal model delta sigma weight residual 110.39 117.13 -6.74 1.66e+00 3.63e-01 1.65e+01 angle pdb=" C ARG B 46 " pdb=" N MET B 47 " pdb=" CA MET B 47 " ideal model delta sigma weight residual 120.72 114.20 6.52 1.67e+00 3.59e-01 1.52e+01 angle pdb=" C VAL K 89 " pdb=" N MET K 90 " pdb=" CA MET K 90 " ideal model delta sigma weight residual 121.14 114.50 6.64 1.75e+00 3.27e-01 1.44e+01 angle pdb=" CB MET C 37 " pdb=" CG MET C 37 " pdb=" SD MET C 37 " ideal model delta sigma weight residual 112.70 124.05 -11.35 3.00e+00 1.11e-01 1.43e+01 ... (remaining 37057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.96: 13099 30.96 - 61.92: 2002 61.92 - 92.88: 80 92.88 - 123.84: 0 123.84 - 154.80: 1 Dihedral angle restraints: 15182 sinusoidal: 8258 harmonic: 6924 Sorted by residual: dihedral pdb=" CA GLN D 541 " pdb=" C GLN D 541 " pdb=" N ILE D 542 " pdb=" CA ILE D 542 " ideal model delta harmonic sigma weight residual 180.00 -155.66 -24.34 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA PHE K 84 " pdb=" C PHE K 84 " pdb=" N GLN K 85 " pdb=" CA GLN K 85 " ideal model delta harmonic sigma weight residual 180.00 159.04 20.96 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA LYS B 153 " pdb=" C LYS B 153 " pdb=" N LYS B 154 " pdb=" CA LYS B 154 " ideal model delta harmonic sigma weight residual 180.00 159.46 20.54 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 15179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3443 0.053 - 0.107: 589 0.107 - 0.160: 46 0.160 - 0.213: 2 0.213 - 0.266: 2 Chirality restraints: 4082 Sorted by residual: chirality pdb=" CA MET K 90 " pdb=" N MET K 90 " pdb=" C MET K 90 " pdb=" CB MET K 90 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA MET B 47 " pdb=" N MET B 47 " pdb=" C MET B 47 " pdb=" CB MET B 47 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB VAL C 257 " pdb=" CA VAL C 257 " pdb=" CG1 VAL C 257 " pdb=" CG2 VAL C 257 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.12e-01 ... (remaining 4079 not shown) Planarity restraints: 3655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 296 " 0.044 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO D 297 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO D 297 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 297 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 118 " 0.043 5.00e-02 4.00e+02 6.62e-02 7.02e+00 pdb=" N PRO D 119 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO D 119 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 119 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 57 " 0.040 5.00e-02 4.00e+02 5.98e-02 5.73e+00 pdb=" N PRO E 58 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO E 58 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 58 " 0.033 5.00e-02 4.00e+02 ... (remaining 3652 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 326 2.58 - 3.16: 21771 3.16 - 3.74: 46740 3.74 - 4.32: 61218 4.32 - 4.90: 92117 Nonbonded interactions: 222172 Sorted by model distance: nonbonded pdb=" OD2 ASP B 186 " pdb="ZN ZN B 501 " model vdw 2.006 2.230 nonbonded pdb=" OD2 ASP B 274 " pdb="ZN ZN B 501 " model vdw 2.016 2.230 nonbonded pdb=" O2 DC O 70 " pdb=" N2 DG P -70 " model vdw 2.054 2.496 nonbonded pdb=" OD1 ASP B 186 " pdb="ZN ZN B 501 " model vdw 2.058 2.230 nonbonded pdb=" O2 DC O -21 " pdb=" N2 DG P 21 " model vdw 2.083 2.496 ... (remaining 222167 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 36 through 109 or (resid 110 through 111 and (name N or na \ me CA or name C or name O or name CB )) or resid 112 through 134)) selection = chain 'K' } ncs_group { reference = chain 'H' selection = (chain 'L' and resid 23 through 101) } ncs_group { reference = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'J' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 31.420 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 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 : 0.006 0.344 26530 Z= 0.261 Angle : 0.667 14.903 37071 Z= 0.377 Chirality : 0.039 0.266 4082 Planarity : 0.004 0.067 3655 Dihedral : 23.555 154.797 10708 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.29 % Allowed : 20.67 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.17), residues: 2307 helix: 1.52 (0.14), residues: 1265 sheet: -0.70 (0.50), residues: 128 loop : -1.57 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 35 TYR 0.015 0.001 TYR B 347 PHE 0.015 0.002 PHE B 301 TRP 0.016 0.002 TRP D 464 HIS 0.010 0.002 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00529 (26514) covalent geometry : angle 0.66450 (37062) hydrogen bonds : bond 0.13331 ( 1388) hydrogen bonds : angle 5.59391 ( 3681) metal coordination : bond 0.08665 ( 16) metal coordination : angle 3.56664 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 315 MET cc_start: 0.2566 (ptp) cc_final: 0.2309 (ptm) REVERT: E 22 MET cc_start: 0.4286 (mpp) cc_final: 0.4010 (mpp) outliers start: 6 outliers final: 1 residues processed: 74 average time/residue: 0.1785 time to fit residues: 21.4978 Evaluate side-chains 68 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 20.0000 chunk 258 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 802 GLN B 144 ASN C 275 GLN C 369 HIS ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 GLN K 39 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.039149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.024528 restraints weight = 365252.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.024926 restraints weight = 189769.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.025171 restraints weight = 122688.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.025255 restraints weight = 99124.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.025262 restraints weight = 91841.646| |-----------------------------------------------------------------------------| r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26530 Z= 0.185 Angle : 0.569 11.007 37071 Z= 0.322 Chirality : 0.037 0.183 4082 Planarity : 0.004 0.051 3655 Dihedral : 26.446 155.558 5896 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.68 % Allowed : 18.08 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.17), residues: 2307 helix: 1.82 (0.14), residues: 1289 sheet: -0.58 (0.47), residues: 140 loop : -1.47 (0.19), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 96 TYR 0.022 0.001 TYR C 38 PHE 0.011 0.001 PHE L 61 TRP 0.015 0.001 TRP D 464 HIS 0.008 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00397 (26514) covalent geometry : angle 0.56738 (37062) hydrogen bonds : bond 0.05215 ( 1388) hydrogen bonds : angle 4.12541 ( 3681) metal coordination : bond 0.00520 ( 16) metal coordination : angle 2.42543 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 69 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1314 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8241 (mm) REVERT: B 128 MET cc_start: 0.7156 (tpp) cc_final: 0.6763 (tpp) REVERT: B 214 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.8231 (t80) REVERT: H 92 ARG cc_start: 0.9406 (OUTLIER) cc_final: 0.9206 (ptm160) REVERT: K 90 MET cc_start: 0.9447 (mpp) cc_final: 0.9237 (mpp) outliers start: 35 outliers final: 8 residues processed: 98 average time/residue: 0.1844 time to fit residues: 29.2319 Evaluate side-chains 79 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain D residue 459 ASN Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain K residue 51 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 217 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 118 optimal weight: 50.0000 chunk 168 optimal weight: 0.9980 chunk 22 optimal weight: 40.0000 chunk 15 optimal weight: 6.9990 chunk 66 optimal weight: 30.0000 chunk 201 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 236 optimal weight: 50.0000 chunk 93 optimal weight: 10.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 ASN A1299 ASN D 376 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 GLN E 82 GLN K 113 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.038319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.023905 restraints weight = 375872.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.024169 restraints weight = 195438.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.024423 restraints weight = 127187.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.024629 restraints weight = 104690.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.024643 restraints weight = 94975.524| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 26530 Z= 0.268 Angle : 0.609 10.974 37071 Z= 0.342 Chirality : 0.039 0.220 4082 Planarity : 0.004 0.043 3655 Dihedral : 26.583 155.184 5896 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.97 % Allowed : 18.18 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.17), residues: 2307 helix: 1.67 (0.14), residues: 1298 sheet: -0.52 (0.46), residues: 134 loop : -1.43 (0.19), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 42 TYR 0.019 0.001 TYR C 38 PHE 0.019 0.001 PHE A 685 TRP 0.012 0.001 TRP D 464 HIS 0.007 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00577 (26514) covalent geometry : angle 0.60697 (37062) hydrogen bonds : bond 0.06638 ( 1388) hydrogen bonds : angle 4.12183 ( 3681) metal coordination : bond 0.00771 ( 16) metal coordination : angle 3.08743 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 65 time to evaluate : 0.851 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: B 128 MET cc_start: 0.7411 (tpp) cc_final: 0.6911 (tpp) REVERT: B 214 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.8279 (t80) REVERT: E 22 MET cc_start: 0.3527 (mpp) cc_final: 0.3218 (mmt) outliers start: 41 outliers final: 19 residues processed: 97 average time/residue: 0.1897 time to fit residues: 29.6277 Evaluate side-chains 83 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 401 MET Chi-restraints excluded: chain D residue 459 ASN Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 105 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 201 optimal weight: 10.0000 chunk 249 optimal weight: 0.9990 chunk 39 optimal weight: 30.0000 chunk 25 optimal weight: 50.0000 chunk 236 optimal weight: 50.0000 chunk 162 optimal weight: 9.9990 chunk 36 optimal weight: 0.5980 chunk 228 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 HIS ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.038852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.024383 restraints weight = 365697.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.024795 restraints weight = 192041.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.025058 restraints weight = 123859.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.025146 restraints weight = 100400.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.025289 restraints weight = 91480.692| |-----------------------------------------------------------------------------| r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26530 Z= 0.176 Angle : 0.550 11.261 37071 Z= 0.311 Chirality : 0.036 0.159 4082 Planarity : 0.004 0.039 3655 Dihedral : 26.502 156.119 5896 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.87 % Allowed : 18.13 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.17), residues: 2307 helix: 1.90 (0.14), residues: 1298 sheet: -0.59 (0.47), residues: 127 loop : -1.32 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 35 TYR 0.015 0.001 TYR C 38 PHE 0.010 0.001 PHE L 61 TRP 0.010 0.001 TRP D 464 HIS 0.006 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00378 (26514) covalent geometry : angle 0.54886 (37062) hydrogen bonds : bond 0.04647 ( 1388) hydrogen bonds : angle 3.82068 ( 3681) metal coordination : bond 0.00485 ( 16) metal coordination : angle 2.34793 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 67 time to evaluate : 0.871 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: B 128 MET cc_start: 0.7283 (tpp) cc_final: 0.6784 (tpp) REVERT: B 214 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.8116 (t80) REVERT: N 68 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8746 (pt0) REVERT: E 22 MET cc_start: 0.3753 (mpp) cc_final: 0.3340 (mmt) REVERT: K 120 MET cc_start: 0.9056 (mmm) cc_final: 0.8802 (mmm) outliers start: 39 outliers final: 24 residues processed: 100 average time/residue: 0.1803 time to fit residues: 29.3204 Evaluate side-chains 90 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 1298 GLU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 443 CYS Chi-restraints excluded: chain D residue 459 ASN Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain N residue 113 LYS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain K residue 51 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 143 optimal weight: 20.0000 chunk 2 optimal weight: 50.0000 chunk 16 optimal weight: 20.0000 chunk 204 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 50 optimal weight: 30.0000 chunk 85 optimal weight: 8.9990 chunk 205 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 35 optimal weight: 0.0970 chunk 142 optimal weight: 8.9990 overall best weight: 7.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 998 HIS D 267 ASN D 325 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.038133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.023781 restraints weight = 373774.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.024235 restraints weight = 193363.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.024432 restraints weight = 125138.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.024498 restraints weight = 103180.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.024634 restraints weight = 96056.340| |-----------------------------------------------------------------------------| r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 26530 Z= 0.264 Angle : 0.610 11.235 37071 Z= 0.342 Chirality : 0.039 0.163 4082 Planarity : 0.004 0.036 3655 Dihedral : 26.758 156.072 5896 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.30 % Allowed : 18.61 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.17), residues: 2307 helix: 1.77 (0.14), residues: 1300 sheet: -0.63 (0.47), residues: 122 loop : -1.29 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 42 TYR 0.014 0.001 TYR B 368 PHE 0.014 0.002 PHE L 61 TRP 0.012 0.001 TRP D 464 HIS 0.007 0.001 HIS A 998 Details of bonding type rmsd covalent geometry : bond 0.00570 (26514) covalent geometry : angle 0.60770 (37062) hydrogen bonds : bond 0.06414 ( 1388) hydrogen bonds : angle 4.01514 ( 3681) metal coordination : bond 0.00945 ( 16) metal coordination : angle 3.21174 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 66 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 MET cc_start: 0.7370 (tpp) cc_final: 0.6792 (tpp) REVERT: B 214 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.8130 (t80) REVERT: B 246 THR cc_start: 0.7051 (OUTLIER) cc_final: 0.6792 (p) REVERT: E 22 MET cc_start: 0.4599 (mpp) cc_final: 0.4210 (mmt) outliers start: 48 outliers final: 29 residues processed: 107 average time/residue: 0.1914 time to fit residues: 32.3471 Evaluate side-chains 95 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 64 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1178 VAL Chi-restraints excluded: chain A residue 1298 GLU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 459 ASN Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain M residue 74 LYS Chi-restraints excluded: chain N residue 113 LYS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 125 optimal weight: 0.0370 chunk 124 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 221 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 200 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 257 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 overall best weight: 2.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 937 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.038986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.024534 restraints weight = 365688.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.024855 restraints weight = 194606.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.025100 restraints weight = 122660.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.025290 restraints weight = 100319.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.025314 restraints weight = 92342.761| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26530 Z= 0.141 Angle : 0.551 12.382 37071 Z= 0.307 Chirality : 0.036 0.200 4082 Planarity : 0.004 0.039 3655 Dihedral : 26.535 157.634 5896 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.53 % Allowed : 19.23 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.18), residues: 2307 helix: 2.01 (0.14), residues: 1302 sheet: -0.72 (0.46), residues: 132 loop : -1.17 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 92 TYR 0.016 0.001 TYR C 38 PHE 0.009 0.001 PHE B 251 TRP 0.007 0.001 TRP A 775 HIS 0.006 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00300 (26514) covalent geometry : angle 0.54996 (37062) hydrogen bonds : bond 0.04344 ( 1388) hydrogen bonds : angle 3.70493 ( 3681) metal coordination : bond 0.00357 ( 16) metal coordination : angle 2.06930 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 67 time to evaluate : 0.938 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 1294 MET cc_start: 0.3348 (ttt) cc_final: 0.3104 (mmp) REVERT: B 128 MET cc_start: 0.7289 (tpp) cc_final: 0.6757 (tpp) REVERT: B 214 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.8104 (t80) REVERT: B 246 THR cc_start: 0.6947 (OUTLIER) cc_final: 0.6688 (p) REVERT: N 68 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8703 (pt0) REVERT: E 22 MET cc_start: 0.4575 (mpp) cc_final: 0.4125 (mmt) REVERT: G 120 MET cc_start: 0.8883 (ptp) cc_final: 0.8438 (mpp) REVERT: K 120 MET cc_start: 0.9051 (mmm) cc_final: 0.8834 (mmm) outliers start: 32 outliers final: 22 residues processed: 94 average time/residue: 0.1883 time to fit residues: 28.5549 Evaluate side-chains 89 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 1298 GLU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 443 CYS Chi-restraints excluded: chain D residue 459 ASN Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 110 ARG Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 64 optimal weight: 50.0000 chunk 183 optimal weight: 8.9990 chunk 127 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 chunk 140 optimal weight: 20.0000 chunk 43 optimal weight: 40.0000 chunk 89 optimal weight: 4.9990 chunk 249 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 222 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 314 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.038216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.023899 restraints weight = 372524.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.024332 restraints weight = 190972.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.024552 restraints weight = 124726.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.024644 restraints weight = 102136.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.024730 restraints weight = 94952.941| |-----------------------------------------------------------------------------| r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 26530 Z= 0.235 Angle : 0.600 11.166 37071 Z= 0.334 Chirality : 0.038 0.206 4082 Planarity : 0.004 0.039 3655 Dihedral : 26.660 158.386 5896 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.01 % Allowed : 19.04 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.18), residues: 2307 helix: 1.96 (0.14), residues: 1302 sheet: -0.73 (0.46), residues: 131 loop : -1.14 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 42 TYR 0.020 0.001 TYR B 262 PHE 0.013 0.001 PHE L 61 TRP 0.010 0.001 TRP D 464 HIS 0.006 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00508 (26514) covalent geometry : angle 0.59879 (37062) hydrogen bonds : bond 0.06009 ( 1388) hydrogen bonds : angle 3.88919 ( 3681) metal coordination : bond 0.00833 ( 16) metal coordination : angle 2.83232 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 63 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 MET cc_start: 0.7290 (tpp) cc_final: 0.6701 (tpp) REVERT: B 204 MET cc_start: 0.0139 (mmt) cc_final: -0.1308 (mmt) REVERT: B 214 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.8129 (t80) REVERT: B 246 THR cc_start: 0.7064 (OUTLIER) cc_final: 0.6806 (p) REVERT: C 22 MET cc_start: 0.6708 (mpp) cc_final: 0.6484 (mpp) REVERT: E 22 MET cc_start: 0.4561 (mpp) cc_final: 0.4108 (mmt) REVERT: G 120 MET cc_start: 0.8784 (ptp) cc_final: 0.8445 (mpp) REVERT: K 120 MET cc_start: 0.9099 (mmm) cc_final: 0.8829 (mmm) outliers start: 42 outliers final: 31 residues processed: 99 average time/residue: 0.1960 time to fit residues: 30.6177 Evaluate side-chains 95 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 62 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 1298 GLU Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain D residue 459 ASN Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain N residue 31 LYS Chi-restraints excluded: chain N residue 113 LYS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 110 ARG Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 174 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 chunk 84 optimal weight: 0.0030 chunk 82 optimal weight: 30.0000 chunk 165 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 194 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 90 optimal weight: 0.0570 chunk 102 optimal weight: 50.0000 chunk 15 optimal weight: 2.9990 overall best weight: 1.7912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 802 GLN C 104 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.039140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.024774 restraints weight = 365661.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.025123 restraints weight = 186693.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.025212 restraints weight = 120943.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.025414 restraints weight = 103162.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.025593 restraints weight = 94101.340| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26530 Z= 0.131 Angle : 0.546 11.693 37071 Z= 0.304 Chirality : 0.036 0.211 4082 Planarity : 0.003 0.038 3655 Dihedral : 26.377 158.429 5896 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.25 % Allowed : 19.52 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.18), residues: 2307 helix: 2.18 (0.14), residues: 1290 sheet: -0.62 (0.46), residues: 132 loop : -0.98 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG J 76 TYR 0.022 0.001 TYR C 38 PHE 0.010 0.001 PHE B 251 TRP 0.007 0.001 TRP A 775 HIS 0.006 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00278 (26514) covalent geometry : angle 0.54494 (37062) hydrogen bonds : bond 0.04148 ( 1388) hydrogen bonds : angle 3.60873 ( 3681) metal coordination : bond 0.00579 ( 16) metal coordination : angle 1.88225 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.885 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 1294 MET cc_start: 0.3437 (ttt) cc_final: 0.3229 (mmp) REVERT: A 1298 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7919 (tm-30) REVERT: B 128 MET cc_start: 0.7331 (tpp) cc_final: 0.6848 (tpp) REVERT: B 246 THR cc_start: 0.6973 (OUTLIER) cc_final: 0.6713 (p) REVERT: N 68 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8653 (pt0) REVERT: E 22 MET cc_start: 0.4582 (mpp) cc_final: 0.4128 (mmt) REVERT: G 120 MET cc_start: 0.8663 (ptp) cc_final: 0.8424 (mpp) REVERT: K 120 MET cc_start: 0.9127 (mmm) cc_final: 0.8844 (mmm) outliers start: 26 outliers final: 20 residues processed: 83 average time/residue: 0.1868 time to fit residues: 25.1824 Evaluate side-chains 85 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 1298 GLU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain N residue 31 LYS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 226 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 227 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 232 optimal weight: 30.0000 chunk 57 optimal weight: 2.9990 chunk 140 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 147 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.038331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.024028 restraints weight = 372737.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.024453 restraints weight = 195373.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.024665 restraints weight = 122503.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.024724 restraints weight = 100525.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.024724 restraints weight = 93308.926| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 26530 Z= 0.210 Angle : 0.589 13.080 37071 Z= 0.327 Chirality : 0.037 0.216 4082 Planarity : 0.004 0.042 3655 Dihedral : 26.564 158.143 5894 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.53 % Allowed : 19.47 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.18), residues: 2307 helix: 2.08 (0.14), residues: 1296 sheet: -0.53 (0.47), residues: 129 loop : -1.03 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 76 TYR 0.023 0.001 TYR C 38 PHE 0.013 0.001 PHE L 61 TRP 0.011 0.001 TRP D 464 HIS 0.006 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00452 (26514) covalent geometry : angle 0.58727 (37062) hydrogen bonds : bond 0.05376 ( 1388) hydrogen bonds : angle 3.82470 ( 3681) metal coordination : bond 0.00668 ( 16) metal coordination : angle 2.52076 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 63 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1294 MET cc_start: 0.3523 (ttt) cc_final: 0.3320 (mmp) REVERT: A 1298 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7919 (tm-30) REVERT: B 128 MET cc_start: 0.7305 (tpp) cc_final: 0.6745 (tpp) REVERT: B 214 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.8012 (t80) REVERT: B 246 THR cc_start: 0.7059 (OUTLIER) cc_final: 0.6803 (p) REVERT: B 305 MET cc_start: 0.9042 (mtt) cc_final: 0.8327 (tpp) REVERT: C 22 MET cc_start: 0.6556 (mpp) cc_final: 0.5870 (mpp) REVERT: C 69 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8688 (tp30) REVERT: E 22 MET cc_start: 0.4508 (mpp) cc_final: 0.4026 (mmt) REVERT: G 120 MET cc_start: 0.8693 (ptp) cc_final: 0.8451 (mpp) REVERT: K 120 MET cc_start: 0.9142 (mmm) cc_final: 0.8867 (mmm) outliers start: 32 outliers final: 24 residues processed: 89 average time/residue: 0.1933 time to fit residues: 27.6137 Evaluate side-chains 90 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 63 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 1298 GLU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain N residue 31 LYS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 110 ARG Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 39 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 239 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 170 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 203 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 305 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.038009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.023771 restraints weight = 376470.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.024099 restraints weight = 188578.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.024303 restraints weight = 125053.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.024466 restraints weight = 103767.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.024480 restraints weight = 96501.530| |-----------------------------------------------------------------------------| r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 26530 Z= 0.242 Angle : 0.626 15.144 37071 Z= 0.346 Chirality : 0.038 0.245 4082 Planarity : 0.004 0.036 3655 Dihedral : 26.889 159.109 5894 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.53 % Allowed : 19.42 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.18), residues: 2307 helix: 1.82 (0.14), residues: 1295 sheet: -0.60 (0.47), residues: 129 loop : -1.01 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 76 TYR 0.024 0.001 TYR C 38 PHE 0.014 0.002 PHE L 61 TRP 0.013 0.001 TRP E 88 HIS 0.006 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00519 (26514) covalent geometry : angle 0.62436 (37062) hydrogen bonds : bond 0.05938 ( 1388) hydrogen bonds : angle 4.02296 ( 3681) metal coordination : bond 0.00954 ( 16) metal coordination : angle 3.25827 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 62 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 MET cc_start: 0.7270 (tpp) cc_final: 0.6677 (tpp) REVERT: B 214 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.8075 (t80) REVERT: B 246 THR cc_start: 0.7211 (OUTLIER) cc_final: 0.6963 (p) REVERT: B 305 MET cc_start: 0.9207 (mtt) cc_final: 0.8542 (tpp) REVERT: C 69 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8779 (tp30) REVERT: C 107 MET cc_start: 0.9533 (ptt) cc_final: 0.9114 (ppp) REVERT: E 22 MET cc_start: 0.4743 (mpp) cc_final: 0.4230 (mmt) outliers start: 32 outliers final: 25 residues processed: 88 average time/residue: 0.1923 time to fit residues: 27.2344 Evaluate side-chains 89 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 62 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 1298 GLU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain N residue 31 LYS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 110 ARG Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 17 optimal weight: 30.0000 chunk 77 optimal weight: 4.9990 chunk 205 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 chunk 227 optimal weight: 8.9990 chunk 223 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 108 optimal weight: 0.1980 chunk 96 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.038384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.024036 restraints weight = 371305.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.024446 restraints weight = 179291.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.024696 restraints weight = 121889.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.024831 restraints weight = 102595.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.024886 restraints weight = 93357.376| |-----------------------------------------------------------------------------| r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 26530 Z= 0.182 Angle : 0.599 15.660 37071 Z= 0.329 Chirality : 0.037 0.224 4082 Planarity : 0.004 0.037 3655 Dihedral : 26.695 158.038 5894 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.77 % Allowed : 19.38 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.18), residues: 2307 helix: 1.98 (0.14), residues: 1290 sheet: -0.58 (0.46), residues: 129 loop : -0.94 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 76 TYR 0.023 0.001 TYR C 38 PHE 0.017 0.001 PHE B 97 TRP 0.011 0.001 TRP D 464 HIS 0.006 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00390 (26514) covalent geometry : angle 0.59718 (37062) hydrogen bonds : bond 0.04870 ( 1388) hydrogen bonds : angle 3.84483 ( 3681) metal coordination : bond 0.00628 ( 16) metal coordination : angle 2.63216 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6200.77 seconds wall clock time: 107 minutes 33.55 seconds (6453.55 seconds total)