Starting phenix.real_space_refine on Sun Jul 5 03:18:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yi5_33852/07_2026/7yi5_33852.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yi5_33852/07_2026/7yi5_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_33852/07_2026/7yi5_33852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yi5_33852/07_2026/7yi5_33852.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7yi5_33852/07_2026/7yi5_33852.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yi5_33852/07_2026/7yi5_33852.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yi5_33852/07_2026/7yi5_33852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yi5_33852/07_2026/7yi5_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 4.52, per 1000 atoms: 0.18 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: 1.62 Conformation dependent library (CDL) restraints added in 811.3 milliseconds 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: 3.26 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: 6.83 Time building geometry restraints manager: 2.10 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=" C3' DA O -14 " pdb=" O3' DA O -14 " ideal model delta sigma weight residual 1.435 1.393 0.042 1.30e-02 5.92e+03 1.07e+01 bond pdb=" C3' DT O 38 " pdb=" O3' DT O 38 " ideal model delta sigma weight residual 1.435 1.395 0.040 1.30e-02 5.92e+03 9.58e+00 bond pdb=" C3' DG P 73 " pdb=" C2' DG P 73 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.24e+00 bond pdb=" C3' DA P 17 " pdb=" O3' DA P 17 " ideal model delta sigma weight residual 1.435 1.396 0.039 1.30e-02 5.92e+03 8.80e+00 ... (remaining 26509 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 36820 2.98 - 5.96: 218 5.96 - 8.94: 18 8.94 - 11.92: 4 11.92 - 14.90: 2 Bond angle restraints: 37062 Sorted by residual: angle pdb=" O4' DG O 26 " pdb=" C4' DG O 26 " pdb=" C3' DG O 26 " ideal model delta sigma weight residual 106.00 102.38 3.62 6.00e-01 2.78e+00 3.64e+01 angle pdb=" O4' DC O 37 " pdb=" C4' DC O 37 " pdb=" C3' DC O 37 " ideal model delta sigma weight residual 106.00 102.82 3.18 6.00e-01 2.78e+00 2.80e+01 angle pdb=" O4' DG O 47 " pdb=" C4' DG O 47 " pdb=" C3' DG O 47 " ideal model delta sigma weight residual 106.00 103.25 2.75 6.00e-01 2.78e+00 2.10e+01 angle pdb=" O4' DT P -29 " pdb=" C4' DT P -29 " pdb=" C3' DT P -29 " ideal model delta sigma weight residual 106.00 103.25 2.75 6.00e-01 2.78e+00 2.10e+01 angle pdb=" O4' DG P -5 " pdb=" C1' DG P -5 " pdb=" N9 DG P -5 " ideal model delta sigma weight residual 108.00 111.18 -3.18 7.00e-01 2.04e+00 2.06e+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: 3264 0.053 - 0.107: 677 0.107 - 0.160: 136 0.160 - 0.213: 3 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=" C3' DA P 17 " pdb=" C4' DA P 17 " pdb=" O3' DA P 17 " pdb=" C2' DA P 17 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.73e-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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 27.800 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 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= 0.492 Angle : 0.739 14.903 37071 Z= 0.554 Chirality : 0.045 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 are 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/Z covalent geometry : bond 0.00576 / 0.49 (26514) covalent geometry : angle 0.73725 / 0.55 (37062) hydrogen bonds : bond 0.13331 / 8.78 ( 1388) hydrogen bonds : angle 5.59391 / 4.01 ( 3681) metal coordination : bond 0.08665 / 4.34 ( 16) metal coordination : angle 3.56664 / 1.67 ( 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 : 0.585 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: 0.1659 time to fit residues: 19.9594 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 : 0.568 ------------------------------------------------------------------------------- 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: 2.9990 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 20.0000 chunk 258 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 144 ASN C 275 GLN C 369 HIS D 430 HIS 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 = 0.3421 r_free = 0.3421 target = 0.039296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.024643 restraints weight = 362876.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.024957 restraints weight = 186556.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.025228 restraints weight = 121439.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.025445 restraints weight = 99762.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.025485 restraints weight = 91515.633| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26530 Z= 0.153 Angle : 0.612 12.871 37071 Z= 0.348 Chirality : 0.041 0.246 4082 Planarity : 0.004 0.051 3655 Dihedral : 26.662 159.265 5896 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.39 % Allowed : 18.47 % Favored : 80.14 % 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 are not related in a simple way. whole: 0.62 (0.17), residues: 2307 helix: 1.75 (0.14), residues: 1283 sheet: -0.43 (0.51), residues: 124 loop : -1.50 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 496 TYR 0.016 0.001 TYR C 38 PHE 0.011 0.001 PHE D 282 TRP 0.014 0.001 TRP D 464 HIS 0.006 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (26514) covalent geometry : angle 0.61113 / 0.35 (37062) hydrogen bonds : bond 0.05630 / 3.76 ( 1388) hydrogen bonds : angle 4.32148 / 3.08 ( 3681) metal coordination : bond 0.00492 / 0.29 ( 16) metal coordination : angle 2.59273 / 1.21 ( 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 98 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 0.592 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 1314 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8245 (mm) REVERT: B 128 MET cc_start: 0.7147 (tpp) cc_final: 0.6781 (tpp) REVERT: E 22 MET cc_start: 0.3560 (mpp) cc_final: 0.3120 (mmt) REVERT: K 120 MET cc_start: 0.8909 (mmm) cc_final: 0.8693 (mmm) outliers start: 29 outliers final: 6 residues processed: 94 average time/residue: 0.1651 time to fit residues: 25.0171 Evaluate side-chains 75 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain D residue 459 ASN Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain N residue 85 THR 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: 50.0000 chunk 230 optimal weight: 40.0000 chunk 118 optimal weight: 0.8980 chunk 168 optimal weight: 4.9990 chunk 22 optimal weight: 40.0000 chunk 15 optimal weight: 40.0000 chunk 66 optimal weight: 30.0000 chunk 201 optimal weight: 40.0000 chunk 65 optimal weight: 6.9990 chunk 236 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 44 GLN K 113 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.038949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.024377 restraints weight = 369651.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.024799 restraints weight = 192201.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.025073 restraints weight = 121562.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.025155 restraints weight = 98536.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.025160 restraints weight = 91676.196| |-----------------------------------------------------------------------------| r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26530 Z= 0.186 Angle : 0.607 11.841 37071 Z= 0.343 Chirality : 0.040 0.230 4082 Planarity : 0.004 0.044 3655 Dihedral : 26.692 159.985 5896 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.39 % Allowed : 18.23 % Favored : 80.38 % 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 are not related in a simple way. whole: 0.66 (0.17), residues: 2307 helix: 1.79 (0.14), residues: 1287 sheet: -0.75 (0.46), residues: 140 loop : -1.47 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 46 TYR 0.017 0.001 TYR C 38 PHE 0.011 0.001 PHE L 61 TRP 0.011 0.001 TRP D 464 HIS 0.007 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.19 (26514) covalent geometry : angle 0.60609 / 0.34 (37062) hydrogen bonds : bond 0.06102 / 4.07 ( 1388) hydrogen bonds : angle 4.17426 / 2.97 ( 3681) metal coordination : bond 0.00708 / 0.43 ( 16) metal coordination : angle 2.47654 / 1.28 ( 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 98 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1314 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8362 (mm) REVERT: B 128 MET cc_start: 0.7256 (tpp) cc_final: 0.6823 (tpp) REVERT: B 214 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.8171 (t80) REVERT: B 315 MET cc_start: 0.0947 (ptm) cc_final: 0.0690 (ptm) outliers start: 29 outliers final: 13 residues processed: 94 average time/residue: 0.1935 time to fit residues: 29.1166 Evaluate side-chains 81 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain D residue 443 CYS Chi-restraints excluded: chain D residue 459 ASN 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 201 optimal weight: 40.0000 chunk 249 optimal weight: 8.9990 chunk 39 optimal weight: 8.9990 chunk 25 optimal weight: 50.0000 chunk 236 optimal weight: 40.0000 chunk 162 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 228 optimal weight: 40.0000 chunk 83 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 779 ASN D 325 ASN D 376 ASN E 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.038629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.024125 restraints weight = 367792.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.024449 restraints weight = 189217.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.024706 restraints weight = 123343.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.024906 restraints weight = 102395.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.024906 restraints weight = 93403.227| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26530 Z= 0.213 Angle : 0.635 11.650 37071 Z= 0.354 Chirality : 0.042 0.388 4082 Planarity : 0.004 0.038 3655 Dihedral : 26.828 160.636 5896 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.97 % Allowed : 18.23 % Favored : 79.81 % 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 are not related in a simple way. whole: 0.58 (0.17), residues: 2307 helix: 1.66 (0.14), residues: 1294 sheet: -0.82 (0.45), residues: 141 loop : -1.41 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 46 TYR 0.018 0.001 TYR C 38 PHE 0.018 0.001 PHE A 723 TRP 0.012 0.001 TRP C 365 HIS 0.007 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.21 (26514) covalent geometry : angle 0.63382 / 0.35 (37062) hydrogen bonds : bond 0.06530 / 4.36 ( 1388) hydrogen bonds : angle 4.13785 / 2.94 ( 3681) metal coordination : bond 0.00678 / 0.43 ( 16) metal coordination : angle 2.76985 / 1.48 ( 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 105 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 64 time to evaluate : 0.907 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: 0.7342 (tpp) cc_final: 0.6862 (tpp) REVERT: B 214 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.8244 (t80) REVERT: E 22 MET cc_start: 0.3653 (mpp) cc_final: 0.3295 (mmt) REVERT: E 107 MET cc_start: 0.2915 (ppp) cc_final: 0.2699 (ppp) REVERT: K 120 MET cc_start: 0.8918 (mmm) cc_final: 0.8676 (mmm) outliers start: 41 outliers final: 25 residues processed: 100 average time/residue: 0.1588 time to fit residues: 26.1486 Evaluate side-chains 88 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 1277 THR 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 323 ILE Chi-restraints excluded: chain C residue 401 MET 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 87 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain L residue 58 LEU 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 G residue 46 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 105 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 143 optimal weight: 50.0000 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 204 optimal weight: 40.0000 chunk 4 optimal weight: 6.9990 chunk 50 optimal weight: 40.0000 chunk 85 optimal weight: 7.9990 chunk 205 optimal weight: 40.0000 chunk 43 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 142 optimal weight: 7.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1299 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.038454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.024078 restraints weight = 370436.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.024369 restraints weight = 192682.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.024599 restraints weight = 126688.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.024781 restraints weight = 105298.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.024797 restraints weight = 96166.012| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 26530 Z= 0.224 Angle : 0.639 11.652 37071 Z= 0.356 Chirality : 0.041 0.225 4082 Planarity : 0.004 0.034 3655 Dihedral : 26.936 161.186 5896 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.73 % Allowed : 18.66 % Favored : 79.62 % 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 are not related in a simple way. whole: 0.57 (0.17), residues: 2307 helix: 1.63 (0.14), residues: 1297 sheet: -0.66 (0.45), residues: 139 loop : -1.41 (0.19), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 46 TYR 0.023 0.001 TYR J 37 PHE 0.017 0.001 PHE E 78 TRP 0.011 0.001 TRP D 464 HIS 0.007 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.22 (26514) covalent geometry : angle 0.63712 / 0.36 (37062) hydrogen bonds : bond 0.06620 / 4.41 ( 1388) hydrogen bonds : angle 4.14357 / 2.94 ( 3681) metal coordination : bond 0.00850 / 0.49 ( 16) metal coordination : angle 3.02172 / 1.61 ( 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 99 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 63 time to evaluate : 0.981 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: 0.3767 (ttt) cc_final: 0.3498 (mmp) REVERT: B 128 MET cc_start: 0.7346 (tpp) cc_final: 0.6830 (tpp) REVERT: B 214 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.8311 (t80) REVERT: C 22 MET cc_start: 0.7109 (mtp) cc_final: 0.6851 (mtm) REVERT: E 22 MET cc_start: 0.3872 (mpp) cc_final: 0.3327 (mmt) outliers start: 36 outliers final: 23 residues processed: 94 average time/residue: 0.1804 time to fit residues: 27.8756 Evaluate side-chains 86 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 1277 THR 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 323 ILE 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 92 ARG 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 65 VAL 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 50 GLU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 105 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 125 optimal weight: 4.9990 chunk 124 optimal weight: 30.0000 chunk 85 optimal weight: 8.9990 chunk 221 optimal weight: 30.0000 chunk 40 optimal weight: 20.0000 chunk 200 optimal weight: 5.9990 chunk 180 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 257 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.038893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.024453 restraints weight = 367146.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.024772 restraints weight = 184175.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.025010 restraints weight = 120945.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.025175 restraints weight = 100466.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.025185 restraints weight = 92816.706| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 26530 Z= 0.143 Angle : 0.583 12.005 37071 Z= 0.328 Chirality : 0.040 0.247 4082 Planarity : 0.004 0.035 3655 Dihedral : 26.872 161.008 5896 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.58 % Allowed : 19.23 % Favored : 79.18 % 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 are not related in a simple way. whole: 0.79 (0.17), residues: 2307 helix: 1.85 (0.14), residues: 1297 sheet: -0.76 (0.44), residues: 143 loop : -1.35 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 917 TYR 0.023 0.001 TYR C 38 PHE 0.012 0.001 PHE L 61 TRP 0.007 0.001 TRP D 464 HIS 0.005 0.001 HIS A 998 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 (26514) covalent geometry : angle 0.58240 / 0.33 (37062) hydrogen bonds : bond 0.05067 / 3.37 ( 1388) hydrogen bonds : angle 3.93480 / 2.79 ( 3681) metal coordination : bond 0.00507 / 0.29 ( 16) metal coordination : angle 2.18467 / 1.13 ( 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 100 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 67 time to evaluate : 0.880 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 1298 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: B 128 MET cc_start: 0.7362 (tpp) cc_final: 0.6876 (tpp) REVERT: B 214 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8190 (t80) REVERT: B 246 THR cc_start: 0.6881 (OUTLIER) cc_final: 0.6618 (p) REVERT: C 22 MET cc_start: 0.7087 (mtp) cc_final: 0.6840 (mtm) REVERT: N 68 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8723 (pt0) REVERT: E 22 MET cc_start: 0.3983 (mpp) cc_final: 0.3725 (mmt) REVERT: G 90 MET cc_start: 0.8998 (mmm) cc_final: 0.8739 (mpp) REVERT: G 120 MET cc_start: 0.8719 (ptp) cc_final: 0.8435 (mpp) outliers start: 33 outliers final: 20 residues processed: 96 average time/residue: 0.1840 time to fit residues: 28.5747 Evaluate side-chains 87 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1298 GLU 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 323 ILE 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 L residue 58 LEU 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 51 ILE 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: 7.9990 chunk 127 optimal weight: 40.0000 chunk 101 optimal weight: 8.9990 chunk 140 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 89 optimal weight: 7.9990 chunk 249 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 222 optimal weight: 30.0000 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 105 ASN ** B 235 ASN ** 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 = 0.3402 r_free = 0.3402 target = 0.038814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.024432 restraints weight = 366558.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.024829 restraints weight = 191886.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.024912 restraints weight = 122221.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.025219 restraints weight = 104230.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.025213 restraints weight = 91808.817| |-----------------------------------------------------------------------------| r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26530 Z= 0.156 Angle : 0.594 12.103 37071 Z= 0.332 Chirality : 0.040 0.234 4082 Planarity : 0.004 0.035 3655 Dihedral : 26.828 162.083 5896 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.53 % Allowed : 19.38 % 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 are not related in a simple way. whole: 0.89 (0.17), residues: 2307 helix: 1.92 (0.14), residues: 1297 sheet: -0.56 (0.46), residues: 136 loop : -1.31 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1291 TYR 0.024 0.001 TYR C 38 PHE 0.014 0.001 PHE A1139 TRP 0.011 0.001 TRP C 91 HIS 0.006 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.16 (26514) covalent geometry : angle 0.59286 / 0.33 (37062) hydrogen bonds : bond 0.05293 / 3.52 ( 1388) hydrogen bonds : angle 3.89610 / 2.77 ( 3681) metal coordination : bond 0.00563 / 0.32 ( 16) metal coordination : angle 2.48884 / 1.32 ( 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 97 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 65 time to evaluate : 0.761 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: 0.7382 (tpp) cc_final: 0.6886 (tpp) REVERT: B 204 MET cc_start: -0.1489 (mmt) cc_final: -0.1772 (mmm) REVERT: B 214 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.8220 (t80) REVERT: B 246 THR cc_start: 0.6876 (OUTLIER) cc_final: 0.6610 (p) REVERT: C 22 MET cc_start: 0.7139 (mtp) cc_final: 0.6936 (mtm) REVERT: N 68 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8720 (pt0) REVERT: E 22 MET cc_start: 0.4022 (mpp) cc_final: 0.3466 (mmt) REVERT: E 107 MET cc_start: 0.2919 (ppp) cc_final: 0.2633 (ppp) outliers start: 32 outliers final: 25 residues processed: 92 average time/residue: 0.1752 time to fit residues: 26.0054 Evaluate side-chains 91 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 1277 THR 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 323 ILE Chi-restraints excluded: chain C residue 401 MET 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 87 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain N residue 87 THR 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 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: 6.9990 chunk 169 optimal weight: 4.9990 chunk 84 optimal weight: 0.0010 chunk 82 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 194 optimal weight: 9.9990 chunk 136 optimal weight: 7.9990 chunk 90 optimal weight: 0.3980 chunk 102 optimal weight: 8.9990 chunk 15 optimal weight: 0.0870 overall best weight: 2.0968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 80 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.039154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.024690 restraints weight = 365220.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.025042 restraints weight = 181689.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.025128 restraints weight = 117932.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.025345 restraints weight = 102793.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.025527 restraints weight = 93538.257| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 26530 Z= 0.121 Angle : 0.575 12.496 37071 Z= 0.323 Chirality : 0.040 0.252 4082 Planarity : 0.004 0.057 3655 Dihedral : 26.735 161.979 5896 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.10 % Allowed : 20.00 % Favored : 78.90 % 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 are not related in a simple way. whole: 1.06 (0.18), residues: 2307 helix: 2.04 (0.14), residues: 1293 sheet: -0.52 (0.48), residues: 131 loop : -1.18 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 92 TYR 0.024 0.001 TYR C 38 PHE 0.010 0.001 PHE E 78 TRP 0.007 0.001 TRP C 91 HIS 0.007 0.001 HIS C 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.12 (26514) covalent geometry : angle 0.57479 / 0.32 (37062) hydrogen bonds : bond 0.04523 / 3.02 ( 1388) hydrogen bonds : angle 3.80723 / 2.70 ( 3681) metal coordination : bond 0.00350 / 0.20 ( 16) metal coordination : angle 1.89042 / 0.98 ( 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 91 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.837 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: 0.7472 (tpp) cc_final: 0.7019 (tpp) REVERT: B 204 MET cc_start: -0.1210 (mmt) cc_final: -0.1582 (mmt) REVERT: B 214 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.8192 (t80) REVERT: B 246 THR cc_start: 0.6946 (OUTLIER) cc_final: 0.6683 (p) REVERT: C 107 MET cc_start: 0.9351 (ptt) cc_final: 0.8999 (ppp) REVERT: N 68 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8701 (pt0) REVERT: E 22 MET cc_start: 0.4145 (mpp) cc_final: 0.3670 (mmt) REVERT: E 107 MET cc_start: 0.3148 (ppp) cc_final: 0.2880 (ppp) REVERT: G 90 MET cc_start: 0.8935 (mmp) cc_final: 0.8714 (mpp) REVERT: G 120 MET cc_start: 0.8757 (ptp) cc_final: 0.8478 (mpp) outliers start: 23 outliers final: 18 residues processed: 87 average time/residue: 0.1889 time to fit residues: 26.0744 Evaluate side-chains 86 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 910 ARG 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 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 L residue 58 LEU Chi-restraints excluded: chain N residue 87 THR 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 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: 30.0000 chunk 38 optimal weight: 10.0000 chunk 227 optimal weight: 30.0000 chunk 16 optimal weight: 8.9990 chunk 232 optimal weight: 50.0000 chunk 57 optimal weight: 40.0000 chunk 140 optimal weight: 50.0000 chunk 4 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 147 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 235 ASN ** 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 = 0.3388 r_free = 0.3388 target = 0.038343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.024082 restraints weight = 372840.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.024436 restraints weight = 200211.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.024670 restraints weight = 126308.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.024722 restraints weight = 103705.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.024818 restraints weight = 96772.912| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 26530 Z= 0.240 Angle : 0.668 13.855 37071 Z= 0.365 Chirality : 0.041 0.242 4082 Planarity : 0.004 0.034 3655 Dihedral : 26.894 163.460 5896 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.39 % Allowed : 19.76 % 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 are not related in a simple way. whole: 0.82 (0.17), residues: 2307 helix: 1.78 (0.14), residues: 1301 sheet: -0.61 (0.45), residues: 141 loop : -1.21 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 92 TYR 0.023 0.002 TYR C 38 PHE 0.012 0.001 PHE L 61 TRP 0.011 0.001 TRP D 464 HIS 0.008 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.24 (26514) covalent geometry : angle 0.66646 / 0.37 (37062) hydrogen bonds : bond 0.06948 / 4.65 ( 1388) hydrogen bonds : angle 4.08940 / 2.91 ( 3681) metal coordination : bond 0.01037 / 0.52 ( 16) metal coordination : angle 3.19518 / 1.72 ( 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 94 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.687 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 61 MET cc_start: 0.7541 (mpp) cc_final: 0.6926 (mpp) REVERT: B 128 MET cc_start: 0.7468 (tpp) cc_final: 0.6944 (tpp) REVERT: B 204 MET cc_start: -0.0986 (mmt) cc_final: -0.1684 (mmt) REVERT: B 214 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8309 (t80) REVERT: B 246 THR cc_start: 0.6971 (OUTLIER) cc_final: 0.6712 (p) REVERT: C 22 MET cc_start: 0.7031 (mtm) cc_final: 0.5818 (mpp) REVERT: N 68 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8734 (pt0) outliers start: 29 outliers final: 23 residues processed: 90 average time/residue: 0.1616 time to fit residues: 24.0481 Evaluate side-chains 89 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 64 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 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 263 HIS 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 87 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain N residue 87 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 39 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 177 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 17 optimal weight: 30.0000 chunk 239 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 203 optimal weight: 30.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 998 HIS ** C 104 ASN ** 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 = 0.3393 r_free = 0.3393 target = 0.038537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.024201 restraints weight = 370317.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.024581 restraints weight = 194388.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.024664 restraints weight = 125200.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.024960 restraints weight = 106770.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.024959 restraints weight = 94217.449| |-----------------------------------------------------------------------------| r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26530 Z= 0.189 Angle : 0.633 11.969 37071 Z= 0.349 Chirality : 0.041 0.247 4082 Planarity : 0.004 0.050 3655 Dihedral : 26.978 163.175 5896 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.20 % Allowed : 20.05 % Favored : 78.75 % 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 are not related in a simple way. whole: 0.85 (0.17), residues: 2307 helix: 1.81 (0.14), residues: 1301 sheet: -0.58 (0.47), residues: 131 loop : -1.20 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 46 TYR 0.023 0.001 TYR C 38 PHE 0.013 0.001 PHE L 61 TRP 0.010 0.001 TRP D 464 HIS 0.006 0.001 HIS A 998 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.19 (26514) covalent geometry : angle 0.63134 / 0.35 (37062) hydrogen bonds : bond 0.05637 / 3.76 ( 1388) hydrogen bonds : angle 4.03612 / 2.87 ( 3681) metal coordination : bond 0.00721 / 0.37 ( 16) metal coordination : angle 2.76762 / 1.44 ( 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 91 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.729 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: A 1164 MET cc_start: 0.9274 (mmp) cc_final: 0.8774 (tpt) REVERT: B 61 MET cc_start: 0.7469 (mpp) cc_final: 0.6842 (mpp) REVERT: B 128 MET cc_start: 0.7447 (tpp) cc_final: 0.6922 (tpp) REVERT: B 204 MET cc_start: 0.0061 (mmt) cc_final: -0.1025 (mmt) REVERT: B 214 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.8179 (t80) REVERT: B 246 THR cc_start: 0.6978 (OUTLIER) cc_final: 0.6718 (p) REVERT: C 22 MET cc_start: 0.7109 (mtm) cc_final: 0.6185 (mpp) REVERT: N 68 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8717 (pt0) REVERT: E 22 MET cc_start: 0.4514 (mpp) cc_final: 0.3911 (mmt) REVERT: G 120 MET cc_start: 0.8814 (ptp) cc_final: 0.8501 (mpp) outliers start: 25 outliers final: 22 residues processed: 86 average time/residue: 0.1715 time to fit residues: 23.5320 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 : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 1298 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 263 HIS 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 H residue 92 ARG 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 N residue 87 THR 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 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: 6.9990 chunk 205 optimal weight: 30.0000 chunk 224 optimal weight: 30.0000 chunk 227 optimal weight: 40.0000 chunk 223 optimal weight: 40.0000 chunk 149 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 104 ASN ** 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 = 0.3406 r_free = 0.3406 target = 0.038918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.024537 restraints weight = 365078.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.024835 restraints weight = 189955.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.025101 restraints weight = 123202.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.025261 restraints weight = 100494.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.025287 restraints weight = 91581.419| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 26530 Z= 0.137 Angle : 0.606 17.042 37071 Z= 0.333 Chirality : 0.040 0.252 4082 Planarity : 0.004 0.036 3655 Dihedral : 26.838 163.854 5896 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.06 % Allowed : 20.24 % Favored : 78.71 % 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 are not related in a simple way. whole: 1.07 (0.18), residues: 2307 helix: 2.00 (0.14), residues: 1295 sheet: -0.56 (0.47), residues: 131 loop : -1.09 (0.20), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 46 TYR 0.024 0.001 TYR C 38 PHE 0.012 0.001 PHE L 61 TRP 0.008 0.001 TRP E 88 HIS 0.005 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.14 (26514) covalent geometry : angle 0.60522 / 0.33 (37062) hydrogen bonds : bond 0.04582 / 3.06 ( 1388) hydrogen bonds : angle 3.86792 / 2.75 ( 3681) metal coordination : bond 0.00477 / 0.23 ( 16) metal coordination : angle 2.13467 / 1.08 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5346.30 seconds wall clock time: 93 minutes 1.07 seconds (5581.07 seconds total)