Starting phenix.real_space_refine on Sat Jun 21 20:33:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yi5_33852/06_2025/7yi5_33852.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yi5_33852/06_2025/7yi5_33852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yi5_33852/06_2025/7yi5_33852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yi5_33852/06_2025/7yi5_33852.map" model { file = "/net/cci-nas-00/data/ceres_data/7yi5_33852/06_2025/7yi5_33852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yi5_33852/06_2025/7yi5_33852.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.97, per 1000 atoms: 0.55 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: 5.89 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 11.11 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: 15.69 Time building geometry restraints manager: 7.10 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=" CA MET A 765 " pdb=" CB MET A 765 " ideal model delta sigma weight residual 1.526 1.552 -0.026 1.20e-02 6.94e+03 4.57e+00 bond pdb=" C SER K 86 " pdb=" N SER K 87 " ideal model delta sigma weight residual 1.335 1.315 0.020 1.32e-02 5.74e+03 2.37e+00 bond pdb=" C CYS D 451 " pdb=" N VAL D 452 " ideal model delta sigma weight residual 1.324 1.336 -0.012 8.60e-03 1.35e+04 1.96e+00 bond pdb=" SD MET B 47 " pdb=" CE MET B 47 " ideal model delta sigma weight residual 1.791 1.756 0.035 2.50e-02 1.60e+03 1.93e+00 ... (remaining 26509 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 36854 2.98 - 5.96: 184 5.96 - 8.94: 18 8.94 - 11.92: 4 11.92 - 14.90: 2 Bond angle restraints: 37062 Sorted by residual: angle pdb=" C LEU N 98 " pdb=" N LEU N 99 " pdb=" CA LEU N 99 " ideal model delta sigma weight residual 122.15 107.25 14.90 3.47e+00 8.31e-02 1.84e+01 angle pdb=" N MET B 47 " pdb=" CA MET B 47 " pdb=" CB MET B 47 " ideal model delta sigma weight residual 110.39 117.13 -6.74 1.66e+00 3.63e-01 1.65e+01 angle pdb=" C ARG B 46 " pdb=" N MET B 47 " pdb=" CA MET B 47 " ideal model delta sigma weight residual 120.72 114.20 6.52 1.67e+00 3.59e-01 1.52e+01 angle pdb=" C VAL K 89 " pdb=" N MET K 90 " pdb=" CA MET K 90 " ideal model delta sigma weight residual 121.14 114.50 6.64 1.75e+00 3.27e-01 1.44e+01 angle pdb=" CB MET C 37 " pdb=" CG MET C 37 " pdb=" SD MET C 37 " ideal model delta sigma weight residual 112.70 124.05 -11.35 3.00e+00 1.11e-01 1.43e+01 ... (remaining 37057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.96: 13099 30.96 - 61.92: 2002 61.92 - 92.88: 80 92.88 - 123.84: 0 123.84 - 154.80: 1 Dihedral angle restraints: 15182 sinusoidal: 8258 harmonic: 6924 Sorted by residual: dihedral pdb=" CA GLN D 541 " pdb=" C GLN D 541 " pdb=" N ILE D 542 " pdb=" CA ILE D 542 " ideal model delta harmonic sigma weight residual 180.00 -155.66 -24.34 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA PHE K 84 " pdb=" C PHE K 84 " pdb=" N GLN K 85 " pdb=" CA GLN K 85 " ideal model delta harmonic sigma weight residual 180.00 159.04 20.96 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA LYS B 153 " pdb=" C LYS B 153 " pdb=" N LYS B 154 " pdb=" CA LYS B 154 " ideal model delta harmonic sigma weight residual 180.00 159.46 20.54 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 15179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3443 0.053 - 0.107: 589 0.107 - 0.160: 46 0.160 - 0.213: 2 0.213 - 0.266: 2 Chirality restraints: 4082 Sorted by residual: chirality pdb=" CA MET K 90 " pdb=" N MET K 90 " pdb=" C MET K 90 " pdb=" CB MET K 90 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA MET B 47 " pdb=" N MET B 47 " pdb=" C MET B 47 " pdb=" CB MET B 47 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB VAL C 257 " pdb=" CA VAL C 257 " pdb=" CG1 VAL C 257 " pdb=" CG2 VAL C 257 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.12e-01 ... (remaining 4079 not shown) Planarity restraints: 3655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 296 " 0.044 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO D 297 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO D 297 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 297 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 118 " 0.043 5.00e-02 4.00e+02 6.62e-02 7.02e+00 pdb=" N PRO D 119 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO D 119 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 119 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 57 " 0.040 5.00e-02 4.00e+02 5.98e-02 5.73e+00 pdb=" N PRO E 58 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO E 58 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 58 " 0.033 5.00e-02 4.00e+02 ... (remaining 3652 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 326 2.58 - 3.16: 21771 3.16 - 3.74: 46740 3.74 - 4.32: 61218 4.32 - 4.90: 92117 Nonbonded interactions: 222172 Sorted by model distance: nonbonded pdb=" OD2 ASP B 186 " pdb="ZN ZN B 501 " model vdw 2.006 2.230 nonbonded pdb=" OD2 ASP B 274 " pdb="ZN ZN B 501 " model vdw 2.016 2.230 nonbonded pdb=" O2 DC O 70 " pdb=" N2 DG P -70 " model vdw 2.054 2.496 nonbonded pdb=" OD1 ASP B 186 " pdb="ZN ZN B 501 " model vdw 2.058 2.230 nonbonded pdb=" O2 DC O -21 " pdb=" N2 DG P 21 " model vdw 2.083 2.496 ... (remaining 222167 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 36 through 109 or (resid 110 through 111 and (name N or na \ me CA or name C or name O or name CB )) or resid 112 through 134)) selection = chain 'K' } ncs_group { reference = chain 'H' selection = (chain 'L' and resid 23 through 101) } ncs_group { reference = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'J' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 73.520 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.344 26530 Z= 0.261 Angle : 0.667 14.903 37071 Z= 0.377 Chirality : 0.039 0.266 4082 Planarity : 0.004 0.067 3655 Dihedral : 23.555 154.797 10708 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 17.91 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (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 TRP 0.016 0.002 TRP D 464 HIS 0.010 0.002 HIS B 43 PHE 0.015 0.002 PHE B 301 TYR 0.015 0.001 TYR B 347 ARG 0.006 0.001 ARG L 35 Details of bonding type rmsd hydrogen bonds : bond 0.13331 ( 1388) hydrogen bonds : angle 5.59391 ( 3681) metal coordination : bond 0.08665 ( 16) metal coordination : angle 3.56664 ( 9) covalent geometry : bond 0.00529 (26514) covalent geometry : angle 0.66450 (37062) *********************** 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 : 2.589 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: 0.2311 (ptm) REVERT: E 22 MET cc_start: 0.4286 (mpp) cc_final: 0.4009 (mpp) outliers start: 6 outliers final: 1 residues processed: 74 average time/residue: 0.4176 time to fit residues: 50.5874 Evaluate side-chains 69 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 2.652 ------------------------------------------------------------------------------- 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 219 optimal weight: 10.0000 chunk 197 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 67 optimal weight: 50.0000 chunk 132 optimal weight: 3.9990 chunk 105 optimal weight: 30.0000 chunk 203 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 151 optimal weight: 7.9990 chunk 236 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 802 GLN B 144 ASN C 275 GLN C 369 HIS ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 GLN N 44 GLN K 39 HIS K 113 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.038919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.024366 restraints weight = 367488.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.024657 restraints weight = 190972.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.024942 restraints weight = 125546.942| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 26530 Z= 0.213 Angle : 0.582 10.470 37071 Z= 0.330 Chirality : 0.037 0.178 4082 Planarity : 0.004 0.054 3655 Dihedral : 26.502 155.692 5896 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.77 % Allowed : 18.27 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.17), residues: 2307 helix: 1.78 (0.14), residues: 1287 sheet: -0.60 (0.47), residues: 140 loop : -1.46 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 464 HIS 0.007 0.001 HIS L 75 PHE 0.012 0.001 PHE L 61 TYR 0.023 0.001 TYR C 38 ARG 0.006 0.001 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.05501 ( 1388) hydrogen bonds : angle 4.15488 ( 3681) metal coordination : bond 0.00596 ( 16) metal coordination : angle 2.70754 ( 9) covalent geometry : bond 0.00459 (26514) covalent geometry : angle 0.58063 (37062) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 67 time to evaluate : 2.635 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 1314 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8269 (mm) REVERT: B 128 MET cc_start: 0.7268 (tpp) cc_final: 0.6846 (tpp) REVERT: B 214 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.8303 (t80) outliers start: 37 outliers final: 9 residues processed: 98 average time/residue: 0.3944 time to fit residues: 63.2702 Evaluate side-chains 76 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain D residue 459 ASN Chi-restraints excluded: chain J residue 85 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 140 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 116 optimal weight: 20.0000 chunk 129 optimal weight: 9.9990 chunk 229 optimal weight: 10.0000 chunk 31 optimal weight: 40.0000 chunk 0 optimal weight: 50.0000 chunk 242 optimal weight: 2.9990 chunk 202 optimal weight: 8.9990 chunk 12 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.039028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.024464 restraints weight = 363647.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.024946 restraints weight = 189984.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.025192 restraints weight = 119578.896| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26530 Z= 0.173 Angle : 0.548 11.052 37071 Z= 0.309 Chirality : 0.036 0.253 4082 Planarity : 0.004 0.045 3655 Dihedral : 26.350 155.470 5896 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.53 % Allowed : 17.99 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.17), residues: 2307 helix: 1.94 (0.14), residues: 1293 sheet: -0.54 (0.46), residues: 138 loop : -1.38 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 464 HIS 0.006 0.001 HIS L 75 PHE 0.022 0.001 PHE A 685 TYR 0.018 0.001 TYR C 38 ARG 0.004 0.000 ARG L 35 Details of bonding type rmsd hydrogen bonds : bond 0.04791 ( 1388) hydrogen bonds : angle 3.86382 ( 3681) metal coordination : bond 0.00400 ( 16) metal coordination : angle 2.22142 ( 9) covalent geometry : bond 0.00372 (26514) covalent geometry : angle 0.54682 (37062) *********************** 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 102 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 70 time to evaluate : 2.817 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: 0.7351 (tpp) cc_final: 0.6937 (tpp) REVERT: E 22 MET cc_start: 0.3563 (mpp) cc_final: 0.3189 (mmt) outliers start: 32 outliers final: 13 residues processed: 96 average time/residue: 0.4070 time to fit residues: 63.5281 Evaluate side-chains 81 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 443 CYS Chi-restraints excluded: chain D residue 459 ASN Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain J residue 85 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 K residue 51 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 248 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 45 optimal weight: 50.0000 chunk 57 optimal weight: 20.0000 chunk 120 optimal weight: 8.9990 chunk 254 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 235 optimal weight: 0.0770 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 HIS ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.039124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.024630 restraints weight = 366080.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.024978 restraints weight = 186231.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.025293 restraints weight = 121626.678| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26530 Z= 0.154 Angle : 0.535 10.952 37071 Z= 0.301 Chirality : 0.036 0.158 4082 Planarity : 0.004 0.040 3655 Dihedral : 26.229 155.848 5896 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.58 % Allowed : 18.23 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.18), residues: 2307 helix: 2.11 (0.14), residues: 1289 sheet: -0.42 (0.48), residues: 127 loop : -1.24 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 464 HIS 0.006 0.001 HIS L 75 PHE 0.009 0.001 PHE A 723 TYR 0.015 0.001 TYR C 38 ARG 0.005 0.000 ARG A 906 Details of bonding type rmsd hydrogen bonds : bond 0.04406 ( 1388) hydrogen bonds : angle 3.66529 ( 3681) metal coordination : bond 0.00368 ( 16) metal coordination : angle 1.81844 ( 9) covalent geometry : bond 0.00329 (26514) covalent geometry : angle 0.53435 (37062) *********************** 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 100 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 67 time to evaluate : 2.417 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: 0.7277 (tpp) cc_final: 0.6805 (tpp) REVERT: B 214 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.8112 (t80) REVERT: N 68 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8738 (pt0) REVERT: E 22 MET cc_start: 0.3598 (mpp) cc_final: 0.3268 (mmt) outliers start: 33 outliers final: 18 residues processed: 91 average time/residue: 0.3922 time to fit residues: 58.1469 Evaluate side-chains 86 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 443 CYS Chi-restraints excluded: chain D residue 459 ASN Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain N residue 113 LYS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain K residue 51 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 156 optimal weight: 10.0000 chunk 59 optimal weight: 40.0000 chunk 167 optimal weight: 8.9990 chunk 128 optimal weight: 50.0000 chunk 3 optimal weight: 50.0000 chunk 7 optimal weight: 7.9990 chunk 214 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 223 optimal weight: 10.0000 chunk 32 optimal weight: 50.0000 chunk 39 optimal weight: 2.9990 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 ASN D 267 ASN D 376 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 73 ASN E 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.038163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.023836 restraints weight = 376727.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.024314 restraints weight = 185649.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.024381 restraints weight = 126289.571| |-----------------------------------------------------------------------------| r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 26530 Z= 0.261 Angle : 0.603 11.017 37071 Z= 0.339 Chirality : 0.038 0.181 4082 Planarity : 0.004 0.036 3655 Dihedral : 26.651 156.172 5896 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.01 % Allowed : 18.56 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.17), residues: 2307 helix: 1.84 (0.14), residues: 1302 sheet: -0.54 (0.46), residues: 127 loop : -1.24 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 464 HIS 0.006 0.001 HIS A 998 PHE 0.014 0.001 PHE L 61 TYR 0.015 0.001 TYR H 51 ARG 0.007 0.001 ARG M 42 Details of bonding type rmsd hydrogen bonds : bond 0.06685 ( 1388) hydrogen bonds : angle 3.96892 ( 3681) metal coordination : bond 0.00947 ( 16) metal coordination : angle 3.17204 ( 9) covalent geometry : bond 0.00561 (26514) covalent geometry : angle 0.60117 (37062) *********************** 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 105 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 63 time to evaluate : 2.795 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: 0.7418 (tpp) cc_final: 0.6850 (tpp) REVERT: B 204 MET cc_start: -0.0407 (mmt) cc_final: -0.0794 (mmt) REVERT: B 214 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.8054 (t80) REVERT: E 22 MET cc_start: 0.4051 (mpp) cc_final: 0.3772 (mmt) REVERT: K 120 MET cc_start: 0.8977 (mmm) cc_final: 0.8759 (mmm) outliers start: 42 outliers final: 24 residues processed: 98 average time/residue: 0.4306 time to fit residues: 68.8780 Evaluate side-chains 88 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 1178 VAL Chi-restraints excluded: chain A residue 1298 GLU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 459 ASN Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain K residue 51 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 246 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 chunk 192 optimal weight: 2.9990 chunk 111 optimal weight: 20.0000 chunk 245 optimal weight: 9.9990 chunk 203 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 25 optimal weight: 50.0000 chunk 94 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 ASN A 998 HIS ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.038342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.024011 restraints weight = 370716.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.024379 restraints weight = 195331.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.024635 restraints weight = 125600.684| |-----------------------------------------------------------------------------| r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 26530 Z= 0.231 Angle : 0.589 11.279 37071 Z= 0.329 Chirality : 0.037 0.201 4082 Planarity : 0.004 0.049 3655 Dihedral : 26.712 157.733 5896 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.63 % Allowed : 19.14 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.17), residues: 2307 helix: 1.86 (0.14), residues: 1302 sheet: -0.73 (0.45), residues: 131 loop : -1.20 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 464 HIS 0.007 0.001 HIS L 75 PHE 0.012 0.001 PHE L 61 TYR 0.015 0.001 TYR C 38 ARG 0.013 0.000 ARG L 92 Details of bonding type rmsd hydrogen bonds : bond 0.05463 ( 1388) hydrogen bonds : angle 3.89914 ( 3681) metal coordination : bond 0.00726 ( 16) metal coordination : angle 2.86402 ( 9) covalent geometry : bond 0.00495 (26514) covalent geometry : angle 0.58731 (37062) *********************** 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 98 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 64 time to evaluate : 3.367 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 906 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7668 (mpt180) REVERT: A 1298 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7922 (tm-30) REVERT: B 61 MET cc_start: 0.7988 (mpp) cc_final: 0.7265 (mpp) REVERT: B 128 MET cc_start: 0.7300 (tpp) cc_final: 0.6718 (tpp) REVERT: B 204 MET cc_start: -0.0088 (mmt) cc_final: -0.0572 (mmt) REVERT: B 214 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.8023 (t80) REVERT: E 22 MET cc_start: 0.4274 (mpp) cc_final: 0.3812 (mmt) REVERT: G 120 MET cc_start: 0.8829 (ptp) cc_final: 0.8418 (mpp) REVERT: K 120 MET cc_start: 0.9022 (mmm) cc_final: 0.8811 (mmm) outliers start: 34 outliers final: 21 residues processed: 93 average time/residue: 0.5489 time to fit residues: 83.7617 Evaluate side-chains 87 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 2.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 1298 GLU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 235 ASP 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 113 LYS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 110 ARG Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain K residue 51 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 20 optimal weight: 30.0000 chunk 87 optimal weight: 40.0000 chunk 41 optimal weight: 20.0000 chunk 110 optimal weight: 9.9990 chunk 104 optimal weight: 40.0000 chunk 167 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 179 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 250 optimal weight: 4.9990 chunk 94 optimal weight: 30.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 314 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.038118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.023836 restraints weight = 374724.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.024162 restraints weight = 200062.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.024245 restraints weight = 129299.090| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 26530 Z= 0.238 Angle : 0.598 11.411 37071 Z= 0.333 Chirality : 0.038 0.194 4082 Planarity : 0.004 0.052 3655 Dihedral : 26.767 158.422 5896 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.92 % Allowed : 18.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.17), residues: 2307 helix: 1.85 (0.14), residues: 1302 sheet: -0.72 (0.45), residues: 129 loop : -1.16 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 464 HIS 0.006 0.001 HIS L 75 PHE 0.012 0.001 PHE L 61 TYR 0.017 0.001 TYR C 38 ARG 0.014 0.000 ARG J 76 Details of bonding type rmsd hydrogen bonds : bond 0.05900 ( 1388) hydrogen bonds : angle 3.95029 ( 3681) metal coordination : bond 0.00671 ( 16) metal coordination : angle 2.94620 ( 9) covalent geometry : bond 0.00513 (26514) covalent geometry : angle 0.59677 (37062) *********************** 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 101 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 61 time to evaluate : 2.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 906 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7631 (mpt180) REVERT: A 1298 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7778 (tm-30) REVERT: B 128 MET cc_start: 0.7299 (tpp) cc_final: 0.6711 (tpp) REVERT: B 204 MET cc_start: 0.0629 (mmt) cc_final: 0.0147 (mmt) REVERT: B 214 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.8134 (t80) REVERT: B 305 MET cc_start: 0.9104 (mtt) cc_final: 0.8387 (tpp) REVERT: E 22 MET cc_start: 0.4443 (mpp) cc_final: 0.3989 (mmt) REVERT: G 120 MET cc_start: 0.8753 (ptp) cc_final: 0.8431 (mpp) outliers start: 40 outliers final: 28 residues processed: 96 average time/residue: 0.4053 time to fit residues: 63.0344 Evaluate side-chains 92 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 61 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 1298 GLU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain 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 82 THR Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain N residue 113 LYS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 110 ARG Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain K residue 51 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 20.0000 chunk 200 optimal weight: 5.9990 chunk 123 optimal weight: 0.0010 chunk 130 optimal weight: 30.0000 chunk 111 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 245 optimal weight: 9.9990 chunk 106 optimal weight: 0.1980 chunk 93 optimal weight: 50.0000 chunk 151 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 802 GLN A 937 GLN C 104 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.039147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.024733 restraints weight = 363787.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.025097 restraints weight = 186504.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.025185 restraints weight = 120549.076| |-----------------------------------------------------------------------------| r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26530 Z= 0.126 Angle : 0.558 11.949 37071 Z= 0.308 Chirality : 0.036 0.208 4082 Planarity : 0.003 0.037 3655 Dihedral : 26.406 158.359 5896 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.25 % Allowed : 19.33 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.18), residues: 2307 helix: 2.16 (0.14), residues: 1293 sheet: -0.60 (0.45), residues: 135 loop : -1.00 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 775 HIS 0.005 0.001 HIS L 75 PHE 0.011 0.001 PHE E 78 TYR 0.018 0.001 TYR C 38 ARG 0.011 0.000 ARG J 76 Details of bonding type rmsd hydrogen bonds : bond 0.04105 ( 1388) hydrogen bonds : angle 3.60041 ( 3681) metal coordination : bond 0.00364 ( 16) metal coordination : angle 1.85866 ( 9) covalent geometry : bond 0.00266 (26514) covalent geometry : angle 0.55693 (37062) *********************** 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 90 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 2.900 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: 0.7330 (tpp) cc_final: 0.6849 (tpp) REVERT: B 204 MET cc_start: 0.0610 (mmt) cc_final: -0.0034 (mmt) REVERT: B 214 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.8137 (t80) REVERT: B 246 THR cc_start: 0.6957 (OUTLIER) cc_final: 0.6691 (p) REVERT: B 305 MET cc_start: 0.9073 (mtt) cc_final: 0.8203 (tpp) REVERT: C 22 MET cc_start: 0.6582 (mpp) cc_final: 0.5776 (mpp) REVERT: N 68 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8621 (pt0) REVERT: E 22 MET cc_start: 0.4101 (mpp) cc_final: 0.3636 (mmt) REVERT: G 120 MET cc_start: 0.8635 (ptp) cc_final: 0.8407 (mpp) outliers start: 26 outliers final: 17 residues processed: 85 average time/residue: 0.4055 time to fit residues: 58.2509 Evaluate side-chains 81 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain H residue 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 31 LYS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 86 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 80 optimal weight: 20.0000 chunk 236 optimal weight: 0.0270 chunk 146 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 177 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 191 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 overall best weight: 4.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 325 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 459 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.038462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.024186 restraints weight = 371642.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.024529 restraints weight = 196460.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.024616 restraints weight = 126457.132| |-----------------------------------------------------------------------------| r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26530 Z= 0.189 Angle : 0.574 11.160 37071 Z= 0.318 Chirality : 0.037 0.207 4082 Planarity : 0.004 0.036 3655 Dihedral : 26.461 158.067 5894 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.10 % Allowed : 19.62 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.18), residues: 2307 helix: 2.18 (0.14), residues: 1292 sheet: -0.53 (0.45), residues: 135 loop : -0.99 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 464 HIS 0.006 0.001 HIS L 75 PHE 0.011 0.001 PHE H 100 TYR 0.025 0.001 TYR C 38 ARG 0.011 0.000 ARG J 76 Details of bonding type rmsd hydrogen bonds : bond 0.05147 ( 1388) hydrogen bonds : angle 3.71765 ( 3681) metal coordination : bond 0.00588 ( 16) metal coordination : angle 2.34068 ( 9) covalent geometry : bond 0.00407 (26514) covalent geometry : angle 0.57267 (37062) *********************** 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 86 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 4.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.7250 (mpp) cc_final: 0.6324 (mpp) REVERT: B 128 MET cc_start: 0.7255 (tpp) cc_final: 0.6690 (tpp) REVERT: B 214 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.8262 (t80) REVERT: B 246 THR cc_start: 0.7058 (OUTLIER) cc_final: 0.6796 (p) REVERT: B 305 MET cc_start: 0.9094 (mtt) cc_final: 0.8253 (tpp) REVERT: C 22 MET cc_start: 0.6729 (mpp) cc_final: 0.6052 (mpp) REVERT: G 90 MET cc_start: 0.9048 (ptt) cc_final: 0.8671 (ppp) REVERT: G 120 MET cc_start: 0.8666 (ptp) cc_final: 0.8443 (mpp) outliers start: 23 outliers final: 18 residues processed: 81 average time/residue: 0.7364 time to fit residues: 99.1777 Evaluate side-chains 82 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 4.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 401 MET 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 N residue 31 LYS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain G residue 46 VAL 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 105 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 195 optimal weight: 0.9990 chunk 59 optimal weight: 50.0000 chunk 233 optimal weight: 8.9990 chunk 119 optimal weight: 40.0000 chunk 8 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 130 optimal weight: 30.0000 chunk 122 optimal weight: 20.0000 chunk 205 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 305 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.038035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.023815 restraints weight = 376120.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.024188 restraints weight = 199210.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.024274 restraints weight = 128491.507| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 26530 Z= 0.239 Angle : 0.625 11.374 37071 Z= 0.344 Chirality : 0.038 0.218 4082 Planarity : 0.004 0.040 3655 Dihedral : 26.750 158.627 5894 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.10 % Allowed : 19.62 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.18), residues: 2307 helix: 1.92 (0.14), residues: 1299 sheet: -0.65 (0.44), residues: 136 loop : -0.98 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 464 HIS 0.006 0.001 HIS L 75 PHE 0.014 0.001 PHE L 61 TYR 0.024 0.001 TYR C 38 ARG 0.012 0.001 ARG J 76 Details of bonding type rmsd hydrogen bonds : bond 0.05959 ( 1388) hydrogen bonds : angle 3.95432 ( 3681) metal coordination : bond 0.00859 ( 16) metal coordination : angle 3.11870 ( 9) covalent geometry : bond 0.00513 (26514) covalent geometry : angle 0.62308 (37062) ********************** 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 85 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 2.498 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 906 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7606 (mpt180) REVERT: B 61 MET cc_start: 0.7321 (mpp) cc_final: 0.6430 (mpp) REVERT: B 128 MET cc_start: 0.7277 (tpp) cc_final: 0.6701 (tpp) REVERT: B 214 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.8108 (t80) REVERT: B 246 THR cc_start: 0.7122 (OUTLIER) cc_final: 0.6854 (p) REVERT: B 305 MET cc_start: 0.9168 (mtt) cc_final: 0.8366 (tpp) REVERT: C 22 MET cc_start: 0.6808 (mpp) cc_final: 0.6204 (mpp) REVERT: C 69 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8805 (tp30) REVERT: G 90 MET cc_start: 0.9012 (ptt) cc_final: 0.8797 (ppp) REVERT: K 90 MET cc_start: 0.9333 (pmm) cc_final: 0.8985 (pmm) outliers start: 23 outliers final: 19 residues processed: 80 average time/residue: 0.4088 time to fit residues: 53.0768 Evaluate side-chains 84 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 401 MET 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 N residue 31 LYS Chi-restraints excluded: chain N residue 113 LYS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain 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 65 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 chunk 121 optimal weight: 30.0000 chunk 74 optimal weight: 20.0000 chunk 238 optimal weight: 30.0000 chunk 35 optimal weight: 7.9990 chunk 86 optimal weight: 20.0000 chunk 179 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 128 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.037832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.023591 restraints weight = 376251.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.024004 restraints weight = 197432.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.024220 restraints weight = 126987.216| |-----------------------------------------------------------------------------| r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 26530 Z= 0.264 Angle : 0.652 13.784 37071 Z= 0.359 Chirality : 0.039 0.209 4082 Planarity : 0.004 0.043 3655 Dihedral : 26.912 158.868 5894 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.29 % Allowed : 19.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.18), residues: 2307 helix: 1.77 (0.14), residues: 1298 sheet: -0.86 (0.44), residues: 136 loop : -0.99 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 88 HIS 0.006 0.001 HIS L 75 PHE 0.016 0.002 PHE B 97 TYR 0.023 0.002 TYR C 38 ARG 0.012 0.001 ARG J 76 Details of bonding type rmsd hydrogen bonds : bond 0.06355 ( 1388) hydrogen bonds : angle 4.10332 ( 3681) metal coordination : bond 0.01052 ( 16) metal coordination : angle 3.44819 ( 9) covalent geometry : bond 0.00568 (26514) covalent geometry : angle 0.64991 (37062) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9984.86 seconds wall clock time: 179 minutes 14.84 seconds (10754.84 seconds total)