Starting phenix.real_space_refine on Wed Mar 4 14:44:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yer_33775/03_2026/7yer_33775.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yer_33775/03_2026/7yer_33775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yer_33775/03_2026/7yer_33775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yer_33775/03_2026/7yer_33775.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yer_33775/03_2026/7yer_33775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yer_33775/03_2026/7yer_33775.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 77 5.16 5 C 9140 2.51 5 N 2408 2.21 5 O 2687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14313 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10540 Classifications: {'peptide': 1316} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 64, 'TRANS': 1249} Chain breaks: 5 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2011 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 260, 1983 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 242} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 260, 1983 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 242} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1990 Chain: "C" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 733 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 515 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 66} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 513 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 65} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9081 SG CYS A1150 46.478 43.940 97.558 1.00 77.65 S ATOM 9103 SG CYS A1153 49.590 41.687 97.882 1.00 79.43 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AGLN B 244 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 244 " occ=0.50 residue: pdb=" N ASER B 266 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER B 266 " occ=0.50 residue: pdb=" N ACYS B 275 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 275 " occ=0.50 residue: pdb=" N ATHR B 335 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR B 335 " occ=0.50 Time building chain proxies: 3.32, per 1000 atoms: 0.23 Number of scatterers: 14313 At special positions: 0 Unit cell: (180.83, 134.82, 113.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 77 16.00 O 2687 8.00 N 2408 7.00 C 9140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 484.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2301 " pdb="ZN ZN A2301 " - pdb=" NE2 HIS A1347 " pdb="ZN ZN A2301 " - pdb=" ND1 HIS A1345 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1153 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1150 " Number of angles added : 1 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3470 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 7 sheets defined 60.4% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 21 through 29 removed outlier: 3.564A pdb=" N VAL A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 51 through 55 removed outlier: 3.689A pdb=" N LYS A 54 " --> pdb=" O TYR A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 63 Processing helix chain 'A' and resid 72 through 75 removed outlier: 3.771A pdb=" N PHE A 75 " --> pdb=" O PRO A 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 75' Processing helix chain 'A' and resid 76 through 84 removed outlier: 3.617A pdb=" N LYS A 82 " --> pdb=" O PRO A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 100 through 112 Processing helix chain 'A' and resid 113 through 122 Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 145 through 166 removed outlier: 3.705A pdb=" N ASN A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 208 through 212 removed outlier: 4.226A pdb=" N ASP A 211 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP A 212 " --> pdb=" O ALA A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 212' Processing helix chain 'A' and resid 216 through 221 removed outlier: 4.027A pdb=" N GLU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 221' Processing helix chain 'A' and resid 235 through 261 removed outlier: 3.689A pdb=" N GLU A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 288 Processing helix chain 'A' and resid 291 through 296 removed outlier: 3.540A pdb=" N ILE A 295 " --> pdb=" O GLY A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 308 Processing helix chain 'A' and resid 317 through 334 Processing helix chain 'A' and resid 343 through 348 removed outlier: 3.555A pdb=" N LYS A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 357 Processing helix chain 'A' and resid 361 through 369 Processing helix chain 'A' and resid 381 through 391 removed outlier: 3.708A pdb=" N ILE A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 422 removed outlier: 3.617A pdb=" N ILE A 404 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 422 " --> pdb=" O HIS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 450 through 454 removed outlier: 3.701A pdb=" N MET A 453 " --> pdb=" O PRO A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 464 removed outlier: 3.594A pdb=" N LEU A 464 " --> pdb=" O PHE A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.520A pdb=" N ILE A 480 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 498 removed outlier: 3.939A pdb=" N TRP A 494 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ASP A 495 " --> pdb=" O THR A 492 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA A 496 " --> pdb=" O CYS A 493 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL A 497 " --> pdb=" O TRP A 494 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE A 498 " --> pdb=" O ASP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 522 Processing helix chain 'A' and resid 527 through 537 Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.504A pdb=" N LEU A 541 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 584 removed outlier: 3.523A pdb=" N ASP A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 600 removed outlier: 3.567A pdb=" N GLU A 600 " --> pdb=" O THR A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 634 through 640 removed outlier: 4.063A pdb=" N LEU A 638 " --> pdb=" O LYS A 635 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE A 640 " --> pdb=" O ASN A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 656 Proline residue: A 647 - end of helix removed outlier: 3.711A pdb=" N TYR A 656 " --> pdb=" O CYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 670 through 672 No H-bonds generated for 'chain 'A' and resid 670 through 672' Processing helix chain 'A' and resid 688 through 692 removed outlier: 3.704A pdb=" N ARG A 691 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN A 692 " --> pdb=" O GLU A 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 688 through 692' Processing helix chain 'A' and resid 712 through 731 removed outlier: 3.546A pdb=" N TRP A 716 " --> pdb=" O GLN A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 783 Processing helix chain 'A' and resid 815 through 820 removed outlier: 3.676A pdb=" N THR A 820 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 850 removed outlier: 3.831A pdb=" N GLU A 850 " --> pdb=" O ARG A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 875 removed outlier: 3.572A pdb=" N ARG A 858 " --> pdb=" O ILE A 854 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 867 " --> pdb=" O PHE A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 891 removed outlier: 3.773A pdb=" N THR A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU A 890 " --> pdb=" O GLY A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 903 removed outlier: 3.584A pdb=" N ILE A 899 " --> pdb=" O ASP A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 910 Processing helix chain 'A' and resid 916 through 921 Processing helix chain 'A' and resid 927 through 943 removed outlier: 3.600A pdb=" N SER A 931 " --> pdb=" O ASP A 927 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY A 932 " --> pdb=" O PRO A 928 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 943 " --> pdb=" O TYR A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 954 removed outlier: 3.767A pdb=" N ILE A 953 " --> pdb=" O PHE A 949 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 954 " --> pdb=" O LEU A 950 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 949 through 954' Processing helix chain 'A' and resid 963 through 968 removed outlier: 3.801A pdb=" N LEU A 967 " --> pdb=" O ILE A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 978 removed outlier: 3.877A pdb=" N SER A 977 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN A 978 " --> pdb=" O PRO A 975 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 974 through 978' Processing helix chain 'A' and resid 980 through 995 Processing helix chain 'A' and resid 1000 through 1005 Processing helix chain 'A' and resid 1008 through 1021 removed outlier: 3.537A pdb=" N LEU A1021 " --> pdb=" O CYS A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1036 removed outlier: 3.766A pdb=" N SER A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1048 removed outlier: 3.610A pdb=" N GLY A1048 " --> pdb=" O LEU A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1059 Processing helix chain 'A' and resid 1061 through 1065 removed outlier: 3.509A pdb=" N ASN A1064 " --> pdb=" O ILE A1061 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN A1065 " --> pdb=" O ILE A1062 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1061 through 1065' Processing helix chain 'A' and resid 1069 through 1085 removed outlier: 3.802A pdb=" N ARG A1073 " --> pdb=" O PRO A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1100 Processing helix chain 'A' and resid 1105 through 1117 Processing helix chain 'A' and resid 1134 through 1139 Processing helix chain 'A' and resid 1150 through 1155 Processing helix chain 'A' and resid 1182 through 1186 removed outlier: 3.701A pdb=" N THR A1186 " --> pdb=" O ILE A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1230 removed outlier: 4.379A pdb=" N ARG A1217 " --> pdb=" O SER A1213 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU A1218 " --> pdb=" O ALA A1214 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A1230 " --> pdb=" O LEU A1226 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1238 removed outlier: 4.364A pdb=" N ASP A1237 " --> pdb=" O SER A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1245 removed outlier: 4.315A pdb=" N PHE A1243 " --> pdb=" O LEU A1239 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1259 Processing helix chain 'A' and resid 1287 through 1290 removed outlier: 3.504A pdb=" N THR A1290 " --> pdb=" O ASN A1287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1287 through 1290' Processing helix chain 'A' and resid 1296 through 1300 removed outlier: 3.529A pdb=" N GLY A1300 " --> pdb=" O ASN A1297 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1331 removed outlier: 3.557A pdb=" N VAL A1319 " --> pdb=" O ILE A1315 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE A1320 " --> pdb=" O PHE A1316 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASN A1321 " --> pdb=" O GLN A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1335 through 1339 removed outlier: 3.573A pdb=" N ILE A1339 " --> pdb=" O ALA A1336 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 117 Processing helix chain 'B' and resid 118 through 123 removed outlier: 3.655A pdb=" N ASP B 123 " --> pdb=" O LYS B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 126 No H-bonds generated for 'chain 'B' and resid 124 through 126' Processing helix chain 'B' and resid 127 through 149 removed outlier: 4.022A pdb=" N LEU B 131 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 163 Processing helix chain 'B' and resid 177 through 187 removed outlier: 3.838A pdb=" N GLU B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 220 through 230 Processing helix chain 'B' and resid 237 through 254 removed outlier: 3.835A pdb=" N GLN B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 269 removed outlier: 3.563A pdb=" N GLU B 269 " --> pdb=" O ALA B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 284 Processing helix chain 'B' and resid 285 through 288 Processing helix chain 'B' and resid 305 through 309 removed outlier: 4.175A pdb=" N LYS B 309 " --> pdb=" O ALA B 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 118 removed outlier: 3.728A pdb=" N LEU C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 144 removed outlier: 3.703A pdb=" N SER C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C 130 " --> pdb=" O LYS C 126 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU C 144 " --> pdb=" O ALA C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 165 removed outlier: 3.567A pdb=" N GLU C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 112 Processing helix chain 'D' and resid 113 through 146 removed outlier: 3.816A pdb=" N GLY D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) Proline residue: D 120 - end of helix removed outlier: 4.292A pdb=" N SER D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER D 130 " --> pdb=" O LYS D 126 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU D 144 " --> pdb=" O ALA D 140 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU D 145 " --> pdb=" O LYS D 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 144 removed outlier: 4.757A pdb=" N LYS E 119 " --> pdb=" O GLU E 115 " (cutoff:3.500A) Proline residue: E 120 - end of helix removed outlier: 3.854A pdb=" N LEU E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 177 Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 399 Processing sheet with id=AA3, first strand: chain 'A' and resid 549 through 552 Processing sheet with id=AA4, first strand: chain 'A' and resid 734 through 740 removed outlier: 3.915A pdb=" N LYS A 734 " --> pdb=" O LEU A 749 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN A 743 " --> pdb=" O MET A 740 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL A 630 " --> pdb=" O PHE A 793 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE A 793 " --> pdb=" O VAL A 630 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 798 through 801 Processing sheet with id=AA6, first strand: chain 'A' and resid 1292 through 1295 Processing sheet with id=AA7, first strand: chain 'B' and resid 294 through 297 removed outlier: 3.996A pdb=" N CYS B 326 " --> pdb=" O LEU B 338 " (cutoff:3.500A) 714 hydrogen bonds defined for protein. 2044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4627 1.34 - 1.46: 2494 1.46 - 1.58: 7397 1.58 - 1.70: 0 1.70 - 1.81: 112 Bond restraints: 14630 Sorted by residual: bond pdb=" N VAL A 595 " pdb=" CA VAL A 595 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.25e-02 6.40e+03 8.40e+00 bond pdb=" N VAL A 596 " pdb=" CA VAL A 596 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.27e-02 6.20e+03 7.84e+00 bond pdb=" N MET A 594 " pdb=" CA MET A 594 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.30e-02 5.92e+03 7.08e+00 bond pdb=" N ASN A 592 " pdb=" CA ASN A 592 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.23e-02 6.61e+03 6.71e+00 bond pdb=" N MET A 593 " pdb=" CA MET A 593 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.91e+00 ... (remaining 14625 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 19496 1.70 - 3.39: 322 3.39 - 5.09: 52 5.09 - 6.79: 11 6.79 - 8.48: 6 Bond angle restraints: 19887 Sorted by residual: angle pdb=" N ILE A 963 " pdb=" CA ILE A 963 " pdb=" C ILE A 963 " ideal model delta sigma weight residual 113.53 108.98 4.55 9.80e-01 1.04e+00 2.15e+01 angle pdb=" C GLY A1190 " pdb=" N ILE A1191 " pdb=" CA ILE A1191 " ideal model delta sigma weight residual 122.13 130.61 -8.48 1.85e+00 2.92e-01 2.10e+01 angle pdb=" C PHE A 526 " pdb=" N SER A 527 " pdb=" CA SER A 527 " ideal model delta sigma weight residual 121.54 129.53 -7.99 1.91e+00 2.74e-01 1.75e+01 angle pdb=" C LEU A 112 " pdb=" N PHE A 113 " pdb=" CA PHE A 113 " ideal model delta sigma weight residual 121.54 128.23 -6.69 1.91e+00 2.74e-01 1.23e+01 angle pdb=" C ALA A 111 " pdb=" N LEU A 112 " pdb=" CA LEU A 112 " ideal model delta sigma weight residual 121.54 127.99 -6.45 1.91e+00 2.74e-01 1.14e+01 ... (remaining 19882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 7943 17.48 - 34.95: 747 34.95 - 52.43: 118 52.43 - 69.91: 14 69.91 - 87.39: 11 Dihedral angle restraints: 8833 sinusoidal: 3490 harmonic: 5343 Sorted by residual: dihedral pdb=" CA LEU A 112 " pdb=" C LEU A 112 " pdb=" N PHE A 113 " pdb=" CA PHE A 113 " ideal model delta harmonic sigma weight residual -180.00 -151.77 -28.23 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA GLY B 167 " pdb=" C GLY B 167 " pdb=" N GLN B 168 " pdb=" CA GLN B 168 " ideal model delta harmonic sigma weight residual 180.00 162.66 17.34 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA HIS C 166 " pdb=" C HIS C 166 " pdb=" N GLY C 167 " pdb=" CA GLY C 167 " ideal model delta harmonic sigma weight residual 180.00 -163.50 -16.50 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 8830 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1769 0.045 - 0.091: 417 0.091 - 0.136: 95 0.136 - 0.182: 6 0.182 - 0.227: 3 Chirality restraints: 2290 Sorted by residual: chirality pdb=" CA VAL A 596 " pdb=" N VAL A 596 " pdb=" C VAL A 596 " pdb=" CB VAL A 596 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE A 482 " pdb=" CA ILE A 482 " pdb=" CG1 ILE A 482 " pdb=" CG2 ILE A 482 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA MET A 593 " pdb=" N MET A 593 " pdb=" C MET A 593 " pdb=" CB MET A 593 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.43e-01 ... (remaining 2287 not shown) Planarity restraints: 2542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 467 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO A 468 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 468 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 468 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1085 " 0.010 2.00e-02 2.50e+03 1.38e-02 4.76e+00 pdb=" CG TRP A1085 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A1085 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A1085 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A1085 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A1085 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A1085 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1085 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1085 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A1085 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 93 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO A 94 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 94 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 94 " -0.024 5.00e-02 4.00e+02 ... (remaining 2539 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2920 2.78 - 3.31: 13372 3.31 - 3.84: 22238 3.84 - 4.37: 25441 4.37 - 4.90: 46144 Nonbonded interactions: 110115 Sorted by model distance: nonbonded pdb=" O GLU A 643 " pdb=" OG1 THR B 148 " model vdw 2.248 3.040 nonbonded pdb=" O LEU A 112 " pdb=" N LEU A 114 " model vdw 2.300 3.120 nonbonded pdb=" OE2 GLU A 643 " pdb=" OG1 THR C 153 " model vdw 2.345 3.040 nonbonded pdb=" NE2 HIS A1006 " pdb=" OH TYR A1374 " model vdw 2.351 3.120 nonbonded pdb=" O LEU A1256 " pdb=" OG1 THR A1259 " model vdw 2.355 3.040 ... (remaining 110110 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 'D' and (resid 82 through 118 or (resid 119 and (name N or name CA or nam \ e C or name O or name CB )) or resid 120 through 146)) selection = (chain 'E' and (resid 82 through 132 or (resid 133 and (name N or name CA or nam \ e C or name O or name CB )) or resid 134 through 146)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.160 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:8.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 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 : 0.003 0.036 14634 Z= 0.135 Angle : 0.553 8.483 19888 Z= 0.293 Chirality : 0.040 0.227 2290 Planarity : 0.004 0.058 2542 Dihedral : 13.651 87.386 5363 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.31 % Favored : 93.24 % Rotamer: Outliers : 0.13 % Allowed : 0.38 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.21), residues: 1802 helix: 2.08 (0.18), residues: 962 sheet: 1.75 (0.56), residues: 87 loop : -1.51 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 546 TYR 0.016 0.001 TYR A 413 PHE 0.024 0.001 PHE A 319 TRP 0.035 0.001 TRP A1085 HIS 0.004 0.001 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00260 (14630) covalent geometry : angle 0.55279 (19887) hydrogen bonds : bond 0.14448 ( 714) hydrogen bonds : angle 4.29387 ( 2044) metal coordination : bond 0.01217 ( 4) metal coordination : angle 2.72373 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 0.558 Fit side-chains REVERT: A 595 VAL cc_start: 0.6174 (OUTLIER) cc_final: 0.5461 (t) REVERT: A 709 GLU cc_start: 0.7206 (tt0) cc_final: 0.6861 (tp30) REVERT: A 968 ASN cc_start: 0.6785 (t0) cc_final: 0.5825 (p0) REVERT: A 997 LYS cc_start: 0.6807 (ptmt) cc_final: 0.6465 (pttt) REVERT: C 138 MET cc_start: 0.6973 (mmm) cc_final: 0.6749 (mmm) outliers start: 1 outliers final: 0 residues processed: 228 average time/residue: 0.6686 time to fit residues: 165.1282 Evaluate side-chains 183 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.0770 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 ASN A 509 HIS A 608 GLN A 808 ASN A 814 GLN A1179 ASN A1342 ASN A1377 ASN B 202 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.167014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.107402 restraints weight = 36315.515| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 3.24 r_work: 0.2781 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14634 Z= 0.202 Angle : 0.654 10.509 19888 Z= 0.336 Chirality : 0.044 0.183 2290 Planarity : 0.005 0.063 2542 Dihedral : 4.363 39.346 1953 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.82 % Favored : 92.68 % Rotamer: Outliers : 2.39 % Allowed : 9.04 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.21), residues: 1802 helix: 1.65 (0.17), residues: 998 sheet: 1.63 (0.57), residues: 87 loop : -1.59 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 546 TYR 0.016 0.002 TYR A 35 PHE 0.041 0.002 PHE A 319 TRP 0.022 0.002 TRP A1085 HIS 0.007 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00501 (14630) covalent geometry : angle 0.65350 (19887) hydrogen bonds : bond 0.06152 ( 714) hydrogen bonds : angle 3.62026 ( 2044) metal coordination : bond 0.02190 ( 4) metal coordination : angle 3.79125 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 192 time to evaluate : 0.462 Fit side-chains REVERT: A 74 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7782 (m-30) REVERT: A 136 ILE cc_start: 0.8055 (mt) cc_final: 0.7855 (mm) REVERT: A 163 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7431 (ttp80) REVERT: A 323 MET cc_start: 0.8577 (mmp) cc_final: 0.8371 (mmm) REVERT: A 523 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.6894 (tm-30) REVERT: A 524 GLU cc_start: 0.8147 (tp30) cc_final: 0.7611 (tp30) REVERT: A 529 GLU cc_start: 0.7762 (tt0) cc_final: 0.7456 (mp0) REVERT: A 578 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6459 (tp30) REVERT: A 767 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7559 (m-30) REVERT: A 968 ASN cc_start: 0.6808 (t0) cc_final: 0.5836 (p0) REVERT: A 997 LYS cc_start: 0.7106 (ptmt) cc_final: 0.6762 (pttt) REVERT: A 1018 LYS cc_start: 0.7846 (ttmt) cc_final: 0.7408 (tttt) REVERT: A 1045 GLN cc_start: 0.8434 (tt0) cc_final: 0.8070 (tt0) REVERT: A 1076 LYS cc_start: 0.7960 (ttpp) cc_final: 0.7278 (pttp) REVERT: A 1217 ARG cc_start: 0.6601 (mtm110) cc_final: 0.6116 (mtm180) REVERT: A 1221 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6728 (pm20) REVERT: A 1376 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.5909 (pp20) REVERT: A 1377 ASN cc_start: 0.8097 (m110) cc_final: 0.7787 (m-40) REVERT: B 137 GLU cc_start: 0.8282 (tt0) cc_final: 0.7839 (tt0) REVERT: B 176 TYR cc_start: 0.8742 (m-80) cc_final: 0.8474 (m-80) REVERT: B 282 LYS cc_start: 0.7336 (OUTLIER) cc_final: 0.7134 (mttt) REVERT: C 138 MET cc_start: 0.6960 (mmm) cc_final: 0.6552 (mmm) REVERT: E 124 MET cc_start: 0.6828 (mmp) cc_final: 0.6058 (mtm) outliers start: 37 outliers final: 16 residues processed: 213 average time/residue: 0.6614 time to fit residues: 152.3667 Evaluate side-chains 208 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1135 MET Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1258 MET Chi-restraints excluded: chain A residue 1376 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain E residue 139 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 7 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 151 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 139 optimal weight: 0.0270 overall best weight: 1.0440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN A 692 ASN A1064 ASN A1342 ASN B 202 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.170367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.110521 restraints weight = 39184.744| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.53 r_work: 0.2807 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14634 Z= 0.131 Angle : 0.560 9.811 19888 Z= 0.291 Chirality : 0.040 0.139 2290 Planarity : 0.004 0.064 2542 Dihedral : 4.129 26.006 1952 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.09 % Favored : 93.46 % Rotamer: Outliers : 2.01 % Allowed : 11.55 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.21), residues: 1802 helix: 1.80 (0.17), residues: 999 sheet: 1.47 (0.57), residues: 87 loop : -1.51 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 546 TYR 0.012 0.001 TYR A 413 PHE 0.027 0.002 PHE A 319 TRP 0.009 0.001 TRP A 191 HIS 0.004 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00305 (14630) covalent geometry : angle 0.55913 (19887) hydrogen bonds : bond 0.04678 ( 714) hydrogen bonds : angle 3.44894 ( 2044) metal coordination : bond 0.01394 ( 4) metal coordination : angle 3.00951 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.356 Fit side-chains REVERT: A 74 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7886 (m-30) REVERT: A 136 ILE cc_start: 0.8216 (mt) cc_final: 0.7963 (mm) REVERT: A 445 ARG cc_start: 0.6964 (mtm110) cc_final: 0.6759 (mtm110) REVERT: A 523 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.6968 (tm-30) REVERT: A 524 GLU cc_start: 0.8144 (tp30) cc_final: 0.7633 (tp30) REVERT: A 529 GLU cc_start: 0.7787 (tt0) cc_final: 0.7480 (mp0) REVERT: A 767 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7653 (m-30) REVERT: A 968 ASN cc_start: 0.6789 (t0) cc_final: 0.5878 (p0) REVERT: A 997 LYS cc_start: 0.7125 (ptmt) cc_final: 0.6899 (pttt) REVERT: A 1018 LYS cc_start: 0.7914 (ttmt) cc_final: 0.7477 (tttt) REVERT: A 1045 GLN cc_start: 0.8501 (tt0) cc_final: 0.8193 (tt0) REVERT: A 1076 LYS cc_start: 0.7892 (ttpp) cc_final: 0.7199 (pttp) REVERT: A 1221 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6864 (pm20) REVERT: A 1376 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.5518 (pp20) REVERT: A 1377 ASN cc_start: 0.8035 (m110) cc_final: 0.7590 (m-40) REVERT: B 176 TYR cc_start: 0.8750 (m-80) cc_final: 0.8492 (m-80) REVERT: C 138 MET cc_start: 0.7025 (mmm) cc_final: 0.6638 (mmm) outliers start: 31 outliers final: 13 residues processed: 202 average time/residue: 0.6980 time to fit residues: 152.1250 Evaluate side-chains 199 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1135 MET Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1376 GLU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain E residue 139 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 81 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 122 optimal weight: 0.0870 chunk 62 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 ASN A1342 ASN B 202 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.167335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.106737 restraints weight = 35978.891| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.43 r_work: 0.2836 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14634 Z= 0.116 Angle : 0.544 9.116 19888 Z= 0.281 Chirality : 0.039 0.147 2290 Planarity : 0.004 0.061 2542 Dihedral : 4.020 25.812 1952 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.42 % Favored : 93.13 % Rotamer: Outliers : 1.95 % Allowed : 12.93 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.21), residues: 1802 helix: 1.94 (0.18), residues: 994 sheet: 0.79 (0.56), residues: 95 loop : -1.38 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 110 TYR 0.014 0.001 TYR A 413 PHE 0.018 0.001 PHE A 319 TRP 0.008 0.001 TRP A1019 HIS 0.005 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00259 (14630) covalent geometry : angle 0.54379 (19887) hydrogen bonds : bond 0.04117 ( 714) hydrogen bonds : angle 3.35844 ( 2044) metal coordination : bond 0.01305 ( 4) metal coordination : angle 2.82643 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 0.537 Fit side-chains REVERT: A 108 MET cc_start: 0.8759 (mmm) cc_final: 0.8362 (mtm) REVERT: A 163 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7609 (ttp80) REVERT: A 491 ARG cc_start: 0.8464 (tpt170) cc_final: 0.8087 (tpt90) REVERT: A 523 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.6967 (tm-30) REVERT: A 524 GLU cc_start: 0.8128 (tp30) cc_final: 0.7602 (tp30) REVERT: A 529 GLU cc_start: 0.7852 (tt0) cc_final: 0.7467 (mp0) REVERT: A 767 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7669 (m-30) REVERT: A 968 ASN cc_start: 0.7021 (t0) cc_final: 0.5957 (p0) REVERT: A 997 LYS cc_start: 0.7099 (ptmt) cc_final: 0.6823 (pttt) REVERT: A 1018 LYS cc_start: 0.7997 (ttmt) cc_final: 0.7591 (tttt) REVERT: A 1045 GLN cc_start: 0.8543 (tt0) cc_final: 0.8243 (tt0) REVERT: A 1076 LYS cc_start: 0.7818 (ttpp) cc_final: 0.7175 (ptmm) REVERT: A 1221 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6878 (pm20) REVERT: A 1376 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.5402 (pp20) REVERT: B 137 GLU cc_start: 0.8255 (tt0) cc_final: 0.7921 (tt0) REVERT: B 176 TYR cc_start: 0.8775 (m-80) cc_final: 0.8568 (m-80) REVERT: C 124 MET cc_start: 0.6247 (mmp) cc_final: 0.5598 (mtp) REVERT: C 138 MET cc_start: 0.7040 (mmm) cc_final: 0.6518 (mmm) REVERT: E 124 MET cc_start: 0.6808 (mmp) cc_final: 0.6106 (mtm) outliers start: 30 outliers final: 16 residues processed: 214 average time/residue: 0.7068 time to fit residues: 163.5361 Evaluate side-chains 204 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 1135 MET Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1376 GLU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain E residue 139 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 30.0000 chunk 24 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 0.0370 chunk 170 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 overall best weight: 1.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 ASN A1342 ASN E 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.164960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.103937 restraints weight = 40852.800| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.82 r_work: 0.2766 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14634 Z= 0.155 Angle : 0.584 9.472 19888 Z= 0.301 Chirality : 0.041 0.152 2290 Planarity : 0.004 0.063 2542 Dihedral : 4.165 26.242 1952 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.54 % Favored : 93.02 % Rotamer: Outliers : 2.64 % Allowed : 12.87 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.21), residues: 1802 helix: 1.87 (0.17), residues: 992 sheet: 1.44 (0.57), residues: 87 loop : -1.50 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 110 TYR 0.016 0.002 TYR A 419 PHE 0.026 0.002 PHE A 319 TRP 0.009 0.001 TRP A1118 HIS 0.005 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00376 (14630) covalent geometry : angle 0.58363 (19887) hydrogen bonds : bond 0.05018 ( 714) hydrogen bonds : angle 3.42344 ( 2044) metal coordination : bond 0.01398 ( 4) metal coordination : angle 2.48358 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 185 time to evaluate : 0.543 Fit side-chains REVERT: A 163 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7661 (ttp80) REVERT: A 445 ARG cc_start: 0.6911 (mtm110) cc_final: 0.6700 (mtm110) REVERT: A 491 ARG cc_start: 0.8479 (tpt170) cc_final: 0.8085 (tpt90) REVERT: A 523 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.6995 (tm-30) REVERT: A 524 GLU cc_start: 0.8241 (tp30) cc_final: 0.7671 (tp30) REVERT: A 529 GLU cc_start: 0.7859 (tt0) cc_final: 0.7439 (mp0) REVERT: A 578 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6618 (tp30) REVERT: A 767 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7721 (m-30) REVERT: A 968 ASN cc_start: 0.7123 (t0) cc_final: 0.6064 (p0) REVERT: A 997 LYS cc_start: 0.7126 (ptmt) cc_final: 0.6885 (pttt) REVERT: A 1015 MET cc_start: 0.7515 (tpp) cc_final: 0.7171 (mmm) REVERT: A 1045 GLN cc_start: 0.8549 (tt0) cc_final: 0.8251 (tt0) REVERT: A 1076 LYS cc_start: 0.7838 (ttpp) cc_final: 0.7269 (ptmm) REVERT: A 1221 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6888 (pm20) REVERT: A 1376 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.5517 (pp20) REVERT: B 176 TYR cc_start: 0.8860 (m-80) cc_final: 0.8591 (m-80) REVERT: C 138 MET cc_start: 0.7150 (mmm) cc_final: 0.6694 (mmm) REVERT: E 124 MET cc_start: 0.6859 (mmp) cc_final: 0.6181 (mtm) outliers start: 41 outliers final: 23 residues processed: 209 average time/residue: 0.7126 time to fit residues: 161.3369 Evaluate side-chains 211 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1135 MET Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1317 GLN Chi-restraints excluded: chain A residue 1376 GLU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain E residue 139 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 155 optimal weight: 10.0000 chunk 99 optimal weight: 0.0970 chunk 43 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 4 optimal weight: 0.1980 chunk 123 optimal weight: 7.9990 chunk 92 optimal weight: 0.2980 chunk 56 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 ASN A 814 GLN A1342 ASN B 202 ASN E 99 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.170047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.109235 restraints weight = 45316.070| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.94 r_work: 0.2859 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14634 Z= 0.102 Angle : 0.528 8.707 19888 Z= 0.272 Chirality : 0.039 0.149 2290 Planarity : 0.004 0.061 2542 Dihedral : 3.953 25.922 1952 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.81 % Favored : 93.74 % Rotamer: Outliers : 1.95 % Allowed : 14.38 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.21), residues: 1802 helix: 2.02 (0.18), residues: 990 sheet: 0.81 (0.56), residues: 95 loop : -1.35 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 225 TYR 0.013 0.001 TYR A 419 PHE 0.017 0.001 PHE A 793 TRP 0.009 0.001 TRP A1019 HIS 0.004 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00215 (14630) covalent geometry : angle 0.52806 (19887) hydrogen bonds : bond 0.03549 ( 714) hydrogen bonds : angle 3.30388 ( 2044) metal coordination : bond 0.01157 ( 4) metal coordination : angle 2.84590 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 0.534 Fit side-chains REVERT: A 108 MET cc_start: 0.8817 (mmm) cc_final: 0.8390 (mtm) REVERT: A 163 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7435 (ttp80) REVERT: A 491 ARG cc_start: 0.8493 (tpt170) cc_final: 0.8112 (tpt90) REVERT: A 529 GLU cc_start: 0.7836 (tt0) cc_final: 0.7416 (mp0) REVERT: A 767 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7695 (m-30) REVERT: A 968 ASN cc_start: 0.6994 (t0) cc_final: 0.5992 (p0) REVERT: A 997 LYS cc_start: 0.7069 (ptmt) cc_final: 0.6757 (pttt) REVERT: A 1015 MET cc_start: 0.7542 (tpp) cc_final: 0.7238 (mmm) REVERT: A 1045 GLN cc_start: 0.8521 (tt0) cc_final: 0.8204 (tt0) REVERT: A 1076 LYS cc_start: 0.7774 (ttpp) cc_final: 0.7179 (ptmm) REVERT: A 1221 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6972 (pm20) REVERT: A 1376 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.5311 (pp20) REVERT: B 176 TYR cc_start: 0.8804 (m-80) cc_final: 0.8594 (m-80) REVERT: B 283 ARG cc_start: 0.7113 (ttp-110) cc_final: 0.6836 (ttp-110) REVERT: C 124 MET cc_start: 0.6252 (mmp) cc_final: 0.5596 (mtp) REVERT: C 138 MET cc_start: 0.7013 (mmm) cc_final: 0.6464 (mmm) REVERT: E 124 MET cc_start: 0.6729 (mmp) cc_final: 0.6182 (mtm) REVERT: E 144 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7253 (pp) outliers start: 30 outliers final: 15 residues processed: 213 average time/residue: 0.6746 time to fit residues: 155.8300 Evaluate side-chains 206 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 1135 MET Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1317 GLN Chi-restraints excluded: chain A residue 1376 GLU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain E residue 144 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 73 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 HIS A1342 ASN B 202 ASN E 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.168930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.108257 restraints weight = 46772.716| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 4.00 r_work: 0.2844 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14634 Z= 0.120 Angle : 0.544 8.498 19888 Z= 0.281 Chirality : 0.039 0.145 2290 Planarity : 0.004 0.059 2542 Dihedral : 3.958 25.990 1952 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.75 % Favored : 93.80 % Rotamer: Outliers : 1.95 % Allowed : 15.00 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.21), residues: 1802 helix: 2.04 (0.18), residues: 984 sheet: 0.83 (0.56), residues: 95 loop : -1.37 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 110 TYR 0.012 0.001 TYR A 419 PHE 0.017 0.001 PHE A 548 TRP 0.008 0.001 TRP A 191 HIS 0.005 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00275 (14630) covalent geometry : angle 0.54406 (19887) hydrogen bonds : bond 0.03962 ( 714) hydrogen bonds : angle 3.30302 ( 2044) metal coordination : bond 0.01243 ( 4) metal coordination : angle 2.62870 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: A 163 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7491 (ttp80) REVERT: A 491 ARG cc_start: 0.8511 (tpt170) cc_final: 0.8130 (tpt90) REVERT: A 529 GLU cc_start: 0.7849 (tt0) cc_final: 0.7430 (mp0) REVERT: A 767 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7719 (m-30) REVERT: A 968 ASN cc_start: 0.6987 (t0) cc_final: 0.6003 (p0) REVERT: A 1018 LYS cc_start: 0.7887 (ttmt) cc_final: 0.7468 (tttt) REVERT: A 1045 GLN cc_start: 0.8509 (tt0) cc_final: 0.8201 (tt0) REVERT: A 1076 LYS cc_start: 0.7776 (ttpp) cc_final: 0.7200 (ptmm) REVERT: A 1221 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6932 (pm20) REVERT: B 137 GLU cc_start: 0.8423 (tt0) cc_final: 0.8062 (tt0) REVERT: B 176 TYR cc_start: 0.8809 (m-80) cc_final: 0.8560 (m-80) REVERT: C 124 MET cc_start: 0.6340 (mmp) cc_final: 0.5593 (mtp) REVERT: C 138 MET cc_start: 0.6992 (mmm) cc_final: 0.6490 (mmm) REVERT: E 144 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7291 (pp) outliers start: 30 outliers final: 21 residues processed: 212 average time/residue: 0.7302 time to fit residues: 167.5885 Evaluate side-chains 208 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1135 MET Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1317 GLN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain E residue 144 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 6 optimal weight: 0.0040 chunk 116 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 144 optimal weight: 0.5980 chunk 137 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 HIS A1342 ASN E 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.168286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.107230 restraints weight = 41044.828| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.80 r_work: 0.2865 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14634 Z= 0.110 Angle : 0.544 9.074 19888 Z= 0.280 Chirality : 0.039 0.145 2290 Planarity : 0.004 0.059 2542 Dihedral : 3.917 25.923 1952 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.92 % Favored : 93.63 % Rotamer: Outliers : 2.13 % Allowed : 15.38 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.21), residues: 1802 helix: 2.08 (0.18), residues: 984 sheet: 0.83 (0.56), residues: 95 loop : -1.34 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 445 TYR 0.011 0.001 TYR A 419 PHE 0.019 0.001 PHE A 793 TRP 0.008 0.001 TRP A1019 HIS 0.005 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00244 (14630) covalent geometry : angle 0.54360 (19887) hydrogen bonds : bond 0.03689 ( 714) hydrogen bonds : angle 3.27188 ( 2044) metal coordination : bond 0.01161 ( 4) metal coordination : angle 2.55391 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 191 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 108 MET cc_start: 0.8894 (mmm) cc_final: 0.8354 (mtm) REVERT: A 163 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7353 (ttp80) REVERT: A 166 ARG cc_start: 0.7126 (ptt-90) cc_final: 0.6221 (ptp-170) REVERT: A 491 ARG cc_start: 0.8503 (tpt170) cc_final: 0.8147 (tpt90) REVERT: A 529 GLU cc_start: 0.7886 (tt0) cc_final: 0.7482 (mp0) REVERT: A 767 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7768 (m-30) REVERT: A 968 ASN cc_start: 0.7050 (t0) cc_final: 0.6084 (p0) REVERT: A 1045 GLN cc_start: 0.8513 (tt0) cc_final: 0.8227 (tt0) REVERT: A 1076 LYS cc_start: 0.7794 (ttpp) cc_final: 0.7221 (ptmm) REVERT: A 1221 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6985 (pm20) REVERT: B 176 TYR cc_start: 0.8827 (m-80) cc_final: 0.8579 (m-80) REVERT: B 283 ARG cc_start: 0.7136 (ttp-110) cc_final: 0.6915 (ttp-110) REVERT: C 124 MET cc_start: 0.6272 (mmp) cc_final: 0.5486 (mtp) REVERT: C 138 MET cc_start: 0.6975 (mmm) cc_final: 0.6544 (mmm) REVERT: E 124 MET cc_start: 0.6807 (mmp) cc_final: 0.6049 (mtm) REVERT: E 144 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7342 (pp) outliers start: 33 outliers final: 20 residues processed: 212 average time/residue: 0.6926 time to fit residues: 159.0571 Evaluate side-chains 215 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 191 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1135 MET Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1317 GLN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain E residue 144 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 139 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN A1342 ASN E 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.166267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.103850 restraints weight = 48444.285| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 4.00 r_work: 0.2753 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14634 Z= 0.164 Angle : 0.601 8.748 19888 Z= 0.309 Chirality : 0.042 0.150 2290 Planarity : 0.004 0.059 2542 Dihedral : 4.148 26.429 1952 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.59 % Favored : 92.91 % Rotamer: Outliers : 2.26 % Allowed : 15.32 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.21), residues: 1802 helix: 1.92 (0.18), residues: 986 sheet: 1.43 (0.56), residues: 87 loop : -1.47 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 445 TYR 0.016 0.002 TYR A 117 PHE 0.023 0.002 PHE A 548 TRP 0.008 0.001 TRP A 191 HIS 0.005 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00404 (14630) covalent geometry : angle 0.60126 (19887) hydrogen bonds : bond 0.05040 ( 714) hydrogen bonds : angle 3.39375 ( 2044) metal coordination : bond 0.01360 ( 4) metal coordination : angle 2.26723 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 163 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7684 (ttp80) REVERT: A 491 ARG cc_start: 0.8501 (tpt170) cc_final: 0.8104 (tpt90) REVERT: A 529 GLU cc_start: 0.7888 (tt0) cc_final: 0.7429 (mp0) REVERT: A 767 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7721 (m-30) REVERT: A 968 ASN cc_start: 0.7040 (t0) cc_final: 0.6056 (p0) REVERT: A 1045 GLN cc_start: 0.8548 (tt0) cc_final: 0.8241 (tt0) REVERT: A 1076 LYS cc_start: 0.7796 (ttpp) cc_final: 0.7213 (ptmm) REVERT: A 1221 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6953 (pm20) REVERT: B 138 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7733 (ttp) REVERT: B 176 TYR cc_start: 0.8944 (m-80) cc_final: 0.8663 (m-80) REVERT: B 283 ARG cc_start: 0.7160 (ttp-110) cc_final: 0.6911 (ttp-110) REVERT: C 124 MET cc_start: 0.6301 (mmp) cc_final: 0.5511 (mtp) REVERT: C 138 MET cc_start: 0.7083 (mmm) cc_final: 0.6580 (mmm) REVERT: E 124 MET cc_start: 0.6844 (mmp) cc_final: 0.6096 (mtm) REVERT: E 144 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7290 (pp) outliers start: 35 outliers final: 20 residues processed: 212 average time/residue: 0.6929 time to fit residues: 159.0241 Evaluate side-chains 212 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1135 MET Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain E residue 144 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 170 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 65 optimal weight: 0.0980 chunk 111 optimal weight: 0.0020 chunk 13 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 160 optimal weight: 10.0000 chunk 162 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 153 optimal weight: 0.0670 chunk 31 optimal weight: 2.9990 overall best weight: 0.8330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 ASN A 509 HIS A 692 ASN A 814 GLN A1342 ASN B 202 ASN E 99 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.168222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.107739 restraints weight = 50871.999| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 4.05 r_work: 0.2770 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14634 Z= 0.122 Angle : 0.562 8.832 19888 Z= 0.291 Chirality : 0.040 0.147 2290 Planarity : 0.004 0.060 2542 Dihedral : 4.048 26.243 1952 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.98 % Favored : 93.58 % Rotamer: Outliers : 2.13 % Allowed : 15.57 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.21), residues: 1802 helix: 2.00 (0.18), residues: 986 sheet: 0.79 (0.55), residues: 95 loop : -1.38 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 445 TYR 0.012 0.001 TYR A 153 PHE 0.021 0.001 PHE A 793 TRP 0.009 0.001 TRP A1118 HIS 0.005 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00278 (14630) covalent geometry : angle 0.56142 (19887) hydrogen bonds : bond 0.04099 ( 714) hydrogen bonds : angle 3.31403 ( 2044) metal coordination : bond 0.01285 ( 4) metal coordination : angle 2.68857 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.544 Fit side-chains REVERT: A 163 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7349 (ttp80) REVERT: A 491 ARG cc_start: 0.8533 (tpt170) cc_final: 0.8134 (tpt90) REVERT: A 529 GLU cc_start: 0.7834 (tt0) cc_final: 0.7363 (mp0) REVERT: A 767 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7645 (m-30) REVERT: A 968 ASN cc_start: 0.7060 (t0) cc_final: 0.6112 (p0) REVERT: A 1015 MET cc_start: 0.7419 (tpp) cc_final: 0.7093 (mmm) REVERT: A 1045 GLN cc_start: 0.8435 (tt0) cc_final: 0.8140 (tt0) REVERT: A 1076 LYS cc_start: 0.7727 (ttpp) cc_final: 0.7141 (ptmm) REVERT: B 138 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7673 (ttp) REVERT: B 176 TYR cc_start: 0.8890 (m-80) cc_final: 0.8638 (m-80) REVERT: B 283 ARG cc_start: 0.7195 (ttp-110) cc_final: 0.6929 (ttp-110) REVERT: C 124 MET cc_start: 0.6240 (mmp) cc_final: 0.5478 (mtp) REVERT: C 138 MET cc_start: 0.6919 (mmm) cc_final: 0.6447 (mmm) REVERT: E 124 MET cc_start: 0.6762 (mmp) cc_final: 0.6033 (mtm) REVERT: E 144 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7255 (pp) outliers start: 33 outliers final: 19 residues processed: 210 average time/residue: 0.7520 time to fit residues: 170.3425 Evaluate side-chains 207 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1135 MET Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain E residue 144 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 138 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 80 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 132 optimal weight: 10.0000 chunk 137 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 7 optimal weight: 0.0020 chunk 123 optimal weight: 2.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 ASN A 509 HIS A 692 ASN A1342 ASN B 202 ASN E 99 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.167906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.107108 restraints weight = 41503.166| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.90 r_work: 0.2821 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14634 Z= 0.120 Angle : 0.563 8.546 19888 Z= 0.292 Chirality : 0.039 0.142 2290 Planarity : 0.004 0.059 2542 Dihedral : 4.002 26.042 1952 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.09 % Favored : 93.46 % Rotamer: Outliers : 1.82 % Allowed : 15.88 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.21), residues: 1802 helix: 2.07 (0.18), residues: 985 sheet: 0.82 (0.55), residues: 95 loop : -1.35 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 445 TYR 0.012 0.001 TYR A 419 PHE 0.015 0.001 PHE A 319 TRP 0.009 0.001 TRP B 324 HIS 0.005 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00259 (14630) covalent geometry : angle 0.56300 (19887) hydrogen bonds : bond 0.03867 ( 714) hydrogen bonds : angle 3.31064 ( 2044) metal coordination : bond 0.01222 ( 4) metal coordination : angle 2.62055 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6103.38 seconds wall clock time: 104 minutes 20.50 seconds (6260.50 seconds total)