Starting phenix.real_space_refine on Mon Sep 14 10:01:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d42_27172/09_2026/8d42_27172_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d42_27172/09_2026/8d42_27172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d42_27172/09_2026/8d42_27172_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d42_27172/09_2026/8d42_27172_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d42_27172/09_2026/8d42_27172.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d42_27172/09_2026/8d42_27172.map" } resolution = 2.91 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= -0.121 sd= 0.790 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: 7 Type Number sf(0) Gaussians Ca 3 9.91 5 P 45 5.49 5 S 82 5.16 5 C 9546 2.51 5 N 2665 2.21 5 O 2852 1.98 5 H 14610 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29803 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 15393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 15393 Classifications: {'peptide': 974} Link IDs: {'PTRANS': 65, 'TRANS': 908} Chain breaks: 6 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 6613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 6613 Classifications: {'peptide': 411} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 392} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 6431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 6431 Classifications: {'peptide': 399} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 666 Classifications: {'DNA': 21} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 20} Chain: "T" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 669 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 31 Unusual residues: {' CA': 3, 'DCP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.85, per 1000 atoms: 0.16 Number of scatterers: 29803 At special positions: 0 Unit cell: (115.6, 105.4, 145.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 3 19.99 S 82 16.00 P 45 15.00 O 2852 8.00 N 2665 7.00 C 9546 6.00 H 14610 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A1077 " distance=2.04 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: 3.75 Conformation dependent library (CDL) restraints added in 867.8 milliseconds 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3322 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 13 sheets defined 48.3% alpha, 13.7% beta 18 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 5.01 Creating SS restraints... Processing helix chain 'A' and resid 80 through 88 removed outlier: 3.633A pdb=" N GLN A 86 " --> pdb=" O GLY A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 111 Processing helix chain 'A' and resid 134 through 159 Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.661A pdb=" N VAL A 229 " --> pdb=" O SER A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 277 through 278 No H-bonds generated for 'chain 'A' and resid 277 through 278' Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.751A pdb=" N TYR A 282 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 283 " --> pdb=" O GLU A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 279 through 283' Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 305 through 316 Processing helix chain 'A' and resid 347 through 351 removed outlier: 3.530A pdb=" N ILE A 350 " --> pdb=" O TRP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 388 through 418 Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 431 removed outlier: 4.419A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 425 " --> pdb=" O PRO A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 472 removed outlier: 4.102A pdb=" N GLN A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 482 removed outlier: 5.268A pdb=" N GLY A 476 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N TYR A 479 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 554 removed outlier: 3.562A pdb=" N GLY A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 576 removed outlier: 3.919A pdb=" N LEU A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 604 removed outlier: 4.011A pdb=" N LYS A 601 " --> pdb=" O ARG A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 661 removed outlier: 3.725A pdb=" N ARG A 650 " --> pdb=" O VAL A 646 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE A 652 " --> pdb=" O PRO A 648 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLU A 653 " --> pdb=" O TYR A 649 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER A 654 " --> pdb=" O ARG A 650 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU A 655 " --> pdb=" O ALA A 651 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 771 Processing helix chain 'A' and resid 787 through 810 removed outlier: 4.767A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 821 Processing helix chain 'A' and resid 822 through 827 Processing helix chain 'A' and resid 871 through 878 removed outlier: 3.819A pdb=" N LEU A 874 " --> pdb=" O GLY A 871 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LYS A 875 " --> pdb=" O SER A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 914 through 923 Processing helix chain 'A' and resid 930 through 940 Processing helix chain 'A' and resid 942 through 955 Processing helix chain 'A' and resid 958 through 970 removed outlier: 3.731A pdb=" N ASN A 970 " --> pdb=" O LEU A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 990 removed outlier: 3.985A pdb=" N GLU A 980 " --> pdb=" O GLN A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1067 Processing helix chain 'A' and resid 1080 through 1083 Processing helix chain 'A' and resid 1084 through 1089 Processing helix chain 'A' and resid 1092 through 1123 removed outlier: 3.686A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1167 Processing helix chain 'A' and resid 1205 through 1210 Processing helix chain 'A' and resid 1219 through 1228 Processing helix chain 'B' and resid 65 through 76 Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 119 Processing helix chain 'B' and resid 151 through 153 No H-bonds generated for 'chain 'B' and resid 151 through 153' Processing helix chain 'B' and resid 165 through 178 removed outlier: 4.195A pdb=" N ALA B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLU B 172 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER B 178 " --> pdb=" O VAL B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 197 removed outlier: 3.547A pdb=" N ALA B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASN B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 201 Processing helix chain 'B' and resid 247 through 266 removed outlier: 3.941A pdb=" N PHE B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 319 through 323 Processing helix chain 'B' and resid 342 through 354 removed outlier: 3.508A pdb=" N PHE B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 391 through 409 Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 424 through 435 removed outlier: 3.541A pdb=" N LEU B 428 " --> pdb=" O SER B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 451 Processing helix chain 'B' and resid 468 through 485 removed outlier: 4.626A pdb=" N LYS B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ASP B 473 " --> pdb=" O SER B 469 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 87 through 94 Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 151 through 156 removed outlier: 3.893A pdb=" N GLU C 155 " --> pdb=" O GLU C 151 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE C 156 " --> pdb=" O THR C 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 151 through 156' Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'C' and resid 163 through 166 removed outlier: 4.427A pdb=" N GLN C 166 " --> pdb=" O SER C 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 163 through 166' Processing helix chain 'C' and resid 167 through 178 removed outlier: 3.916A pdb=" N LEU C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU C 172 " --> pdb=" O VAL C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 192 removed outlier: 3.634A pdb=" N HIS C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 200 removed outlier: 3.870A pdb=" N ASP C 198 " --> pdb=" O VAL C 194 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU C 199 " --> pdb=" O ASN C 195 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL C 200 " --> pdb=" O CYS C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 266 removed outlier: 4.188A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 318 through 323 removed outlier: 3.716A pdb=" N LYS C 321 " --> pdb=" O ASN C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 353 Processing helix chain 'C' and resid 391 through 409 removed outlier: 4.484A pdb=" N GLN C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 444 through 451 removed outlier: 3.583A pdb=" N LEU C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 485 removed outlier: 4.323A pdb=" N LYS C 472 " --> pdb=" O ILE C 468 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASP C 473 " --> pdb=" O SER C 469 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 72 removed outlier: 3.804A pdb=" N ILE A 76 " --> pdb=" O ASN A 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 184 through 186 removed outlier: 3.721A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLU A 200 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ALA A 212 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASP A 198 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA A 214 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL A 196 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU A 195 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLN A 264 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU A 292 " --> pdb=" O GLN A 264 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 435 through 438 removed outlier: 4.826A pdb=" N TYR A 837 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 814 " --> pdb=" O ALA A 839 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 606 through 607 Processing sheet with id=AA5, first strand: chain 'A' and resid 1127 through 1133 removed outlier: 6.704A pdb=" N GLY A1127 " --> pdb=" O ARG A1142 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ARG A1142 " --> pdb=" O GLY A1127 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N PHE A1129 " --> pdb=" O LEU A1140 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LEU A1140 " --> pdb=" O PHE A1129 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A1186 " --> pdb=" O LEU A 886 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.292A pdb=" N PHE B 126 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N ILE B 211 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL B 335 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LYS B 297 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHE B 293 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU B 301 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 133 through 134 removed outlier: 3.614A pdb=" N LYS B 180 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 149 removed outlier: 3.611A pdb=" N ARG B 146 " --> pdb=" O VAL C 148 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AB1, first strand: chain 'B' and resid 413 through 415 removed outlier: 6.688A pdb=" N LYS B 382 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N VAL B 441 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA B 384 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N VAL B 443 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ASP B 386 " --> pdb=" O VAL B 443 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.090A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL C 335 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LYS C 297 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N PHE C 293 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU C 301 " --> pdb=" O LEU C 289 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AB4, first strand: chain 'C' and resid 413 through 414 removed outlier: 7.132A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) 656 hydrogen bonds defined for protein. 1839 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 7.54 Time building geometry restraints manager: 4.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14576 1.03 - 1.23: 66 1.23 - 1.42: 6671 1.42 - 1.62: 8825 1.62 - 1.81: 131 Bond restraints: 30269 Sorted by residual: bond pdb=" O5' DCP A1304 " pdb=" PA DCP A1304 " ideal model delta sigma weight residual 1.654 1.805 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" O3A DCP A1304 " pdb=" PA DCP A1304 " ideal model delta sigma weight residual 1.632 1.528 0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" O3B DCP A1304 " pdb=" PG DCP A1304 " ideal model delta sigma weight residual 1.746 1.651 0.095 2.00e-02 2.50e+03 2.23e+01 bond pdb=" C5' DCP A1304 " pdb=" O5' DCP A1304 " ideal model delta sigma weight residual 1.413 1.323 0.090 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C2 DCP A1304 " pdb=" N3 DCP A1304 " ideal model delta sigma weight residual 1.350 1.410 -0.060 2.00e-02 2.50e+03 8.95e+00 ... (remaining 30264 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.51: 54673 3.51 - 7.01: 49 7.01 - 10.52: 4 10.52 - 14.03: 1 14.03 - 17.53: 1 Bond angle restraints: 54728 Sorted by residual: angle pdb=" O1A DCP A1304 " pdb=" PA DCP A1304 " pdb=" O3A DCP A1304 " ideal model delta sigma weight residual 106.39 123.92 -17.53 3.00e+00 1.11e-01 3.42e+01 angle pdb=" N3 DT T 8 " pdb=" C4 DT T 8 " pdb=" O4 DT T 8 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.03e+01 angle pdb=" N3 DT T 23 " pdb=" C4 DT T 23 " pdb=" O4 DT T 23 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.03e+01 angle pdb=" N3 DT P 17 " pdb=" C4 DT P 17 " pdb=" O4 DT P 17 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT T 20 " pdb=" C4 DT T 20 " pdb=" O4 DT T 20 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 ... (remaining 54723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.74: 13600 34.74 - 69.48: 463 69.48 - 104.22: 8 104.22 - 138.95: 0 138.95 - 173.69: 1 Dihedral angle restraints: 14072 sinusoidal: 7909 harmonic: 6163 Sorted by residual: dihedral pdb=" CA LYS C 164 " pdb=" C LYS C 164 " pdb=" N GLU C 165 " pdb=" CA GLU C 165 " ideal model delta harmonic sigma weight residual -180.00 -159.27 -20.73 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA ASP B 159 " pdb=" C ASP B 159 " pdb=" N LYS B 160 " pdb=" CA LYS B 160 " ideal model delta harmonic sigma weight residual 180.00 159.37 20.63 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" C4' DG T 5 " pdb=" C3' DG T 5 " pdb=" O3' DG T 5 " pdb=" P DT T 6 " ideal model delta sinusoidal sigma weight residual -140.00 33.69 -173.69 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 14069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1638 0.033 - 0.066: 446 0.066 - 0.098: 108 0.098 - 0.131: 83 0.131 - 0.164: 31 Chirality restraints: 2306 Sorted by residual: chirality pdb=" C3' DG T 22 " pdb=" C4' DG T 22 " pdb=" O3' DG T 22 " pdb=" C2' DG T 22 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" C3' DC P 19 " pdb=" C4' DC P 19 " pdb=" O3' DC P 19 " pdb=" C2' DC P 19 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.30e-01 chirality pdb=" C3' DA P 23 " pdb=" C4' DA P 23 " pdb=" O3' DA P 23 " pdb=" C2' DA P 23 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.15e-01 ... (remaining 2303 not shown) Planarity restraints: 4303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 485 " 0.029 2.00e-02 2.50e+03 5.94e-02 3.53e+01 pdb=" C VAL C 485 " -0.103 2.00e-02 2.50e+03 pdb=" O VAL C 485 " 0.037 2.00e-02 2.50e+03 pdb=" OXT VAL C 485 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 448 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.39e+00 pdb=" C ALA A 448 " 0.027 2.00e-02 2.50e+03 pdb=" O ALA A 448 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN A 449 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 457 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C ARG A 457 " -0.025 2.00e-02 2.50e+03 pdb=" O ARG A 457 " 0.009 2.00e-02 2.50e+03 pdb=" N GLU A 458 " 0.008 2.00e-02 2.50e+03 ... (remaining 4300 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 989 2.16 - 2.77: 56145 2.77 - 3.38: 81540 3.38 - 3.99: 104571 3.99 - 4.60: 163799 Nonbonded interactions: 407044 Sorted by model distance: nonbonded pdb=" OE1 GLU A1144 " pdb=" H GLU A1144 " model vdw 1.552 2.450 nonbonded pdb=" H VAL A 201 " pdb=" O3' DT P 24 " model vdw 1.564 2.450 nonbonded pdb=" HH TYR A 150 " pdb=" O ARG A 288 " model vdw 1.587 2.450 nonbonded pdb=" OE1 GLU C 310 " pdb=" H GLU C 310 " model vdw 1.617 2.450 nonbonded pdb=" OE1 GLU A 231 " pdb=" H GLU A 231 " model vdw 1.623 2.450 ... (remaining 407039 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 'B' and ((resid 67 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3)) or resid 68 through 218 or (resid 219 and (name N or \ name CA or name C or name O or name CB or name H or name HA or name HB2 or name \ HB3)) or (resid 228 and (name N or name CA or name C or name O or name CB or nam \ e HA or name HB )) or resid 229 through 355 or (resid 368 and (name N or name CA \ or name C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 o \ r name NE2 or name HA or name HB2 or name HB3)) or resid 369 through 485)) selection = (chain 'C' and (resid 67 through 215 or (resid 216 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 217 through 355 or (resid 368 and (name N or name CA or name C o \ r name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 o \ r name HA or name HB2 or name HB3)) or resid 369 through 485)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.500 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: 0.190 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 34.340 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 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 : 0.004 0.151 15660 Z= 0.235 Angle : 0.570 17.533 21408 Z= 0.351 Chirality : 0.041 0.164 2306 Planarity : 0.004 0.059 2600 Dihedral : 14.552 173.693 5928 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.84 % Allowed : 5.81 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.21), residues: 1758 helix: 0.92 (0.21), residues: 713 sheet: 0.56 (0.31), residues: 258 loop : -0.20 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 257 TYR 0.008 0.001 TYR A 434 PHE 0.012 0.001 PHE C 403 TRP 0.007 0.001 TRP A 620 HIS 0.003 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.24 (15659) covalent geometry : angle 0.56979 / 0.35 (21406) SS BOND : bond 0.00432 / 0.23 ( 1) SS BOND : angle 0.56495 / 0.32 ( 2) hydrogen bonds : bond 0.14215 / 9.60 ( 703) hydrogen bonds : angle 6.63000 / 4.62 ( 1933) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 990 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Evaluate side-chains 448 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 435 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 ASN cc_start: 0.8163 (t0) cc_final: 0.7824 (t0) REVERT: A 361 ARG cc_start: 0.7615 (tmt-80) cc_final: 0.7139 (tpm170) REVERT: A 610 PHE cc_start: 0.7513 (m-80) cc_final: 0.7262 (m-80) REVERT: A 743 ASP cc_start: 0.7132 (p0) cc_final: 0.6831 (p0) REVERT: A 793 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8051 (mm-30) REVERT: A 797 MET cc_start: 0.8071 (mtt) cc_final: 0.7760 (mtp) REVERT: A 994 TRP cc_start: 0.4383 (m-90) cc_final: 0.3987 (m-10) REVERT: A 1138 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8083 (mmt-90) REVERT: A 1192 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7514 (mm-30) REVERT: B 74 GLN cc_start: 0.7915 (tm-30) cc_final: 0.7522 (pt0) REVERT: B 249 ASN cc_start: 0.8076 (m-40) cc_final: 0.7773 (t0) REVERT: C 107 ARG cc_start: 0.7917 (mtm110) cc_final: 0.7414 (mtm110) REVERT: C 129 ASP cc_start: 0.8193 (t70) cc_final: 0.7963 (t0) outliers start: 13 outliers final: 5 residues processed: 443 average time/residue: 1.0246 time to fit residues: 515.3558 Evaluate side-chains 396 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 390 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 419 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN A 264 GLN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 HIS A 843 GLN A1202 ASN B 124 GLN B 192 HIS B 250 GLN B 258 HIS B 292 ASN B 339 ASN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.132989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.121508 restraints weight = 81858.748| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.16 r_work: 0.3574 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15660 Z= 0.231 Angle : 0.611 7.320 21408 Z= 0.336 Chirality : 0.042 0.252 2306 Planarity : 0.005 0.098 2600 Dihedral : 14.688 168.127 2434 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.17 % Allowed : 14.41 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.41 (0.20), residues: 1758 helix: 1.13 (0.20), residues: 720 sheet: 0.34 (0.31), residues: 251 loop : -0.50 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 852 TYR 0.016 0.002 TYR A 656 PHE 0.014 0.002 PHE A1092 TRP 0.010 0.002 TRP B 262 HIS 0.006 0.001 HIS C 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.23 (15659) covalent geometry : angle 0.61053 / 0.34 (21406) SS BOND : bond 0.00870 / 0.46 ( 1) SS BOND : angle 0.96764 / 0.57 ( 2) hydrogen bonds : bond 0.05611 / 3.86 ( 703) hydrogen bonds : angle 5.29669 / 3.69 ( 1933) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 990 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Evaluate side-chains 451 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 402 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 ASN cc_start: 0.8329 (t0) cc_final: 0.7791 (t0) REVERT: A 297 MET cc_start: 0.8249 (mmm) cc_final: 0.8037 (ttm) REVERT: A 443 ARG cc_start: 0.8174 (mtp85) cc_final: 0.7943 (ttp-110) REVERT: A 779 LEU cc_start: 0.6295 (OUTLIER) cc_final: 0.6016 (tt) REVERT: A 793 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8139 (mp0) REVERT: A 797 MET cc_start: 0.8312 (mtt) cc_final: 0.8003 (mtp) REVERT: A 1091 GLU cc_start: 0.7181 (tt0) cc_final: 0.6962 (tt0) REVERT: A 1138 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7922 (mmt90) REVERT: A 1192 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7590 (mm-30) REVERT: A 1226 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8601 (mt) REVERT: B 74 GLN cc_start: 0.8033 (tm-30) cc_final: 0.7552 (pt0) REVERT: B 259 ARG cc_start: 0.8811 (mmm160) cc_final: 0.8488 (mmp-170) REVERT: C 107 ARG cc_start: 0.8365 (mtm110) cc_final: 0.7933 (mtm110) REVERT: C 129 ASP cc_start: 0.8412 (t70) cc_final: 0.8153 (t0) REVERT: C 146 ARG cc_start: 0.6591 (mtp180) cc_final: 0.6033 (mtt90) REVERT: C 201 ASN cc_start: 0.8815 (t0) cc_final: 0.8613 (t0) outliers start: 49 outliers final: 32 residues processed: 422 average time/residue: 0.9836 time to fit residues: 473.7176 Evaluate side-chains 410 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 375 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 806 LYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain A residue 1219 ASP Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN A 843 GLN B 192 HIS B 250 GLN B 292 ASN B 339 ASN C 261 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.130726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.119503 restraints weight = 81945.394| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.15 r_work: 0.3545 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15660 Z= 0.250 Angle : 0.632 7.084 21408 Z= 0.348 Chirality : 0.042 0.250 2306 Planarity : 0.006 0.086 2600 Dihedral : 14.747 167.737 2429 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.62 % Allowed : 15.96 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.02 (0.20), residues: 1758 helix: 0.96 (0.19), residues: 718 sheet: 0.22 (0.32), residues: 241 loop : -0.97 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1128 TYR 0.016 0.002 TYR C 206 PHE 0.016 0.002 PHE A 197 TRP 0.012 0.002 TRP B 262 HIS 0.007 0.002 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.25 (15659) covalent geometry : angle 0.63177 / 0.35 (21406) SS BOND : bond 0.00048 / 0.03 ( 1) SS BOND : angle 0.67155 / 0.37 ( 2) hydrogen bonds : bond 0.05675 / 3.91 ( 703) hydrogen bonds : angle 5.22547 / 3.64 ( 1933) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 990 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Evaluate side-chains 441 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 385 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 ASN cc_start: 0.8365 (t0) cc_final: 0.7968 (t0) REVERT: A 443 ARG cc_start: 0.8189 (mtp85) cc_final: 0.7963 (ttp-110) REVERT: A 544 MET cc_start: 0.8115 (tmm) cc_final: 0.7885 (tmt) REVERT: A 610 PHE cc_start: 0.7717 (m-80) cc_final: 0.7499 (m-80) REVERT: A 793 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8198 (mp0) REVERT: A 797 MET cc_start: 0.8323 (mtt) cc_final: 0.8035 (mtp) REVERT: A 1138 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8063 (mmt90) REVERT: A 1192 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7559 (mm-30) REVERT: A 1226 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8644 (mt) REVERT: A 1233 LYS cc_start: 0.7193 (OUTLIER) cc_final: 0.6022 (tptp) REVERT: C 107 ARG cc_start: 0.8435 (mtm110) cc_final: 0.8033 (mmm-85) REVERT: C 129 ASP cc_start: 0.8427 (t70) cc_final: 0.8107 (t70) REVERT: C 201 ASN cc_start: 0.8880 (t0) cc_final: 0.8579 (t0) REVERT: C 400 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7870 (tm-30) outliers start: 56 outliers final: 35 residues processed: 407 average time/residue: 0.9521 time to fit residues: 443.9594 Evaluate side-chains 405 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 366 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 806 LYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1219 ASP Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1233 LYS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 154 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 chunk 137 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 843 GLN B 192 HIS B 258 HIS B 292 ASN C 261 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.129818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.118731 restraints weight = 81579.160| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.13 r_work: 0.3534 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15660 Z= 0.252 Angle : 0.641 7.227 21408 Z= 0.352 Chirality : 0.042 0.248 2306 Planarity : 0.006 0.059 2600 Dihedral : 14.915 166.913 2429 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.94 % Allowed : 17.18 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.25 (0.20), residues: 1758 helix: 0.79 (0.19), residues: 718 sheet: 0.20 (0.32), residues: 238 loop : -1.15 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 76 TYR 0.017 0.002 TYR C 206 PHE 0.016 0.002 PHE A 197 TRP 0.012 0.002 TRP B 262 HIS 0.008 0.002 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.25 (15659) covalent geometry : angle 0.64104 / 0.35 (21406) SS BOND : bond 0.01086 / 0.57 ( 1) SS BOND : angle 1.45699 / 0.86 ( 2) hydrogen bonds : bond 0.05529 / 3.82 ( 703) hydrogen bonds : angle 5.17162 / 3.61 ( 1933) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 990 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Evaluate side-chains 442 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 381 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7606 (tp30) REVERT: A 270 ASN cc_start: 0.8346 (t0) cc_final: 0.7922 (t0) REVERT: A 430 MET cc_start: 0.8105 (tpt) cc_final: 0.7770 (tpt) REVERT: A 443 ARG cc_start: 0.8233 (mtp85) cc_final: 0.8032 (ttp-110) REVERT: A 544 MET cc_start: 0.8109 (tmm) cc_final: 0.7874 (tmt) REVERT: A 610 PHE cc_start: 0.7751 (m-80) cc_final: 0.7376 (m-80) REVERT: A 797 MET cc_start: 0.8359 (mtt) cc_final: 0.8058 (mtp) REVERT: A 1138 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7880 (mmt90) REVERT: A 1192 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7539 (mm-30) REVERT: A 1226 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8632 (mt) REVERT: A 1233 LYS cc_start: 0.7187 (OUTLIER) cc_final: 0.6027 (tptp) REVERT: C 107 ARG cc_start: 0.8453 (mtm110) cc_final: 0.8056 (mmm-85) REVERT: C 129 ASP cc_start: 0.8408 (t70) cc_final: 0.7996 (t70) REVERT: C 201 ASN cc_start: 0.8907 (t0) cc_final: 0.8611 (t0) REVERT: C 400 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7735 (tm-30) REVERT: C 404 ASN cc_start: 0.7872 (m110) cc_final: 0.7420 (m110) REVERT: C 465 MET cc_start: 0.6298 (OUTLIER) cc_final: 0.4849 (mpp) outliers start: 61 outliers final: 42 residues processed: 409 average time/residue: 0.9730 time to fit residues: 454.5527 Evaluate side-chains 413 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 366 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 396 CYS Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 806 LYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain A residue 1219 ASP Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1233 LYS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 20 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN A 540 GLN A 843 GLN B 192 HIS B 258 HIS B 292 ASN C 261 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.130396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.119298 restraints weight = 81803.967| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.14 r_work: 0.3542 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15660 Z= 0.195 Angle : 0.609 6.890 21408 Z= 0.334 Chirality : 0.041 0.244 2306 Planarity : 0.005 0.054 2600 Dihedral : 14.909 168.087 2429 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.01 % Allowed : 17.51 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.17 (0.20), residues: 1758 helix: 0.93 (0.19), residues: 724 sheet: 0.24 (0.32), residues: 236 loop : -1.19 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 146 TYR 0.014 0.002 TYR C 206 PHE 0.019 0.002 PHE A1092 TRP 0.013 0.001 TRP A 897 HIS 0.007 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (15659) covalent geometry : angle 0.60885 / 0.33 (21406) SS BOND : bond 0.02379 / 1.25 ( 1) SS BOND : angle 2.59160 / 1.52 ( 2) hydrogen bonds : bond 0.05055 / 3.51 ( 703) hydrogen bonds : angle 5.02590 / 3.51 ( 1933) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 990 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Evaluate side-chains 443 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 381 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7551 (tp30) REVERT: A 191 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6569 (pm20) REVERT: A 270 ASN cc_start: 0.8367 (t0) cc_final: 0.7927 (t0) REVERT: A 430 MET cc_start: 0.8119 (tpt) cc_final: 0.7782 (tpt) REVERT: A 443 ARG cc_start: 0.8230 (mtp85) cc_final: 0.8001 (ttp-110) REVERT: A 473 LEU cc_start: 0.8076 (mm) cc_final: 0.7871 (mm) REVERT: A 610 PHE cc_start: 0.7685 (m-80) cc_final: 0.7345 (m-80) REVERT: A 793 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8148 (mp0) REVERT: A 797 MET cc_start: 0.8358 (mtt) cc_final: 0.8059 (mtp) REVERT: A 1138 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7858 (mmt90) REVERT: A 1192 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7561 (mm-30) REVERT: A 1226 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8637 (mt) REVERT: B 139 LEU cc_start: 0.6161 (OUTLIER) cc_final: 0.5371 (pt) REVERT: C 107 ARG cc_start: 0.8456 (mtm110) cc_final: 0.8005 (mtp180) REVERT: C 129 ASP cc_start: 0.8406 (t70) cc_final: 0.8052 (t0) REVERT: C 201 ASN cc_start: 0.8872 (t0) cc_final: 0.8581 (t0) REVERT: C 400 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7749 (tm-30) REVERT: C 404 ASN cc_start: 0.7888 (m110) cc_final: 0.7448 (m110) REVERT: C 465 MET cc_start: 0.6336 (OUTLIER) cc_final: 0.4900 (mpp) outliers start: 62 outliers final: 43 residues processed: 408 average time/residue: 0.9523 time to fit residues: 443.3503 Evaluate side-chains 418 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 369 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 396 CYS Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 806 LYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1219 ASP Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 58 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 135 optimal weight: 8.9990 chunk 166 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 843 GLN B 192 HIS B 292 ASN C 261 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.129054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.118177 restraints weight = 82023.199| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.13 r_work: 0.3524 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 15660 Z= 0.238 Angle : 0.653 15.419 21408 Z= 0.356 Chirality : 0.042 0.248 2306 Planarity : 0.006 0.057 2600 Dihedral : 15.031 167.639 2429 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.26 % Allowed : 18.60 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.20), residues: 1758 helix: 0.78 (0.19), residues: 724 sheet: 0.31 (0.33), residues: 230 loop : -1.32 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 924 TYR 0.016 0.002 TYR C 206 PHE 0.016 0.002 PHE A 197 TRP 0.011 0.002 TRP B 262 HIS 0.008 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.24 (15659) covalent geometry : angle 0.64922 / 0.35 (21406) SS BOND : bond 0.02632 / 1.39 ( 1) SS BOND : angle 7.41744 / 4.25 ( 2) hydrogen bonds : bond 0.05296 / 3.66 ( 703) hydrogen bonds : angle 5.08132 / 3.54 ( 1933) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 990 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Evaluate side-chains 441 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 375 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8457 (ttm110) REVERT: A 270 ASN cc_start: 0.8386 (t0) cc_final: 0.8004 (t0) REVERT: A 430 MET cc_start: 0.8142 (tpt) cc_final: 0.7813 (tpt) REVERT: A 610 PHE cc_start: 0.7736 (m-80) cc_final: 0.7374 (m-80) REVERT: A 793 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8179 (mp0) REVERT: A 797 MET cc_start: 0.8337 (mtt) cc_final: 0.8045 (mtp) REVERT: A 1138 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7873 (mmt90) REVERT: A 1192 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7587 (mm-30) REVERT: A 1226 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8639 (mt) REVERT: A 1233 LYS cc_start: 0.7197 (OUTLIER) cc_final: 0.6075 (tptp) REVERT: B 139 LEU cc_start: 0.6077 (OUTLIER) cc_final: 0.5255 (pt) REVERT: C 107 ARG cc_start: 0.8453 (mtm110) cc_final: 0.8030 (mtp180) REVERT: C 129 ASP cc_start: 0.8423 (t70) cc_final: 0.8094 (t0) REVERT: C 201 ASN cc_start: 0.8864 (t0) cc_final: 0.8588 (t0) REVERT: C 344 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7310 (mmt-90) REVERT: C 400 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7759 (tm-30) REVERT: C 404 ASN cc_start: 0.7883 (m110) cc_final: 0.7420 (m110) outliers start: 66 outliers final: 44 residues processed: 405 average time/residue: 1.0293 time to fit residues: 475.7079 Evaluate side-chains 422 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 371 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 396 CYS Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 806 LYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain A residue 1219 ASP Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1233 LYS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 344 ARG Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 65 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 146 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 45 optimal weight: 0.0770 chunk 101 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 150 optimal weight: 8.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN A 540 GLN A 843 GLN B 192 HIS B 292 ASN C 261 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.130162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.119344 restraints weight = 81685.440| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.12 r_work: 0.3544 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 15660 Z= 0.165 Angle : 0.615 17.076 21408 Z= 0.333 Chirality : 0.040 0.241 2306 Planarity : 0.005 0.056 2600 Dihedral : 14.965 169.467 2429 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.55 % Allowed : 19.19 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.09 (0.20), residues: 1758 helix: 1.04 (0.20), residues: 718 sheet: 0.29 (0.33), residues: 236 loop : -1.20 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 924 TYR 0.013 0.001 TYR C 206 PHE 0.016 0.002 PHE A 197 TRP 0.014 0.001 TRP A 897 HIS 0.007 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (15659) covalent geometry : angle 0.61134 / 0.33 (21406) SS BOND : bond 0.03392 / 1.79 ( 1) SS BOND : angle 6.90887 / 3.97 ( 2) hydrogen bonds : bond 0.04744 / 3.30 ( 703) hydrogen bonds : angle 4.91033 / 3.42 ( 1933) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 990 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Evaluate side-chains 438 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 383 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8477 (ttm110) REVERT: A 270 ASN cc_start: 0.8353 (t0) cc_final: 0.7919 (t0) REVERT: A 430 MET cc_start: 0.8152 (tpt) cc_final: 0.7827 (tpt) REVERT: A 610 PHE cc_start: 0.7611 (m-80) cc_final: 0.7232 (m-80) REVERT: A 793 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8145 (mp0) REVERT: A 797 MET cc_start: 0.8298 (mtt) cc_final: 0.7994 (mtp) REVERT: A 1138 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7852 (mmt90) REVERT: A 1144 GLU cc_start: 0.7890 (mp0) cc_final: 0.7638 (mp0) REVERT: B 139 LEU cc_start: 0.6088 (OUTLIER) cc_final: 0.5276 (pt) REVERT: C 107 ARG cc_start: 0.8427 (mtm110) cc_final: 0.8001 (mtp180) REVERT: C 129 ASP cc_start: 0.8423 (t70) cc_final: 0.8049 (t0) REVERT: C 201 ASN cc_start: 0.8847 (t0) cc_final: 0.8596 (t0) REVERT: C 400 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7756 (tm-30) REVERT: C 404 ASN cc_start: 0.7857 (m110) cc_final: 0.7393 (m110) outliers start: 55 outliers final: 40 residues processed: 410 average time/residue: 0.9790 time to fit residues: 458.8771 Evaluate side-chains 413 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 369 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 806 LYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain A residue 1219 ASP Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 64 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 179 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 41 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 843 GLN B 192 HIS B 292 ASN C 261 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.129945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.119141 restraints weight = 81835.238| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.12 r_work: 0.3540 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 15660 Z= 0.175 Angle : 0.614 14.128 21408 Z= 0.332 Chirality : 0.040 0.245 2306 Planarity : 0.005 0.056 2600 Dihedral : 14.993 170.094 2429 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.55 % Allowed : 19.77 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.07 (0.20), residues: 1758 helix: 1.07 (0.20), residues: 717 sheet: 0.36 (0.33), residues: 230 loop : -1.20 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 290 TYR 0.017 0.002 TYR B 291 PHE 0.017 0.002 PHE A 197 TRP 0.013 0.001 TRP A 897 HIS 0.006 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (15659) covalent geometry : angle 0.61142 / 0.33 (21406) SS BOND : bond 0.02383 / 1.25 ( 1) SS BOND : angle 5.69838 / 3.29 ( 2) hydrogen bonds : bond 0.04681 / 3.25 ( 703) hydrogen bonds : angle 4.85261 / 3.37 ( 1933) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 990 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Evaluate side-chains 433 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 378 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8472 (ttm110) REVERT: A 270 ASN cc_start: 0.8382 (t0) cc_final: 0.7949 (t0) REVERT: A 430 MET cc_start: 0.8139 (tpt) cc_final: 0.7814 (tpt) REVERT: A 610 PHE cc_start: 0.7622 (m-80) cc_final: 0.7249 (m-80) REVERT: A 793 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8228 (mm-30) REVERT: A 797 MET cc_start: 0.8301 (mtt) cc_final: 0.7994 (mtp) REVERT: A 1138 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7888 (mmt90) REVERT: B 139 LEU cc_start: 0.6073 (OUTLIER) cc_final: 0.5260 (pt) REVERT: C 107 ARG cc_start: 0.8463 (mtm110) cc_final: 0.8041 (mtp180) REVERT: C 129 ASP cc_start: 0.8433 (t70) cc_final: 0.8100 (t0) REVERT: C 201 ASN cc_start: 0.8851 (t0) cc_final: 0.8609 (t0) REVERT: C 344 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7096 (mmt-90) REVERT: C 400 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7747 (tm-30) REVERT: C 404 ASN cc_start: 0.7825 (m110) cc_final: 0.7350 (m110) outliers start: 55 outliers final: 39 residues processed: 411 average time/residue: 0.9902 time to fit residues: 464.8043 Evaluate side-chains 416 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 372 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 806 LYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1219 ASP Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 344 ARG Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 46 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 82 optimal weight: 0.1980 chunk 103 optimal weight: 7.9990 chunk 154 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 843 GLN B 192 HIS B 292 ASN C 261 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.130005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.119201 restraints weight = 81882.496| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.12 r_work: 0.3542 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15660 Z= 0.175 Angle : 0.621 13.023 21408 Z= 0.335 Chirality : 0.040 0.245 2306 Planarity : 0.005 0.056 2600 Dihedral : 15.018 170.563 2429 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.62 % Allowed : 20.03 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.04 (0.20), residues: 1758 helix: 1.13 (0.20), residues: 716 sheet: 0.32 (0.33), residues: 233 loop : -1.20 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 290 TYR 0.013 0.002 TYR C 206 PHE 0.017 0.002 PHE A 197 TRP 0.012 0.001 TRP A 897 HIS 0.007 0.001 HIS C 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (15659) covalent geometry : angle 0.61917 / 0.33 (21406) SS BOND : bond 0.02125 / 1.12 ( 1) SS BOND : angle 5.34267 / 3.06 ( 2) hydrogen bonds : bond 0.04662 / 3.23 ( 703) hydrogen bonds : angle 4.83828 / 3.36 ( 1933) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 990 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Evaluate side-chains 432 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 376 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8472 (ttm110) REVERT: A 270 ASN cc_start: 0.8386 (t0) cc_final: 0.7969 (t0) REVERT: A 430 MET cc_start: 0.8145 (tpt) cc_final: 0.7819 (tpt) REVERT: A 610 PHE cc_start: 0.7670 (m-80) cc_final: 0.7323 (m-80) REVERT: A 793 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8238 (mm-30) REVERT: A 797 MET cc_start: 0.8308 (mtt) cc_final: 0.7999 (mtp) REVERT: A 1138 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7878 (mmt90) REVERT: B 139 LEU cc_start: 0.6074 (OUTLIER) cc_final: 0.5265 (pt) REVERT: C 107 ARG cc_start: 0.8453 (mtm110) cc_final: 0.8029 (mtp180) REVERT: C 129 ASP cc_start: 0.8420 (t70) cc_final: 0.8016 (t0) REVERT: C 201 ASN cc_start: 0.8837 (t0) cc_final: 0.8611 (t0) REVERT: C 344 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7243 (mmt-90) REVERT: C 400 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: C 404 ASN cc_start: 0.7803 (m110) cc_final: 0.7324 (m110) outliers start: 56 outliers final: 43 residues processed: 406 average time/residue: 1.0085 time to fit residues: 466.2478 Evaluate side-chains 422 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 374 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 806 LYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1219 ASP Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 344 ARG Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 105 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 843 GLN B 192 HIS B 292 ASN C 261 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.129127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.118380 restraints weight = 81677.339| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.12 r_work: 0.3528 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 15660 Z= 0.210 Angle : 0.645 12.627 21408 Z= 0.348 Chirality : 0.041 0.252 2306 Planarity : 0.006 0.061 2600 Dihedral : 15.110 170.174 2429 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.42 % Allowed : 20.41 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.20 (0.20), residues: 1758 helix: 1.00 (0.19), residues: 715 sheet: 0.27 (0.33), residues: 233 loop : -1.31 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 290 TYR 0.017 0.002 TYR B 291 PHE 0.017 0.002 PHE A 197 TRP 0.010 0.001 TRP B 262 HIS 0.007 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.21 (15659) covalent geometry : angle 0.64263 / 0.35 (21406) SS BOND : bond 0.02219 / 1.17 ( 1) SS BOND : angle 5.52236 / 3.18 ( 2) hydrogen bonds : bond 0.04956 / 3.43 ( 703) hydrogen bonds : angle 4.91512 / 3.41 ( 1933) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 990 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 365 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Evaluate side-chains 426 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 373 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8432 (ttm110) REVERT: A 270 ASN cc_start: 0.8362 (t0) cc_final: 0.7983 (t0) REVERT: A 430 MET cc_start: 0.8108 (tpt) cc_final: 0.7784 (tpt) REVERT: A 610 PHE cc_start: 0.7622 (m-80) cc_final: 0.7218 (m-80) REVERT: A 793 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8241 (mm-30) REVERT: A 797 MET cc_start: 0.8309 (mtt) cc_final: 0.8004 (mtp) REVERT: A 1138 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7863 (mmt90) REVERT: B 139 LEU cc_start: 0.6055 (OUTLIER) cc_final: 0.5203 (pp) REVERT: C 107 ARG cc_start: 0.8459 (mtm110) cc_final: 0.8044 (mtp180) REVERT: C 129 ASP cc_start: 0.8416 (t70) cc_final: 0.8078 (t0) REVERT: C 201 ASN cc_start: 0.8854 (t0) cc_final: 0.8620 (t0) REVERT: C 310 GLU cc_start: 0.8215 (mp0) cc_final: 0.7930 (mp0) REVERT: C 344 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7254 (mmt-90) REVERT: C 400 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7778 (tm-30) REVERT: C 404 ASN cc_start: 0.7828 (m110) cc_final: 0.7381 (m110) outliers start: 53 outliers final: 43 residues processed: 401 average time/residue: 1.0139 time to fit residues: 463.2348 Evaluate side-chains 419 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 371 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 806 LYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1219 ASP Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 344 ARG Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 150 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 843 GLN B 192 HIS B 292 ASN C 261 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.130668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.119934 restraints weight = 81419.714| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.12 r_work: 0.3550 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15660 Z= 0.144 Angle : 0.612 11.721 21408 Z= 0.329 Chirality : 0.040 0.240 2306 Planarity : 0.005 0.059 2600 Dihedral : 15.017 172.022 2429 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.97 % Allowed : 21.12 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.05 (0.20), residues: 1758 helix: 1.17 (0.20), residues: 723 sheet: 0.31 (0.33), residues: 233 loop : -1.11 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 290 TYR 0.013 0.001 TYR C 206 PHE 0.017 0.001 PHE A 197 TRP 0.015 0.001 TRP A 897 HIS 0.007 0.001 HIS C 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (15659) covalent geometry : angle 0.61035 / 0.33 (21406) SS BOND : bond 0.01930 / 1.02 ( 1) SS BOND : angle 4.71248 / 2.70 ( 2) hydrogen bonds : bond 0.04432 / 3.07 ( 703) hydrogen bonds : angle 4.77323 / 3.32 ( 1933) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10795.43 seconds wall clock time: 183 minutes 5.03 seconds (10985.03 seconds total)