Starting phenix.real_space_refine on Fri Mar 6 09:05:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d42_27172/03_2026/8d42_27172_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d42_27172/03_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_27172/03_2026/8d42_27172_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d42_27172/03_2026/8d42_27172_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d42_27172/03_2026/8d42_27172.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d42_27172/03_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-dev-5986/lib/python3.9/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: 5.52, per 1000 atoms: 0.19 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: 2.70 Conformation dependent library (CDL) restraints added in 850.1 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: 5.23 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: 7.06 Time building geometry restraints manager: 3.85 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 1.579 1.805 -0.226 1.50e-02 4.44e+03 2.27e+02 bond pdb=" C5' DCP A1304 " pdb=" O5' DCP A1304 " ideal model delta sigma weight residual 1.443 1.323 0.120 1.10e-02 8.26e+03 1.20e+02 bond pdb=" O3A DCP A1304 " pdb=" PB DCP A1304 " ideal model delta sigma weight residual 1.592 1.710 -0.118 1.10e-02 8.26e+03 1.14e+02 bond pdb=" C4' DCP A1304 " pdb=" C5' DCP A1304 " ideal model delta sigma weight residual 1.508 1.563 -0.055 1.10e-02 8.26e+03 2.52e+01 bond pdb=" O3B DCP A1304 " pdb=" PG DCP A1304 " ideal model delta sigma weight residual 1.600 1.651 -0.051 1.10e-02 8.26e+03 2.19e+01 ... (remaining 30264 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 54564 2.56 - 5.12: 150 5.12 - 7.67: 6 7.67 - 10.23: 5 10.23 - 12.79: 3 Bond angle restraints: 54728 Sorted by residual: angle pdb=" O1G DCP A1304 " pdb=" PG DCP A1304 " pdb=" O3B DCP A1304 " ideal model delta sigma weight residual 110.47 98.05 12.42 1.64e+00 3.70e-01 5.71e+01 angle pdb=" PB DCP A1304 " pdb=" O3B DCP A1304 " pdb=" PG DCP A1304 " ideal model delta sigma weight residual 139.87 133.43 6.44 1.00e+00 1.00e+00 4.14e+01 angle pdb=" O2A DCP A1304 " pdb=" PA DCP A1304 " pdb=" O3A DCP A1304 " ideal model delta sigma weight residual 106.94 116.95 -10.01 1.88e+00 2.83e-01 2.84e+01 angle pdb=" C1' DCP A1304 " pdb=" N1 DCP A1304 " pdb=" C6 DCP A1304 " ideal model delta sigma weight residual 121.66 114.29 7.37 1.39e+00 5.21e-01 2.82e+01 angle pdb=" O3A DCP A1304 " pdb=" PB DCP A1304 " pdb=" O3B DCP A1304 " ideal model delta sigma weight residual 101.57 93.51 8.06 1.54e+00 4.24e-01 2.76e+01 ... (remaining 54723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.74: 13596 34.74 - 69.48: 459 69.48 - 104.22: 9 104.22 - 138.95: 0 138.95 - 173.69: 1 Dihedral angle restraints: 14065 sinusoidal: 7902 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 14062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1550 0.029 - 0.058: 497 0.058 - 0.087: 143 0.087 - 0.116: 96 0.116 - 0.145: 20 Chirality restraints: 2306 Sorted by residual: chirality pdb=" C1' DCP A1304 " pdb=" C2' DCP A1304 " pdb=" N1 DCP A1304 " pdb=" O4' DCP A1304 " both_signs ideal model delta sigma weight residual False 2.45 2.30 0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA ILE B 437 " pdb=" N ILE B 437 " pdb=" C ILE B 437 " pdb=" CB ILE B 437 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA VAL C 338 " pdb=" N VAL C 338 " pdb=" C VAL C 338 " pdb=" CB VAL C 338 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.27e-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: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.200 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 32.830 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 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 0.226 15660 Z= 0.225 Angle : 0.555 12.790 21408 Z= 0.310 Chirality : 0.037 0.145 2306 Planarity : 0.004 0.059 2600 Dihedral : 14.520 173.693 5921 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 covalent geometry : bond 0.00351 (15659) covalent geometry : angle 0.55501 (21406) SS BOND : bond 0.00432 ( 1) SS BOND : angle 0.56495 ( 2) hydrogen bonds : bond 0.14215 ( 703) hydrogen bonds : angle 6.63000 ( 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 : 0.619 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: 1.0700 time to fit residues: 529.9111 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 : 0.716 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 264 GLN A 388 ASN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 843 GLN A1202 ASN B 124 GLN B 192 HIS B 250 GLN B 258 HIS B 279 GLN 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.131972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.120622 restraints weight = 81990.560| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.16 r_work: 0.3560 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15660 Z= 0.234 Angle : 0.618 5.055 21408 Z= 0.333 Chirality : 0.042 0.160 2306 Planarity : 0.006 0.098 2600 Dihedral : 14.666 172.257 2427 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.04 % Allowed : 14.60 % Favored : 82.36 % 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: 0.32 (0.20), residues: 1758 helix: 1.11 (0.20), residues: 720 sheet: 0.28 (0.32), residues: 251 loop : -0.59 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1128 TYR 0.016 0.002 TYR C 206 PHE 0.015 0.002 PHE A 197 TRP 0.010 0.002 TRP B 262 HIS 0.006 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00516 (15659) covalent geometry : angle 0.61748 (21406) SS BOND : bond 0.00246 ( 1) SS BOND : angle 2.12361 ( 2) hydrogen bonds : bond 0.05300 ( 703) hydrogen bonds : angle 5.16774 ( 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 448 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 401 time to evaluate : 0.762 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: A 191 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6811 (pm20) REVERT: A 270 ASN cc_start: 0.8310 (t0) cc_final: 0.7796 (t0) REVERT: A 610 PHE cc_start: 0.7754 (m-80) cc_final: 0.7467 (m-80) REVERT: A 793 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8147 (mp0) REVERT: A 797 MET cc_start: 0.8324 (mtt) cc_final: 0.8012 (mtp) REVERT: A 1116 MET cc_start: 0.7812 (mmm) cc_final: 0.7576 (mmm) REVERT: A 1138 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7970 (mmt90) REVERT: A 1192 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7635 (mm-30) REVERT: A 1226 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8638 (mt) REVERT: C 107 ARG cc_start: 0.8357 (mtm110) cc_final: 0.7921 (mtm110) REVERT: C 129 ASP cc_start: 0.8417 (t70) cc_final: 0.8144 (t0) REVERT: C 201 ASN cc_start: 0.8839 (t0) cc_final: 0.8605 (t0) outliers start: 47 outliers final: 30 residues processed: 419 average time/residue: 0.9990 time to fit residues: 471.6913 Evaluate side-chains 404 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 371 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 191 GLU 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 586 THR 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 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 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: 0.9990 chunk 14 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 120 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 843 GLN B 192 HIS B 250 GLN B 292 ASN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.130831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.119652 restraints weight = 81758.656| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.14 r_work: 0.3547 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15660 Z= 0.227 Angle : 0.606 5.849 21408 Z= 0.326 Chirality : 0.041 0.140 2306 Planarity : 0.006 0.060 2600 Dihedral : 14.693 171.688 2422 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.20 % Allowed : 15.83 % Favored : 79.97 % 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: 1.01 (0.19), residues: 719 sheet: 0.26 (0.32), residues: 241 loop : -0.85 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 290 TYR 0.015 0.002 TYR C 206 PHE 0.018 0.002 PHE A1092 TRP 0.011 0.002 TRP B 262 HIS 0.007 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00504 (15659) covalent geometry : angle 0.60509 (21406) SS BOND : bond 0.00217 ( 1) SS BOND : angle 3.52284 ( 2) hydrogen bonds : bond 0.05302 ( 703) hydrogen bonds : angle 5.12186 ( 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: 65 poor density : 376 time to evaluate : 0.802 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: A 270 ASN cc_start: 0.8309 (t0) cc_final: 0.7850 (t0) REVERT: A 610 PHE cc_start: 0.7768 (m-80) cc_final: 0.7424 (m-80) REVERT: A 659 HIS cc_start: 0.2791 (OUTLIER) cc_final: 0.2382 (m90) REVERT: A 793 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8186 (mp0) REVERT: A 797 MET cc_start: 0.8344 (mtt) cc_final: 0.8046 (mtp) REVERT: A 1138 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8045 (mmt90) REVERT: A 1192 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7549 (mm-30) REVERT: A 1226 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8637 (mt) REVERT: A 1233 LYS cc_start: 0.7183 (OUTLIER) cc_final: 0.5997 (tptp) REVERT: B 122 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8523 (mtt-85) REVERT: C 107 ARG cc_start: 0.8448 (mtm110) cc_final: 0.7963 (mtm110) REVERT: C 116 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8716 (t) REVERT: C 129 ASP cc_start: 0.8426 (t70) cc_final: 0.8073 (t70) REVERT: C 201 ASN cc_start: 0.8868 (t0) cc_final: 0.8592 (t0) REVERT: C 400 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7830 (tm-30) outliers start: 65 outliers final: 38 residues processed: 406 average time/residue: 1.0150 time to fit residues: 463.8871 Evaluate side-chains 415 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 370 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 659 HIS 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 A residue 1233 LYS Chi-restraints excluded: chain B residue 122 ARG 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 325 ARG 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 116 THR 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 374 LEU 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: 10.0000 chunk 62 optimal weight: 5.9990 chunk 161 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS 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 258 HIS B 279 GLN 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 = 0.3742 r_free = 0.3742 target = 0.127752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.117005 restraints weight = 82279.468| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.12 r_work: 0.3505 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 15660 Z= 0.309 Angle : 0.699 6.224 21408 Z= 0.380 Chirality : 0.044 0.161 2306 Planarity : 0.007 0.060 2600 Dihedral : 15.010 170.017 2422 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 4.91 % Allowed : 16.67 % Favored : 78.42 % 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: -0.62 (0.19), residues: 1758 helix: 0.45 (0.19), residues: 724 sheet: 0.32 (0.34), residues: 219 loop : -1.41 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 146 TYR 0.020 0.003 TYR C 206 PHE 0.018 0.002 PHE A 389 TRP 0.015 0.002 TRP B 262 HIS 0.010 0.002 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00683 (15659) covalent geometry : angle 0.69677 (21406) SS BOND : bond 0.00733 ( 1) SS BOND : angle 5.37014 ( 2) hydrogen bonds : bond 0.05988 ( 703) hydrogen bonds : angle 5.28368 ( 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 452 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 376 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: A 81 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8410 (ttm110) REVERT: A 270 ASN cc_start: 0.8389 (t0) cc_final: 0.8099 (t0) REVERT: A 430 MET cc_start: 0.8139 (tpt) cc_final: 0.7833 (tpt) REVERT: A 473 LEU cc_start: 0.8129 (mm) cc_final: 0.7881 (mm) REVERT: A 610 PHE cc_start: 0.7625 (m-80) cc_final: 0.7266 (m-80) REVERT: A 793 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8272 (mm-30) REVERT: A 797 MET cc_start: 0.8359 (mtt) cc_final: 0.8058 (mtp) REVERT: A 1138 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7906 (mmt90) REVERT: A 1192 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7539 (mm-30) REVERT: A 1233 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6093 (tptp) REVERT: B 139 LEU cc_start: 0.6068 (OUTLIER) cc_final: 0.5219 (pt) REVERT: C 107 ARG cc_start: 0.8476 (mtm110) cc_final: 0.7988 (mmm-85) REVERT: C 129 ASP cc_start: 0.8428 (t70) cc_final: 0.7928 (t0) REVERT: C 201 ASN cc_start: 0.8890 (t0) cc_final: 0.8593 (t0) REVERT: C 344 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7318 (mmt-90) REVERT: C 400 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7730 (tm-30) REVERT: C 404 ASN cc_start: 0.7863 (m110) cc_final: 0.7418 (m110) REVERT: C 465 MET cc_start: 0.6403 (OUTLIER) cc_final: 0.4985 (mpp) outliers start: 76 outliers final: 45 residues processed: 415 average time/residue: 0.9913 time to fit residues: 464.8959 Evaluate side-chains 420 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 368 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 238 GLN 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 779 LEU 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 1212 ILE Chi-restraints excluded: chain A residue 1233 LYS 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 444 THR 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 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: 4.9990 chunk 10 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 151 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 110 HIS 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 258 HIS B 292 ASN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.129403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.118617 restraints weight = 81892.827| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.12 r_work: 0.3531 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15660 Z= 0.186 Angle : 0.610 6.219 21408 Z= 0.329 Chirality : 0.040 0.146 2306 Planarity : 0.005 0.060 2600 Dihedral : 14.845 171.472 2422 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.33 % Allowed : 17.89 % Favored : 77.78 % 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: -0.31 (0.20), residues: 1758 helix: 0.78 (0.19), residues: 724 sheet: 0.19 (0.32), residues: 238 loop : -1.25 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 76 TYR 0.014 0.002 TYR C 206 PHE 0.015 0.002 PHE A 197 TRP 0.014 0.001 TRP A 897 HIS 0.008 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00412 (15659) covalent geometry : angle 0.60790 (21406) SS BOND : bond 0.00340 ( 1) SS BOND : angle 5.05025 ( 2) hydrogen bonds : bond 0.05038 ( 703) hydrogen bonds : angle 5.03216 ( 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 444 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 377 time to evaluate : 0.765 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 191 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6575 (pm20) REVERT: A 270 ASN cc_start: 0.8365 (t0) cc_final: 0.7941 (t0) REVERT: A 430 MET cc_start: 0.8170 (tpt) cc_final: 0.7846 (tpt) REVERT: A 793 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8255 (mm-30) REVERT: A 797 MET cc_start: 0.8320 (mtt) cc_final: 0.8012 (mtp) REVERT: A 1138 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7921 (mmt90) REVERT: A 1192 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7595 (mm-30) REVERT: A 1226 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8651 (mt) REVERT: A 1233 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6022 (tptp) REVERT: B 139 LEU cc_start: 0.6051 (OUTLIER) cc_final: 0.5240 (pt) REVERT: B 478 TYR cc_start: 0.8422 (t80) cc_final: 0.8215 (t80) REVERT: C 107 ARG cc_start: 0.8449 (mtm110) cc_final: 0.8025 (mtp180) REVERT: C 129 ASP cc_start: 0.8448 (t70) cc_final: 0.8015 (t0) REVERT: C 201 ASN cc_start: 0.8858 (t0) cc_final: 0.8583 (t0) REVERT: C 400 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7751 (tm-30) REVERT: C 404 ASN cc_start: 0.7865 (m110) cc_final: 0.7426 (m110) outliers start: 67 outliers final: 44 residues processed: 411 average time/residue: 1.0318 time to fit residues: 478.1753 Evaluate side-chains 416 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 366 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 196 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 342 ILE 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 1212 ILE 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 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 446 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 58 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 93 optimal weight: 0.0870 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 110 HIS A 115 GLN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN A 843 GLN B 192 HIS B 258 HIS B 292 ASN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.128997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.118223 restraints weight = 82085.364| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.13 r_work: 0.3526 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 15660 Z= 0.208 Angle : 0.635 11.723 21408 Z= 0.340 Chirality : 0.041 0.203 2306 Planarity : 0.005 0.052 2600 Dihedral : 14.882 172.044 2422 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.33 % Allowed : 18.86 % Favored : 76.81 % 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: -0.30 (0.20), residues: 1758 helix: 0.82 (0.19), residues: 725 sheet: 0.27 (0.33), residues: 232 loop : -1.30 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 193 TYR 0.017 0.002 TYR B 291 PHE 0.016 0.002 PHE A 197 TRP 0.012 0.001 TRP A 897 HIS 0.007 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00469 (15659) covalent geometry : angle 0.62976 (21406) SS BOND : bond 0.02009 ( 1) SS BOND : angle 8.39817 ( 2) hydrogen bonds : bond 0.04962 ( 703) hydrogen bonds : angle 4.97113 ( 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 446 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 379 time to evaluate : 0.767 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 81 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8446 (ttm110) REVERT: A 191 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6655 (pm20) REVERT: A 270 ASN cc_start: 0.8391 (t0) cc_final: 0.8003 (t0) REVERT: A 430 MET cc_start: 0.8166 (tpt) cc_final: 0.7850 (tpt) REVERT: A 793 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8267 (mm-30) REVERT: A 797 MET cc_start: 0.8329 (mtt) cc_final: 0.8021 (mtp) REVERT: A 1138 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7942 (mmt90) REVERT: A 1226 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8628 (mt) REVERT: A 1233 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.5988 (tptp) REVERT: B 139 LEU cc_start: 0.6005 (OUTLIER) cc_final: 0.5197 (pt) REVERT: B 478 TYR cc_start: 0.8465 (t80) cc_final: 0.8260 (t80) REVERT: C 107 ARG cc_start: 0.8465 (mtm110) cc_final: 0.8071 (mtp180) REVERT: C 201 ASN cc_start: 0.8856 (t0) cc_final: 0.8605 (t0) REVERT: C 400 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7755 (tm-30) outliers start: 67 outliers final: 45 residues processed: 414 average time/residue: 1.0078 time to fit residues: 470.7199 Evaluate side-chains 416 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 364 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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 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 647 CYS Chi-restraints excluded: chain A residue 659 HIS 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 1212 ILE 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 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 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 446 THR Chi-restraints excluded: chain C residue 471 LEU 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: 0.3980 chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 110 HIS A 115 GLN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN A 843 GLN B 192 HIS B 292 ASN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.129242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.118492 restraints weight = 81858.821| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.12 r_work: 0.3530 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2579 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= 0.188 Angle : 0.623 15.548 21408 Z= 0.332 Chirality : 0.040 0.156 2306 Planarity : 0.005 0.058 2600 Dihedral : 14.858 172.580 2422 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.13 % Allowed : 19.77 % Favored : 76.10 % 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: -0.19 (0.20), residues: 1758 helix: 0.95 (0.19), residues: 723 sheet: 0.29 (0.33), residues: 232 loop : -1.26 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 290 TYR 0.014 0.002 TYR B 291 PHE 0.016 0.002 PHE A 197 TRP 0.013 0.001 TRP A 897 HIS 0.007 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00422 (15659) covalent geometry : angle 0.62045 (21406) SS BOND : bond 0.02528 ( 1) SS BOND : angle 6.22217 ( 2) hydrogen bonds : bond 0.04815 ( 703) hydrogen bonds : angle 4.92313 ( 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 437 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 373 time to evaluate : 0.780 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: A 270 ASN cc_start: 0.8391 (t0) cc_final: 0.7975 (t0) REVERT: A 430 MET cc_start: 0.8131 (tpt) cc_final: 0.7794 (tpt) REVERT: A 793 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8243 (mm-30) REVERT: A 797 MET cc_start: 0.8347 (mtt) cc_final: 0.8031 (mtp) REVERT: A 896 LEU cc_start: 0.7978 (mt) cc_final: 0.7768 (mp) REVERT: A 1138 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7892 (mmt90) REVERT: B 139 LEU cc_start: 0.6009 (OUTLIER) cc_final: 0.5197 (pt) REVERT: B 371 VAL cc_start: 0.8904 (OUTLIER) cc_final: 0.8682 (p) REVERT: B 478 TYR cc_start: 0.8461 (t80) cc_final: 0.8253 (t80) REVERT: C 107 ARG cc_start: 0.8482 (mtm110) cc_final: 0.8093 (mtp180) REVERT: C 129 ASP cc_start: 0.8460 (t0) cc_final: 0.8143 (t0) REVERT: C 201 ASN cc_start: 0.8829 (t0) cc_final: 0.8592 (t0) REVERT: C 400 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7826 (tm-30) REVERT: C 465 MET cc_start: 0.6406 (OUTLIER) cc_final: 0.4882 (mpp) outliers start: 64 outliers final: 44 residues processed: 410 average time/residue: 1.0147 time to fit residues: 468.8896 Evaluate side-chains 419 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 370 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 196 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 342 ILE 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 659 HIS 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 1212 ILE 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 371 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 64 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 110 HIS ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN A 843 GLN B 192 HIS B 292 ASN B 305 ASN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.126480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.116068 restraints weight = 81817.061| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.09 r_work: 0.3488 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 15660 Z= 0.325 Angle : 0.728 14.342 21408 Z= 0.393 Chirality : 0.045 0.161 2306 Planarity : 0.007 0.058 2600 Dihedral : 15.246 171.507 2422 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 4.84 % Allowed : 19.64 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.88 (0.19), residues: 1758 helix: 0.31 (0.19), residues: 729 sheet: 0.21 (0.34), residues: 219 loop : -1.66 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 193 TYR 0.024 0.003 TYR B 291 PHE 0.018 0.003 PHE A 389 TRP 0.015 0.002 TRP B 262 HIS 0.011 0.002 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00720 (15659) covalent geometry : angle 0.72538 (21406) SS BOND : bond 0.02837 ( 1) SS BOND : angle 6.75630 ( 2) hydrogen bonds : bond 0.06089 ( 703) hydrogen bonds : angle 5.27221 ( 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 445 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 370 time to evaluate : 0.699 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: 0.8625 (OUTLIER) cc_final: 0.8391 (ttm110) REVERT: A 270 ASN cc_start: 0.8391 (t0) cc_final: 0.8143 (t0) REVERT: A 430 MET cc_start: 0.8214 (tpt) cc_final: 0.7889 (tpt) REVERT: A 797 MET cc_start: 0.8395 (mtt) cc_final: 0.7996 (mtp) REVERT: A 1138 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8011 (mmt90) REVERT: A 1233 LYS cc_start: 0.7233 (OUTLIER) cc_final: 0.6746 (tptp) REVERT: B 139 LEU cc_start: 0.6055 (OUTLIER) cc_final: 0.5168 (pt) REVERT: B 310 GLU cc_start: 0.8347 (mp0) cc_final: 0.8142 (mp0) REVERT: B 371 VAL cc_start: 0.8900 (OUTLIER) cc_final: 0.8659 (p) REVERT: B 478 TYR cc_start: 0.8542 (t80) cc_final: 0.8330 (t80) REVERT: C 107 ARG cc_start: 0.8445 (mtm110) cc_final: 0.8087 (mtp180) REVERT: C 129 ASP cc_start: 0.8460 (t0) cc_final: 0.8084 (t0) REVERT: C 201 ASN cc_start: 0.8857 (t0) cc_final: 0.8603 (t0) REVERT: C 344 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7281 (mmt-90) REVERT: C 400 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7787 (tm-30) REVERT: C 465 MET cc_start: 0.6317 (OUTLIER) cc_final: 0.4939 (mpp) outliers start: 75 outliers final: 50 residues processed: 410 average time/residue: 1.0156 time to fit residues: 469.4292 Evaluate side-chains 422 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 364 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 196 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 369 LEU 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 659 HIS 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 1195 MET Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1233 LYS 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 256 LEU 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 371 VAL 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 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 465 MET 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: 0.8980 chunk 116 optimal weight: 3.9990 chunk 81 optimal weight: 0.0040 chunk 12 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS A 115 GLN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN B 192 HIS B 292 ASN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.130112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.119463 restraints weight = 81324.803| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.13 r_work: 0.3544 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15660 Z= 0.134 Angle : 0.613 12.124 21408 Z= 0.325 Chirality : 0.039 0.153 2306 Planarity : 0.005 0.057 2600 Dihedral : 14.849 173.389 2422 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.10 % Allowed : 21.90 % Favored : 75.00 % 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: -0.12 (0.20), residues: 1758 helix: 1.05 (0.19), residues: 720 sheet: 0.28 (0.33), residues: 233 loop : -1.24 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 290 TYR 0.012 0.001 TYR A1108 PHE 0.015 0.001 PHE A 197 TRP 0.019 0.001 TRP A 897 HIS 0.006 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00302 (15659) covalent geometry : angle 0.61140 (21406) SS BOND : bond 0.01779 ( 1) SS BOND : angle 4.75962 ( 2) hydrogen bonds : bond 0.04451 ( 703) hydrogen bonds : angle 4.84857 ( 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 429 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 381 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: A 81 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8437 (ttm110) REVERT: A 270 ASN cc_start: 0.8385 (t0) cc_final: 0.7989 (t0) REVERT: A 430 MET cc_start: 0.8179 (tpt) cc_final: 0.7859 (tpt) REVERT: A 793 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8279 (mm-30) REVERT: A 797 MET cc_start: 0.8376 (mtt) cc_final: 0.8053 (mtp) REVERT: A 896 LEU cc_start: 0.7962 (mt) cc_final: 0.7717 (mp) REVERT: A 1138 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7910 (mmt90) REVERT: B 139 LEU cc_start: 0.5926 (OUTLIER) cc_final: 0.5115 (pt) REVERT: B 310 GLU cc_start: 0.8300 (mp0) cc_final: 0.8093 (mp0) REVERT: B 371 VAL cc_start: 0.8902 (OUTLIER) cc_final: 0.8667 (p) REVERT: C 107 ARG cc_start: 0.8422 (mtm110) cc_final: 0.8058 (mtp180) REVERT: C 129 ASP cc_start: 0.8440 (t0) cc_final: 0.8143 (t0) REVERT: C 201 ASN cc_start: 0.8824 (t0) cc_final: 0.8591 (t0) REVERT: C 400 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7769 (tm-30) outliers start: 48 outliers final: 27 residues processed: 406 average time/residue: 1.0175 time to fit residues: 464.6325 Evaluate side-chains 410 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 378 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 196 VAL Chi-restraints excluded: chain A residue 342 ILE 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 586 THR Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 806 LYS Chi-restraints excluded: chain A residue 851 THR 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 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 337 SER Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 215 PHE 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 400 GLN 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: 1.9990 chunk 94 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN B 192 HIS B 292 ASN B 305 ASN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.129729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.119130 restraints weight = 81211.352| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.11 r_work: 0.3538 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15660 Z= 0.158 Angle : 0.620 11.629 21408 Z= 0.328 Chirality : 0.040 0.159 2306 Planarity : 0.005 0.055 2600 Dihedral : 14.818 173.644 2422 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.20 % Allowed : 22.80 % Favored : 75.00 % 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: -0.01 (0.20), residues: 1758 helix: 1.23 (0.20), residues: 715 sheet: 0.33 (0.33), residues: 233 loop : -1.26 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 290 TYR 0.012 0.001 TYR C 206 PHE 0.020 0.001 PHE C 254 TRP 0.014 0.001 TRP A 897 HIS 0.006 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00360 (15659) covalent geometry : angle 0.61870 (21406) SS BOND : bond 0.01937 ( 1) SS BOND : angle 4.82941 ( 2) hydrogen bonds : bond 0.04493 ( 703) hydrogen bonds : angle 4.81368 ( 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 415 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 381 time to evaluate : 0.676 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: A 81 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8446 (ttm110) REVERT: A 270 ASN cc_start: 0.8351 (t0) cc_final: 0.7965 (t0) REVERT: A 430 MET cc_start: 0.8171 (tpt) cc_final: 0.7844 (tpt) REVERT: A 793 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8174 (mp0) REVERT: A 797 MET cc_start: 0.8361 (mtt) cc_final: 0.8053 (mtp) REVERT: A 896 LEU cc_start: 0.7983 (mt) cc_final: 0.7741 (mp) REVERT: A 1049 TRP cc_start: 0.7146 (OUTLIER) cc_final: 0.6810 (m-10) REVERT: A 1138 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7882 (mmt90) REVERT: B 139 LEU cc_start: 0.5976 (OUTLIER) cc_final: 0.5194 (pt) REVERT: B 371 VAL cc_start: 0.8894 (OUTLIER) cc_final: 0.8658 (p) REVERT: B 480 SER cc_start: 0.8995 (m) cc_final: 0.8746 (m) REVERT: C 107 ARG cc_start: 0.8409 (mtm110) cc_final: 0.8061 (mtp180) REVERT: C 129 ASP cc_start: 0.8450 (t0) cc_final: 0.8201 (t0) REVERT: C 201 ASN cc_start: 0.8810 (t0) cc_final: 0.8593 (t0) REVERT: C 400 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7788 (tm-30) outliers start: 34 outliers final: 28 residues processed: 402 average time/residue: 1.0208 time to fit residues: 461.4270 Evaluate side-chains 410 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 376 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 196 VAL Chi-restraints excluded: chain A residue 342 ILE 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 586 THR Chi-restraints excluded: chain A residue 659 HIS 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 1049 TRP 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 B residue 138 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 371 VAL 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 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 400 GLN 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: 7.9990 chunk 135 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS A 264 GLN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 843 GLN B 192 HIS ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.131152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.120486 restraints weight = 81602.004| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.13 r_work: 0.3560 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15660 Z= 0.127 Angle : 0.597 10.747 21408 Z= 0.314 Chirality : 0.039 0.167 2306 Planarity : 0.005 0.054 2600 Dihedral : 14.688 174.113 2422 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.00 % Allowed : 23.00 % Favored : 75.00 % 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: 1.39 (0.20), residues: 721 sheet: 0.33 (0.33), residues: 233 loop : -1.12 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 290 TYR 0.013 0.001 TYR A1108 PHE 0.018 0.001 PHE B 403 TRP 0.018 0.001 TRP A 897 HIS 0.004 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00288 (15659) covalent geometry : angle 0.59597 (21406) SS BOND : bond 0.01714 ( 1) SS BOND : angle 4.17761 ( 2) hydrogen bonds : bond 0.04070 ( 703) hydrogen bonds : angle 4.69384 ( 1933) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10764.92 seconds wall clock time: 182 minutes 15.21 seconds (10935.21 seconds total)