Starting phenix.real_space_refine on Sat Sep 12 10:15:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d3r_27163/09_2026/8d3r_27163.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d3r_27163/09_2026/8d3r_27163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d3r_27163/09_2026/8d3r_27163.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d3r_27163/09_2026/8d3r_27163.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8d3r_27163/09_2026/8d3r_27163.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d3r_27163/09_2026/8d3r_27163.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d3r_27163/09_2026/8d3r_27163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d3r_27163/09_2026/8d3r_27163.map" } resolution = 3.04 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= 0.339 sd= 0.597 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 48 5.49 5 S 82 5.16 5 C 9490 2.51 5 N 2647 2.21 5 O 2845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15113 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 958, 7629 Classifications: {'peptide': 958} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 64, 'TRANS': 893} Chain breaks: 6 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 3308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3308 Classifications: {'peptide': 411} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} 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: 3222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3222 Classifications: {'peptide': 399} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 2 Chain: "P" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 452 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "T" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 473 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' CA': 1, 'DCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.98, per 1000 atoms: 0.20 Number of scatterers: 15113 At special positions: 0 Unit cell: (107.95, 114.75, 151.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 82 16.00 P 48 15.00 O 2845 8.00 N 2647 7.00 C 9490 6.00 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 628.1 milliseconds 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3294 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 14 sheets defined 48.0% alpha, 13.6% beta 17 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 72 through 76 removed outlier: 4.233A pdb=" N ILE A 76 " --> pdb=" O PRO A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 88 removed outlier: 3.535A pdb=" N HIS A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU A 85 " --> pdb=" O ARG A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 110 Processing helix chain 'A' and resid 134 through 160 Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.767A pdb=" N VAL A 229 " --> pdb=" O SER A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 244 removed outlier: 3.591A pdb=" N LEU A 244 " --> pdb=" O PRO A 241 " (cutoff:3.500A) 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: 3.946A pdb=" N TYR A 282 " --> pdb=" O ARG A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 305 through 316 removed outlier: 4.299A pdb=" N SER A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 removed outlier: 3.899A pdb=" N ASP A 349 " --> pdb=" O ASP A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 removed outlier: 3.516A pdb=" N VAL A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 388 removed outlier: 3.581A pdb=" N GLU A 387 " --> pdb=" O LYS A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 418 removed outlier: 3.618A pdb=" N GLN A 398 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP A 399 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 400 " --> pdb=" O CYS A 396 " (cutoff:3.500A) Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 431 removed outlier: 4.085A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 431 " --> pdb=" O MET A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 471 Processing helix chain 'A' and resid 472 through 482 removed outlier: 3.825A pdb=" N SER A 475 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N GLY A 476 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N TYR A 479 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 488 removed outlier: 4.114A pdb=" N ASP A 487 " --> pdb=" O TRP A 484 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A 488 " --> pdb=" O LEU A 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 484 through 488' Processing helix chain 'A' and resid 538 through 554 removed outlier: 4.162A pdb=" N ASP A 542 " --> pdb=" O GLU A 538 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A 543 " --> pdb=" O PHE A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 559 removed outlier: 3.580A pdb=" N LEU A 558 " --> pdb=" O THR A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 577 removed outlier: 3.750A pdb=" N LEU A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 603 Processing helix chain 'A' and resid 648 through 661 Processing helix chain 'A' and resid 769 through 776 removed outlier: 4.382A pdb=" N LYS A 773 " --> pdb=" O ASP A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 810 removed outlier: 4.889A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.481A 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 826 Processing helix chain 'A' and resid 871 through 878 removed outlier: 4.524A pdb=" N LYS A 875 " --> pdb=" O SER A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 908 removed outlier: 4.353A pdb=" N ALA A 899 " --> pdb=" O GLU A 895 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE A 907 " --> pdb=" O GLY A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 921 Processing helix chain 'A' and resid 930 through 940 Processing helix chain 'A' and resid 945 through 955 removed outlier: 4.426A pdb=" N PHE A 949 " --> pdb=" O HIS A 945 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG A 953 " --> pdb=" O PHE A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 970 removed outlier: 4.029A pdb=" N PHE A 961 " --> pdb=" O ALA A 957 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 966 " --> pdb=" O ALA A 962 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASN A 970 " --> pdb=" O LEU A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 981 through 987 removed outlier: 3.728A pdb=" N MET A 985 " --> pdb=" O LYS A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1056 removed outlier: 3.596A pdb=" N GLU A1056 " --> pdb=" O THR A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1065 removed outlier: 3.530A pdb=" N LEU A1061 " --> pdb=" O MET A1057 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N SER A1063 " --> pdb=" O ASN A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1084 removed outlier: 3.547A pdb=" N GLU A1084 " --> pdb=" O ARG A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1124 removed outlier: 3.783A pdb=" N VAL A1100 " --> pdb=" O ARG A1096 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1168 Processing helix chain 'A' and resid 1205 through 1210 removed outlier: 3.622A pdb=" N TYR A1210 " --> pdb=" O MET A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1228 removed outlier: 3.501A pdb=" N ILE A1223 " --> pdb=" O ASP A1219 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 76 removed outlier: 4.083A pdb=" N LEU B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 119 Processing helix chain 'B' and resid 150 through 157 removed outlier: 4.029A pdb=" N GLU B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 177 removed outlier: 4.543A pdb=" N LEU B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLU B 172 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 191 removed outlier: 4.656A pdb=" N GLY B 188 " --> pdb=" O ASN B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 193 No H-bonds generated for 'chain 'B' and resid 192 through 193' Processing helix chain 'B' and resid 194 through 199 removed outlier: 3.890A pdb=" N ASP B 198 " --> pdb=" O ASN B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 266 removed outlier: 4.125A 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 removed outlier: 3.504A pdb=" N TYR B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 323 Processing helix chain 'B' and resid 342 through 353 Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 391 through 409 removed outlier: 3.713A pdb=" N ASN B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 435 Processing helix chain 'B' and resid 444 through 450 Processing helix chain 'B' and resid 470 through 484 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 149 through 159 removed outlier: 3.583A pdb=" N LEU C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 178 removed outlier: 4.228A pdb=" N ALA C 169 " --> pdb=" O GLU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 192 removed outlier: 4.615A pdb=" N GLY C 188 " --> pdb=" O ASN C 184 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N HIS C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 198 removed outlier: 3.842A pdb=" N ASP C 198 " --> pdb=" O VAL C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 201 No H-bonds generated for 'chain 'C' and resid 199 through 201' 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: 4.108A 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 342 through 354 Processing helix chain 'C' and resid 391 through 409 removed outlier: 3.632A pdb=" N ASN C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'C' and resid 424 through 435 Processing helix chain 'C' and resid 444 through 450 removed outlier: 3.831A pdb=" N LEU C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 485 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187 removed outlier: 3.925A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 211 " --> pdb=" O GLU A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 268 removed outlier: 6.316A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 435 through 437 removed outlier: 4.819A pdb=" N TYR A 837 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 816 " --> pdb=" O TYR A 837 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 814 " --> pdb=" O ALA A 839 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 747 through 751 removed outlier: 3.583A pdb=" N SER A 615 " --> pdb=" O GLY A 619 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1128 through 1131 removed outlier: 6.843A pdb=" N ARG A1138 " --> pdb=" O CYS A1130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.568A pdb=" N PHE B 126 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N ILE B 211 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL B 335 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LYS B 297 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE B 293 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 301 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN B 305 " --> pdb=" O LYS B 285 " (cutoff:3.500A) removed outlier: 5.191A 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 Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 149 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: 6.231A pdb=" N ALA B 384 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL B 443 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 7.074A 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: 6.151A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU C 301 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LYS C 285 " --> pdb=" O ASN C 305 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 133 through 134 removed outlier: 3.698A pdb=" N LYS C 134 " --> pdb=" O LYS C 180 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS C 180 " --> pdb=" O LYS C 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 324 through 325 Processing sheet with id=AB5, first strand: chain 'C' and resid 413 through 415 removed outlier: 6.415A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) 641 hydrogen bonds defined for protein. 1785 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 2.52 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3059 1.33 - 1.45: 3885 1.45 - 1.57: 8422 1.57 - 1.69: 89 1.69 - 1.81: 130 Bond restraints: 15585 Sorted by residual: bond pdb=" O5' DCP A1301 " pdb=" PA DCP A1301 " ideal model delta sigma weight residual 1.579 1.804 -0.225 1.50e-02 4.44e+03 2.25e+02 bond pdb=" C5' DCP A1301 " pdb=" O5' DCP A1301 " ideal model delta sigma weight residual 1.443 1.322 0.121 1.10e-02 8.26e+03 1.21e+02 bond pdb=" O3A DCP A1301 " pdb=" PB DCP A1301 " ideal model delta sigma weight residual 1.592 1.710 -0.118 1.10e-02 8.26e+03 1.14e+02 bond pdb=" O3B DCP A1301 " pdb=" PG DCP A1301 " ideal model delta sigma weight residual 1.600 1.652 -0.052 1.10e-02 8.26e+03 2.25e+01 bond pdb=" C4 DCP A1301 " pdb=" N4 DCP A1301 " ideal model delta sigma weight residual 1.334 1.390 -0.056 1.20e-02 6.94e+03 2.17e+01 ... (remaining 15580 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 21083 2.60 - 5.21: 219 5.21 - 7.81: 10 7.81 - 10.42: 7 10.42 - 13.02: 2 Bond angle restraints: 21321 Sorted by residual: angle pdb=" C1' DCP A1301 " pdb=" O4' DCP A1301 " pdb=" C4' DCP A1301 " ideal model delta sigma weight residual 109.55 101.71 7.84 1.31e+00 5.82e-01 3.58e+01 angle pdb=" PB DCP A1301 " pdb=" O3B DCP A1301 " pdb=" PG DCP A1301 " ideal model delta sigma weight residual 139.87 133.96 5.91 1.00e+00 1.00e+00 3.49e+01 angle pdb=" O2G DCP A1301 " pdb=" PG DCP A1301 " pdb=" O3B DCP A1301 " ideal model delta sigma weight residual 104.48 98.01 6.47 1.14e+00 7.76e-01 3.25e+01 angle pdb=" O4' DA P 23 " pdb=" C1' DA P 23 " pdb=" N9 DA P 23 " ideal model delta sigma weight residual 108.00 111.84 -3.84 7.00e-01 2.04e+00 3.01e+01 angle pdb=" O3A DCP A1301 " pdb=" PB DCP A1301 " pdb=" O3B DCP A1301 " ideal model delta sigma weight residual 101.57 93.17 8.40 1.54e+00 4.24e-01 2.99e+01 ... (remaining 21316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7673 17.99 - 35.97: 1034 35.97 - 53.96: 348 53.96 - 71.95: 84 71.95 - 89.94: 29 Dihedral angle restraints: 9168 sinusoidal: 4066 harmonic: 5102 Sorted by residual: dihedral pdb=" CA GLN A 159 " pdb=" C GLN A 159 " pdb=" N ALA A 160 " pdb=" CA ALA A 160 " ideal model delta harmonic sigma weight residual -180.00 -161.17 -18.83 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CB CYS A 418 " pdb=" SG CYS A 418 " pdb=" SG CYS A1077 " pdb=" CB CYS A1077 " ideal model delta sinusoidal sigma weight residual 93.00 123.82 -30.82 1 1.00e+01 1.00e-02 1.36e+01 dihedral pdb=" CA VAL A 196 " pdb=" C VAL A 196 " pdb=" N PHE A 197 " pdb=" CA PHE A 197 " ideal model delta harmonic sigma weight residual 180.00 -163.22 -16.78 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 9165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1750 0.038 - 0.076: 346 0.076 - 0.114: 132 0.114 - 0.152: 66 0.152 - 0.190: 7 Chirality restraints: 2301 Sorted by residual: chirality pdb=" CA VAL C 228 " pdb=" N VAL C 228 " pdb=" C VAL C 228 " pdb=" CB VAL C 228 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.07e-01 chirality pdb=" C3' DT T 6 " pdb=" C4' DT T 6 " pdb=" O3' DT T 6 " pdb=" C2' DT T 6 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" C1' DCP A1301 " pdb=" C2' DCP A1301 " pdb=" N1 DCP A1301 " pdb=" O4' DCP A1301 " both_signs ideal model delta sigma weight residual False 2.45 2.28 0.16 2.00e-01 2.50e+01 6.66e-01 ... (remaining 2298 not shown) Planarity restraints: 2577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 532 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.69e+00 pdb=" C PRO A 532 " 0.033 2.00e-02 2.50e+03 pdb=" O PRO A 532 " -0.013 2.00e-02 2.50e+03 pdb=" N CYS A 533 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA P 23 " 0.025 2.00e-02 2.50e+03 1.15e-02 3.64e+00 pdb=" N9 DA P 23 " -0.028 2.00e-02 2.50e+03 pdb=" C8 DA P 23 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA P 23 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA P 23 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA P 23 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA P 23 " 0.005 2.00e-02 2.50e+03 pdb=" N1 DA P 23 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA P 23 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA P 23 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA P 23 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A1152 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C ALA A1152 " 0.028 2.00e-02 2.50e+03 pdb=" O ALA A1152 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU A1153 " -0.009 2.00e-02 2.50e+03 ... (remaining 2574 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 119 2.53 - 3.12: 11471 3.12 - 3.72: 23490 3.72 - 4.31: 31204 4.31 - 4.90: 52743 Nonbonded interactions: 119027 Sorted by model distance: nonbonded pdb=" O LEU A1153 " pdb=" OG1 THR A1156 " model vdw 1.941 3.040 nonbonded pdb=" O LEU C 147 " pdb=" OG SER C 178 " model vdw 2.032 3.040 nonbonded pdb=" OG SER A 302 " pdb=" O ILE A 350 " model vdw 2.051 3.040 nonbonded pdb=" OG1 THR C 444 " pdb=" OE1 GLU C 445 " model vdw 2.064 3.040 nonbonded pdb=" OG1 THR A1199 " pdb=" OD1 ASN A1202 " model vdw 2.107 3.040 ... (remaining 119022 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 through 219 or resid 228 through 355 or resid 368 throu \ gh 485)) selection = chain 'C' } 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: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.020 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 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 0.225 15586 Z= 0.286 Angle : 0.636 13.020 21323 Z= 0.399 Chirality : 0.042 0.190 2301 Planarity : 0.004 0.061 2577 Dihedral : 18.890 89.937 5871 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.20 % Allowed : 22.37 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.21), residues: 1742 helix: 0.29 (0.20), residues: 710 sheet: 0.50 (0.33), residues: 225 loop : -0.39 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 146 TYR 0.014 0.001 TYR A1108 PHE 0.014 0.001 PHE C 242 TRP 0.010 0.001 TRP B 241 HIS 0.003 0.001 HIS A 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.29 (15585) covalent geometry : angle 0.63597 / 0.40 (21321) SS BOND : bond 0.00332 / 0.17 ( 1) SS BOND : angle 1.91243 / 1.12 ( 2) hydrogen bonds : bond 0.15261 / 10.96 ( 685) hydrogen bonds : angle 6.86512 / 4.81 ( 1873) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 440 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 PHE cc_start: 0.7336 (t80) cc_final: 0.6866 (t80) REVERT: A 304 LEU cc_start: 0.6400 (mt) cc_final: 0.6038 (mm) REVERT: A 438 ASN cc_start: 0.7586 (t0) cc_final: 0.7225 (t0) REVERT: A 461 LYS cc_start: 0.8044 (ttpt) cc_final: 0.7717 (ptpt) REVERT: A 793 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7697 (mt-10) REVERT: A 875 LYS cc_start: 0.8710 (mtmt) cc_final: 0.8452 (mttp) REVERT: A 877 MET cc_start: 0.8233 (mmm) cc_final: 0.7878 (mmp) REVERT: A 919 MET cc_start: 0.6904 (mtt) cc_final: 0.6691 (mtt) REVERT: A 943 ARG cc_start: 0.5633 (tmt170) cc_final: 0.5397 (ttt-90) REVERT: A 963 GLU cc_start: 0.6446 (tm-30) cc_final: 0.6064 (tm-30) REVERT: A 965 LEU cc_start: 0.4927 (mm) cc_final: 0.4218 (tt) REVERT: A 967 MET cc_start: 0.5754 (mmm) cc_final: 0.5137 (ptt) REVERT: A 1196 ASP cc_start: 0.6939 (t0) cc_final: 0.6724 (t0) REVERT: B 301 GLU cc_start: 0.7672 (tt0) cc_final: 0.7433 (tt0) REVERT: B 305 ASN cc_start: 0.8463 (t0) cc_final: 0.8174 (t0) REVERT: B 373 LYS cc_start: 0.8891 (mtmt) cc_final: 0.8512 (mttt) REVERT: B 408 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7814 (tm-30) REVERT: C 107 ARG cc_start: 0.7341 (ttp-170) cc_final: 0.7005 (ttp-170) REVERT: C 279 GLN cc_start: 0.7717 (mt0) cc_final: 0.7032 (mm-40) REVERT: C 325 ARG cc_start: 0.6716 (mtt-85) cc_final: 0.6351 (mtt90) REVERT: C 394 GLU cc_start: 0.7380 (mm-30) cc_final: 0.6939 (mm-30) outliers start: 3 outliers final: 0 residues processed: 440 average time/residue: 0.1399 time to fit residues: 87.5674 Evaluate side-chains 377 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 HIS A 493 GLN A 975 GLN B 397 GLN C 258 HIS C 313 HIS C 397 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.141090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.126962 restraints weight = 32937.865| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.60 r_work: 0.3717 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15586 Z= 0.145 Angle : 0.634 7.298 21323 Z= 0.334 Chirality : 0.043 0.267 2301 Planarity : 0.005 0.044 2577 Dihedral : 15.251 81.034 2402 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.13 % Allowed : 20.74 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.20), residues: 1742 helix: 0.81 (0.20), residues: 721 sheet: 0.58 (0.34), residues: 214 loop : -0.35 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 146 TYR 0.019 0.002 TYR A 363 PHE 0.028 0.002 PHE C 242 TRP 0.015 0.001 TRP B 241 HIS 0.005 0.001 HIS C 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (15585) covalent geometry : angle 0.63344 / 0.33 (21321) SS BOND : bond 0.01652 / 0.87 ( 1) SS BOND : angle 1.34506 / 0.78 ( 2) hydrogen bonds : bond 0.04960 / 3.46 ( 685) hydrogen bonds : angle 5.08725 / 3.56 ( 1873) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 397 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 PHE cc_start: 0.7356 (t80) cc_final: 0.6961 (t80) REVERT: A 220 TRP cc_start: 0.8175 (m100) cc_final: 0.7892 (m100) REVERT: A 438 ASN cc_start: 0.7561 (t0) cc_final: 0.7274 (t0) REVERT: A 461 LYS cc_start: 0.8008 (ttpt) cc_final: 0.7628 (ptpt) REVERT: A 875 LYS cc_start: 0.8773 (mtmt) cc_final: 0.8436 (mttp) REVERT: A 919 MET cc_start: 0.7486 (mtt) cc_final: 0.7236 (mtt) REVERT: A 943 ARG cc_start: 0.5599 (tmt170) cc_final: 0.5360 (ttt-90) REVERT: A 965 LEU cc_start: 0.5125 (OUTLIER) cc_final: 0.4575 (tt) REVERT: A 966 LEU cc_start: 0.7523 (mm) cc_final: 0.7230 (mm) REVERT: A 967 MET cc_start: 0.5617 (mmm) cc_final: 0.4920 (ptt) REVERT: A 986 TYR cc_start: 0.7474 (m-80) cc_final: 0.7058 (m-80) REVERT: A 1136 GLU cc_start: 0.6746 (mp0) cc_final: 0.6097 (mp0) REVERT: A 1142 ARG cc_start: 0.6243 (ttm-80) cc_final: 0.6011 (ttm-80) REVERT: A 1186 ASP cc_start: 0.6718 (t0) cc_final: 0.6451 (t0) REVERT: B 373 LYS cc_start: 0.8993 (mtmt) cc_final: 0.8631 (mttt) REVERT: C 107 ARG cc_start: 0.7751 (ttp-170) cc_final: 0.7399 (ttp-170) REVERT: C 325 ARG cc_start: 0.6802 (mtt-85) cc_final: 0.6405 (mtt90) REVERT: C 385 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8116 (tt) outliers start: 48 outliers final: 27 residues processed: 416 average time/residue: 0.1239 time to fit residues: 75.8534 Evaluate side-chains 405 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 376 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 363 TYR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 149 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 104 optimal weight: 0.0060 chunk 116 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 47 optimal weight: 0.0020 chunk 136 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 171 optimal weight: 6.9990 overall best weight: 3.0010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN A 493 GLN A1171 ASN B 132 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.137530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.123551 restraints weight = 33313.263| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.59 r_work: 0.3665 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15586 Z= 0.203 Angle : 0.688 8.405 21323 Z= 0.361 Chirality : 0.045 0.194 2301 Planarity : 0.005 0.055 2577 Dihedral : 15.497 79.828 2402 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.41 % Allowed : 18.26 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.20), residues: 1742 helix: 0.62 (0.19), residues: 722 sheet: 0.47 (0.34), residues: 212 loop : -0.59 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 203 TYR 0.018 0.002 TYR A 622 PHE 0.038 0.002 PHE C 242 TRP 0.027 0.002 TRP A 175 HIS 0.007 0.002 HIS A 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (15585) covalent geometry : angle 0.68757 / 0.36 (21321) SS BOND : bond 0.00208 / 0.11 ( 1) SS BOND : angle 1.58945 / 0.91 ( 2) hydrogen bonds : bond 0.05305 / 3.67 ( 685) hydrogen bonds : angle 5.01515 / 3.55 ( 1873) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 384 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 438 ASN cc_start: 0.7828 (t0) cc_final: 0.7546 (t0) REVERT: A 461 LYS cc_start: 0.8051 (ttpt) cc_final: 0.7484 (ptpt) REVERT: A 875 LYS cc_start: 0.8769 (mtmt) cc_final: 0.8431 (mttp) REVERT: A 919 MET cc_start: 0.7577 (mtt) cc_final: 0.7123 (mtp) REVERT: A 943 ARG cc_start: 0.5515 (tmt170) cc_final: 0.5276 (ttt-90) REVERT: A 965 LEU cc_start: 0.4708 (OUTLIER) cc_final: 0.3922 (tt) REVERT: A 966 LEU cc_start: 0.7474 (mm) cc_final: 0.7218 (mm) REVERT: A 967 MET cc_start: 0.5524 (mmm) cc_final: 0.4883 (ptt) REVERT: A 986 TYR cc_start: 0.7565 (m-80) cc_final: 0.7217 (m-80) REVERT: A 1136 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6277 (mp0) REVERT: A 1148 ARG cc_start: 0.8078 (mtp85) cc_final: 0.7821 (mtp85) REVERT: B 301 GLU cc_start: 0.7765 (tt0) cc_final: 0.7493 (tt0) REVERT: B 373 LYS cc_start: 0.9021 (mtmt) cc_final: 0.8666 (mttt) REVERT: C 107 ARG cc_start: 0.7820 (ttp-170) cc_final: 0.7444 (ttp-170) REVERT: C 325 ARG cc_start: 0.6731 (mtt-85) cc_final: 0.6482 (mtt-85) REVERT: C 385 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8193 (tt) outliers start: 83 outliers final: 51 residues processed: 436 average time/residue: 0.1224 time to fit residues: 79.1498 Evaluate side-chains 415 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 361 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 363 TYR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 823 ARG Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 864 ASN Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 81 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 72 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 10 optimal weight: 0.1980 chunk 150 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN C 279 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.138783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.124771 restraints weight = 32980.567| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.60 r_work: 0.3682 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15586 Z= 0.146 Angle : 0.632 11.902 21323 Z= 0.329 Chirality : 0.042 0.186 2301 Planarity : 0.005 0.051 2577 Dihedral : 15.492 78.496 2402 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.44 % Allowed : 20.03 % Favored : 75.54 % 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: 0.15 (0.20), residues: 1742 helix: 0.71 (0.19), residues: 731 sheet: 0.50 (0.34), residues: 219 loop : -0.52 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1187 TYR 0.015 0.002 TYR C 432 PHE 0.035 0.002 PHE B 403 TRP 0.017 0.001 TRP B 241 HIS 0.004 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (15585) covalent geometry : angle 0.63139 / 0.33 (21321) SS BOND : bond 0.00376 / 0.20 ( 1) SS BOND : angle 1.71454 / 1.00 ( 2) hydrogen bonds : bond 0.04590 / 3.17 ( 685) hydrogen bonds : angle 4.85170 / 3.42 ( 1873) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 376 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7730 (m-80) cc_final: 0.7399 (m-10) REVERT: A 438 ASN cc_start: 0.7813 (t0) cc_final: 0.7537 (t0) REVERT: A 461 LYS cc_start: 0.8027 (ttpt) cc_final: 0.7515 (ptpt) REVERT: A 875 LYS cc_start: 0.8750 (mtmt) cc_final: 0.8404 (mttp) REVERT: A 919 MET cc_start: 0.7623 (mtt) cc_final: 0.7203 (mtt) REVERT: A 965 LEU cc_start: 0.4750 (OUTLIER) cc_final: 0.4126 (tt) REVERT: A 966 LEU cc_start: 0.7484 (mm) cc_final: 0.7180 (mm) REVERT: A 967 MET cc_start: 0.5439 (mmm) cc_final: 0.4805 (ptt) REVERT: A 986 TYR cc_start: 0.7521 (m-80) cc_final: 0.7158 (m-80) REVERT: A 1136 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6208 (mp0) REVERT: B 70 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8040 (mm) REVERT: B 373 LYS cc_start: 0.9000 (mtmt) cc_final: 0.8645 (mttt) REVERT: B 400 GLN cc_start: 0.7536 (tp40) cc_final: 0.7248 (mt0) REVERT: C 107 ARG cc_start: 0.7797 (ttp-170) cc_final: 0.7404 (ttp-170) REVERT: C 325 ARG cc_start: 0.6720 (mtt-85) cc_final: 0.6478 (mtt-85) REVERT: C 385 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8177 (tt) outliers start: 68 outliers final: 48 residues processed: 412 average time/residue: 0.1204 time to fit residues: 73.2365 Evaluate side-chains 408 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 356 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 363 TYR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 823 ARG Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1102 GLN Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 178 optimal weight: 20.0000 chunk 115 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN B 279 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.136924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.123079 restraints weight = 32960.887| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.57 r_work: 0.3658 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15586 Z= 0.198 Angle : 0.676 9.931 21323 Z= 0.353 Chirality : 0.044 0.191 2301 Planarity : 0.005 0.053 2577 Dihedral : 15.662 78.664 2402 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.67 % Favored : 96.27 % Rotamer: Outliers : 5.54 % Allowed : 21.07 % Favored : 73.39 % 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: -0.11 (0.20), residues: 1742 helix: 0.51 (0.19), residues: 736 sheet: 0.35 (0.35), residues: 216 loop : -0.66 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1187 TYR 0.019 0.002 TYR A 622 PHE 0.032 0.002 PHE B 403 TRP 0.024 0.002 TRP A 175 HIS 0.005 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 (15585) covalent geometry : angle 0.67587 / 0.35 (21321) SS BOND : bond 0.00433 / 0.23 ( 1) SS BOND : angle 2.15363 / 1.23 ( 2) hydrogen bonds : bond 0.05080 / 3.51 ( 685) hydrogen bonds : angle 4.97854 / 3.54 ( 1873) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 374 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8646 (mp) REVERT: A 438 ASN cc_start: 0.7806 (t0) cc_final: 0.7531 (t0) REVERT: A 461 LYS cc_start: 0.8053 (ttpt) cc_final: 0.7570 (ptpt) REVERT: A 491 ASP cc_start: 0.8082 (p0) cc_final: 0.7870 (p0) REVERT: A 875 LYS cc_start: 0.8766 (mtmt) cc_final: 0.8443 (mttp) REVERT: A 919 MET cc_start: 0.7702 (mtt) cc_final: 0.7357 (mtt) REVERT: A 965 LEU cc_start: 0.4744 (OUTLIER) cc_final: 0.3931 (tt) REVERT: A 966 LEU cc_start: 0.7451 (mm) cc_final: 0.7189 (mm) REVERT: A 967 MET cc_start: 0.5331 (mmm) cc_final: 0.4772 (ptt) REVERT: A 986 TYR cc_start: 0.7563 (m-80) cc_final: 0.7123 (m-80) REVERT: A 1133 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.6746 (mt) REVERT: A 1136 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6277 (mp0) REVERT: B 70 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8160 (mm) REVERT: B 373 LYS cc_start: 0.9013 (mtmt) cc_final: 0.8661 (mttt) REVERT: B 400 GLN cc_start: 0.7597 (tp40) cc_final: 0.7180 (mt0) REVERT: C 71 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7423 (mm-30) REVERT: C 107 ARG cc_start: 0.7775 (ttp-170) cc_final: 0.7380 (ttp-170) REVERT: C 325 ARG cc_start: 0.6720 (mtt-85) cc_final: 0.6311 (mtt90) REVERT: C 385 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8221 (tt) outliers start: 85 outliers final: 59 residues processed: 419 average time/residue: 0.1184 time to fit residues: 73.8551 Evaluate side-chains 435 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 369 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 823 ARG Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 864 ASN Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1102 GLN Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1175 GLN Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 106 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 GLN A 493 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.138817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.124828 restraints weight = 32995.856| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.60 r_work: 0.3683 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15586 Z= 0.136 Angle : 0.626 11.990 21323 Z= 0.325 Chirality : 0.042 0.179 2301 Planarity : 0.005 0.051 2577 Dihedral : 15.622 77.265 2402 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.04 % Favored : 96.90 % Rotamer: Outliers : 4.57 % Allowed : 22.83 % Favored : 72.60 % 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: 0.11 (0.20), residues: 1742 helix: 0.70 (0.19), residues: 735 sheet: 0.48 (0.35), residues: 216 loop : -0.56 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1187 TYR 0.017 0.001 TYR C 432 PHE 0.032 0.001 PHE C 242 TRP 0.023 0.001 TRP A 175 HIS 0.004 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (15585) covalent geometry : angle 0.62616 / 0.32 (21321) SS BOND : bond 0.00054 / 0.03 ( 1) SS BOND : angle 2.00046 / 1.15 ( 2) hydrogen bonds : bond 0.04433 / 3.06 ( 685) hydrogen bonds : angle 4.78637 / 3.39 ( 1873) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 375 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7735 (m-80) cc_final: 0.7400 (m-10) REVERT: A 195 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8577 (mp) REVERT: A 438 ASN cc_start: 0.7738 (t0) cc_final: 0.7465 (t0) REVERT: A 461 LYS cc_start: 0.8008 (ttpt) cc_final: 0.7530 (ptpt) REVERT: A 875 LYS cc_start: 0.8766 (mtmt) cc_final: 0.8433 (mttp) REVERT: A 919 MET cc_start: 0.7736 (mtt) cc_final: 0.7407 (mtt) REVERT: A 965 LEU cc_start: 0.4756 (OUTLIER) cc_final: 0.4060 (tt) REVERT: A 966 LEU cc_start: 0.7496 (mm) cc_final: 0.7193 (mm) REVERT: A 967 MET cc_start: 0.5278 (mmm) cc_final: 0.4693 (ptt) REVERT: A 986 TYR cc_start: 0.7518 (m-80) cc_final: 0.7003 (m-80) REVERT: A 1091 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.5883 (mp0) REVERT: A 1133 ILE cc_start: 0.7717 (OUTLIER) cc_final: 0.6551 (mt) REVERT: A 1136 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6203 (mp0) REVERT: B 70 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8041 (mm) REVERT: B 373 LYS cc_start: 0.8990 (mtmt) cc_final: 0.8634 (mttt) REVERT: B 400 GLN cc_start: 0.7601 (tp40) cc_final: 0.7212 (mt0) REVERT: C 71 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7396 (mm-30) REVERT: C 107 ARG cc_start: 0.7774 (ttp-170) cc_final: 0.7376 (ttp-170) REVERT: C 229 LYS cc_start: 0.7919 (mmtt) cc_final: 0.7678 (tptt) REVERT: C 325 ARG cc_start: 0.6726 (mtt-85) cc_final: 0.6318 (mtt90) REVERT: C 385 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8237 (tt) REVERT: C 425 LEU cc_start: 0.7922 (mt) cc_final: 0.7552 (mt) outliers start: 70 outliers final: 54 residues processed: 412 average time/residue: 0.1247 time to fit residues: 75.8751 Evaluate side-chains 424 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 362 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 823 ARG Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 864 ASN Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1091 GLU Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1175 GLN Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 151 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 45 optimal weight: 0.3980 chunk 95 optimal weight: 9.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.136451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.122641 restraints weight = 32975.672| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.54 r_work: 0.3655 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15586 Z= 0.199 Angle : 0.687 11.278 21323 Z= 0.356 Chirality : 0.045 0.189 2301 Planarity : 0.005 0.054 2577 Dihedral : 15.776 77.385 2402 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.85 % Favored : 96.10 % Rotamer: Outliers : 5.41 % Allowed : 22.50 % Favored : 72.08 % 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: -0.18 (0.20), residues: 1742 helix: 0.49 (0.19), residues: 737 sheet: 0.30 (0.34), residues: 224 loop : -0.76 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 146 TYR 0.018 0.002 TYR C 206 PHE 0.028 0.002 PHE C 242 TRP 0.025 0.001 TRP A 175 HIS 0.005 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.20 (15585) covalent geometry : angle 0.68635 / 0.36 (21321) SS BOND : bond 0.00561 / 0.30 ( 1) SS BOND : angle 2.10470 / 1.15 ( 2) hydrogen bonds : bond 0.05074 / 3.50 ( 685) hydrogen bonds : angle 4.93180 / 3.50 ( 1873) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 363 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8591 (mp) REVERT: A 438 ASN cc_start: 0.7862 (t0) cc_final: 0.7565 (t0) REVERT: A 461 LYS cc_start: 0.7999 (ttpt) cc_final: 0.7551 (ptpt) REVERT: A 875 LYS cc_start: 0.8785 (mtmt) cc_final: 0.8472 (mttp) REVERT: A 919 MET cc_start: 0.7830 (mtt) cc_final: 0.7507 (mtt) REVERT: A 965 LEU cc_start: 0.4707 (OUTLIER) cc_final: 0.3914 (tt) REVERT: A 966 LEU cc_start: 0.7561 (mm) cc_final: 0.7329 (mm) REVERT: A 986 TYR cc_start: 0.7550 (m-80) cc_final: 0.7097 (m-80) REVERT: A 1081 ARG cc_start: 0.7389 (mtm-85) cc_final: 0.6979 (mtm-85) REVERT: A 1091 GLU cc_start: 0.6625 (OUTLIER) cc_final: 0.5966 (mp0) REVERT: A 1133 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.6863 (mt) REVERT: A 1136 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6574 (mp0) REVERT: A 1161 ARG cc_start: 0.6674 (OUTLIER) cc_final: 0.5940 (mmt-90) REVERT: B 70 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8173 (mm) REVERT: B 373 LYS cc_start: 0.9004 (mtmt) cc_final: 0.8654 (mttt) REVERT: B 400 GLN cc_start: 0.7620 (tp40) cc_final: 0.7182 (mt0) REVERT: C 71 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7378 (mm-30) REVERT: C 107 ARG cc_start: 0.7777 (ttp-170) cc_final: 0.7377 (ttp-170) REVERT: C 229 LYS cc_start: 0.7984 (mmtt) cc_final: 0.7745 (tptt) REVERT: C 325 ARG cc_start: 0.6667 (mtt-85) cc_final: 0.6426 (mtt-85) REVERT: C 385 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8284 (tt) REVERT: C 425 LEU cc_start: 0.7922 (mt) cc_final: 0.7505 (mt) outliers start: 83 outliers final: 65 residues processed: 406 average time/residue: 0.1197 time to fit residues: 71.9424 Evaluate side-chains 431 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 357 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 823 ARG Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 864 ASN Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1091 GLU Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1161 ARG Chi-restraints excluded: chain A residue 1175 GLN Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 479 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 137 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 145 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 GLN B 366 ASN ** C 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.138423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.124369 restraints weight = 32988.977| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.62 r_work: 0.3678 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15586 Z= 0.138 Angle : 0.641 11.691 21323 Z= 0.330 Chirality : 0.043 0.173 2301 Planarity : 0.005 0.052 2577 Dihedral : 15.724 75.895 2402 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.10 % Favored : 96.84 % Rotamer: Outliers : 4.83 % Allowed : 23.61 % Favored : 71.56 % 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: 0.03 (0.20), residues: 1742 helix: 0.64 (0.19), residues: 737 sheet: 0.40 (0.35), residues: 220 loop : -0.61 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1187 TYR 0.023 0.002 TYR A 178 PHE 0.027 0.002 PHE B 403 TRP 0.029 0.001 TRP A 175 HIS 0.004 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (15585) covalent geometry : angle 0.64062 / 0.33 (21321) SS BOND : bond 0.00115 / 0.06 ( 1) SS BOND : angle 1.44490 / 0.78 ( 2) hydrogen bonds : bond 0.04445 / 3.08 ( 685) hydrogen bonds : angle 4.77403 / 3.39 ( 1873) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 370 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.7574 (ptt) cc_final: 0.7370 (ptp) REVERT: A 178 TYR cc_start: 0.7606 (m-80) cc_final: 0.7134 (m-80) REVERT: A 195 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8542 (mp) REVERT: A 438 ASN cc_start: 0.7762 (t0) cc_final: 0.7467 (t0) REVERT: A 461 LYS cc_start: 0.7982 (ttpt) cc_final: 0.7529 (ptpt) REVERT: A 875 LYS cc_start: 0.8761 (mtmt) cc_final: 0.8432 (mttp) REVERT: A 919 MET cc_start: 0.7790 (mtt) cc_final: 0.7464 (mtt) REVERT: A 965 LEU cc_start: 0.4678 (OUTLIER) cc_final: 0.3938 (tt) REVERT: A 966 LEU cc_start: 0.7576 (mm) cc_final: 0.7344 (mm) REVERT: A 1081 ARG cc_start: 0.7313 (mtm-85) cc_final: 0.6875 (mtm-85) REVERT: A 1091 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.5929 (mp0) REVERT: A 1133 ILE cc_start: 0.7735 (OUTLIER) cc_final: 0.6566 (mt) REVERT: A 1136 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6185 (mp0) REVERT: A 1142 ARG cc_start: 0.6719 (ttm-80) cc_final: 0.6480 (ttt180) REVERT: A 1221 TYR cc_start: 0.6187 (OUTLIER) cc_final: 0.4172 (m-80) REVERT: B 70 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8062 (mm) REVERT: B 373 LYS cc_start: 0.8977 (mtmt) cc_final: 0.8622 (mttt) REVERT: B 396 ARG cc_start: 0.7971 (tpt90) cc_final: 0.7269 (tpt170) REVERT: B 400 GLN cc_start: 0.7595 (tp40) cc_final: 0.7104 (mt0) REVERT: C 71 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7312 (mm-30) REVERT: C 107 ARG cc_start: 0.7771 (ttp-170) cc_final: 0.7382 (ttp-170) REVERT: C 229 LYS cc_start: 0.7940 (mmtt) cc_final: 0.7680 (tptt) REVERT: C 325 ARG cc_start: 0.6678 (mtt-85) cc_final: 0.6397 (mtt-85) REVERT: C 425 LEU cc_start: 0.7843 (mt) cc_final: 0.7496 (mt) outliers start: 74 outliers final: 53 residues processed: 409 average time/residue: 0.1208 time to fit residues: 73.3158 Evaluate side-chains 422 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 361 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 823 ARG Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 864 ASN Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1091 GLU Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1175 GLN Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 153 optimal weight: 0.0470 chunk 98 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 56 optimal weight: 0.0570 chunk 55 optimal weight: 0.7980 chunk 168 optimal weight: 0.0030 chunk 5 optimal weight: 10.0000 overall best weight: 0.3808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN A1098 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.141329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.127116 restraints weight = 32760.437| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.64 r_work: 0.3719 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15586 Z= 0.121 Angle : 0.622 12.133 21323 Z= 0.320 Chirality : 0.042 0.208 2301 Planarity : 0.005 0.102 2577 Dihedral : 15.600 74.020 2402 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.27 % Favored : 96.67 % Rotamer: Outliers : 3.13 % Allowed : 24.59 % Favored : 72.28 % 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: 0.28 (0.20), residues: 1742 helix: 0.83 (0.19), residues: 735 sheet: 0.52 (0.34), residues: 233 loop : -0.47 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1187 TYR 0.019 0.001 TYR A 622 PHE 0.026 0.001 PHE B 403 TRP 0.036 0.001 TRP A 175 HIS 0.003 0.001 HIS A 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (15585) covalent geometry : angle 0.62218 / 0.32 (21321) SS BOND : bond 0.01137 / 0.60 ( 1) SS BOND : angle 1.41702 / 0.76 ( 2) hydrogen bonds : bond 0.03985 / 2.75 ( 685) hydrogen bonds : angle 4.58848 / 3.25 ( 1873) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 382 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.7573 (ptt) cc_final: 0.7322 (ptp) REVERT: A 144 GLN cc_start: 0.6781 (mm-40) cc_final: 0.6524 (mt0) REVERT: A 175 TRP cc_start: 0.7881 (m100) cc_final: 0.7632 (m100) REVERT: A 195 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8367 (mp) REVERT: A 438 ASN cc_start: 0.7640 (t0) cc_final: 0.7343 (t0) REVERT: A 461 LYS cc_start: 0.7903 (ttpt) cc_final: 0.7506 (ptpt) REVERT: A 875 LYS cc_start: 0.8728 (mtmt) cc_final: 0.8393 (mttp) REVERT: A 919 MET cc_start: 0.7757 (mtt) cc_final: 0.7432 (mtt) REVERT: A 965 LEU cc_start: 0.4704 (OUTLIER) cc_final: 0.4068 (tt) REVERT: A 966 LEU cc_start: 0.7425 (mm) cc_final: 0.7165 (mm) REVERT: A 1081 ARG cc_start: 0.7251 (mtm-85) cc_final: 0.6823 (mtm-85) REVERT: A 1091 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.5913 (mp0) REVERT: A 1093 MET cc_start: 0.3557 (pmm) cc_final: 0.3312 (pmm) REVERT: A 1136 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6620 (mp0) REVERT: B 373 LYS cc_start: 0.8923 (mtmt) cc_final: 0.8558 (mttt) REVERT: B 396 ARG cc_start: 0.7954 (tpt90) cc_final: 0.7322 (tpt170) REVERT: B 400 GLN cc_start: 0.7526 (tp40) cc_final: 0.7110 (mt0) REVERT: C 107 ARG cc_start: 0.7737 (ttp-170) cc_final: 0.7356 (ttp-170) REVERT: C 325 ARG cc_start: 0.6644 (mtt-85) cc_final: 0.6371 (mtt-85) outliers start: 48 outliers final: 28 residues processed: 406 average time/residue: 0.1178 time to fit residues: 71.6430 Evaluate side-chains 405 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 373 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 823 ARG Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1091 GLU Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 69 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 134 optimal weight: 3.9990 chunk 63 optimal weight: 0.3980 chunk 6 optimal weight: 0.0370 chunk 40 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 167 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1175 GLN B 250 GLN B 258 HIS B 454 HIS C 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.141463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.127295 restraints weight = 32828.573| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.64 r_work: 0.3719 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15586 Z= 0.115 Angle : 0.621 11.844 21323 Z= 0.317 Chirality : 0.042 0.196 2301 Planarity : 0.004 0.072 2577 Dihedral : 15.580 72.717 2402 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.99 % Favored : 96.96 % Rotamer: Outliers : 2.67 % Allowed : 26.42 % Favored : 70.91 % 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: 0.34 (0.20), residues: 1742 helix: 0.86 (0.19), residues: 736 sheet: 0.60 (0.34), residues: 233 loop : -0.42 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 122 TYR 0.020 0.001 TYR C 432 PHE 0.022 0.001 PHE B 403 TRP 0.022 0.001 TRP A 175 HIS 0.005 0.001 HIS C 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 (15585) covalent geometry : angle 0.62057 / 0.32 (21321) SS BOND : bond 0.00546 / 0.29 ( 1) SS BOND : angle 1.49275 / 0.80 ( 2) hydrogen bonds : bond 0.03916 / 2.66 ( 685) hydrogen bonds : angle 4.56719 / 3.23 ( 1873) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 378 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.7608 (ptt) cc_final: 0.7338 (ptp) REVERT: A 144 GLN cc_start: 0.6816 (mm-40) cc_final: 0.6553 (mt0) REVERT: A 195 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8257 (mp) REVERT: A 382 MET cc_start: 0.6285 (tpp) cc_final: 0.6027 (tpt) REVERT: A 438 ASN cc_start: 0.7635 (t0) cc_final: 0.7314 (t0) REVERT: A 461 LYS cc_start: 0.7855 (ttpt) cc_final: 0.7465 (ptpt) REVERT: A 875 LYS cc_start: 0.8721 (mtmt) cc_final: 0.8365 (mttp) REVERT: A 919 MET cc_start: 0.7752 (mtt) cc_final: 0.7427 (mtt) REVERT: A 965 LEU cc_start: 0.4721 (OUTLIER) cc_final: 0.4047 (tt) REVERT: A 966 LEU cc_start: 0.7481 (mm) cc_final: 0.7243 (mm) REVERT: A 1081 ARG cc_start: 0.7277 (mtm-85) cc_final: 0.6815 (mtm-85) REVERT: A 1091 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.5938 (mp0) REVERT: A 1093 MET cc_start: 0.3501 (pmm) cc_final: 0.3220 (pmm) REVERT: A 1136 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6669 (mp0) REVERT: B 373 LYS cc_start: 0.8920 (mtmt) cc_final: 0.8542 (mttt) REVERT: B 385 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7674 (tp) REVERT: B 396 ARG cc_start: 0.7982 (tpt90) cc_final: 0.7339 (tpt170) REVERT: B 400 GLN cc_start: 0.7525 (tp40) cc_final: 0.7113 (mt0) REVERT: C 107 ARG cc_start: 0.7738 (ttp-170) cc_final: 0.7358 (ttp-170) REVERT: C 325 ARG cc_start: 0.6654 (mtt-85) cc_final: 0.6237 (mtt90) outliers start: 41 outliers final: 28 residues processed: 396 average time/residue: 0.1137 time to fit residues: 67.3513 Evaluate side-chains 404 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 371 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 823 ARG Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1091 GLU Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 454 HIS Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 42 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 2 optimal weight: 0.5980 chunk 166 optimal weight: 0.9990 chunk 145 optimal weight: 8.9990 chunk 170 optimal weight: 0.8980 chunk 164 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 HIS B 454 HIS ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.140962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.126824 restraints weight = 32948.161| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.63 r_work: 0.3714 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15586 Z= 0.123 Angle : 0.622 11.713 21323 Z= 0.318 Chirality : 0.042 0.208 2301 Planarity : 0.004 0.050 2577 Dihedral : 15.580 72.515 2402 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.10 % Favored : 96.84 % Rotamer: Outliers : 2.87 % Allowed : 26.42 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.20), residues: 1742 helix: 0.89 (0.19), residues: 736 sheet: 0.47 (0.34), residues: 235 loop : -0.42 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 122 TYR 0.023 0.002 TYR C 432 PHE 0.023 0.001 PHE C 242 TRP 0.032 0.001 TRP A 175 HIS 0.011 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (15585) covalent geometry : angle 0.62202 / 0.32 (21321) SS BOND : bond 0.00550 / 0.29 ( 1) SS BOND : angle 1.49175 / 0.80 ( 2) hydrogen bonds : bond 0.03946 / 2.69 ( 685) hydrogen bonds : angle 4.55455 / 3.22 ( 1873) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3472.68 seconds wall clock time: 60 minutes 19.12 seconds (3619.12 seconds total)