Starting phenix.real_space_refine on Fri Jun 13 16:22:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d3r_27163/06_2025/8d3r_27163.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d3r_27163/06_2025/8d3r_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d3r_27163/06_2025/8d3r_27163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d3r_27163/06_2025/8d3r_27163.map" model { file = "/net/cci-nas-00/data/ceres_data/8d3r_27163/06_2025/8d3r_27163.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d3r_27163/06_2025/8d3r_27163.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.339 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS: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: 9.88, per 1000 atoms: 0.65 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: 3.38 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 5.06 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: 8.78 Time building geometry restraints manager: 4.03 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: 21119 2.60 - 5.21: 183 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=" 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 angle pdb=" O2A DCP A1301 " pdb=" PA DCP A1301 " pdb=" O3A DCP A1301 " ideal model delta sigma weight residual 106.94 116.49 -9.55 1.88e+00 2.83e-01 2.58e+01 ... (remaining 21316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7689 17.99 - 35.97: 1039 35.97 - 53.96: 349 53.96 - 71.95: 85 71.95 - 89.94: 30 Dihedral angle restraints: 9192 sinusoidal: 4090 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 9189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1757 0.038 - 0.076: 375 0.076 - 0.114: 134 0.114 - 0.152: 33 0.152 - 0.190: 2 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=" 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 chirality pdb=" CA ILE A1185 " pdb=" N ILE A1185 " pdb=" C ILE A1185 " pdb=" CB ILE A1185 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-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: 2.110 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: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 42.430 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 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= 0.229 Angle : 0.611 13.020 21323 Z= 0.336 Chirality : 0.039 0.190 2301 Planarity : 0.004 0.061 2577 Dihedral : 18.931 89.937 5895 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (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 TRP 0.010 0.001 TRP B 241 HIS 0.003 0.001 HIS A 71 PHE 0.014 0.001 PHE C 242 TYR 0.014 0.001 TYR A1108 ARG 0.007 0.000 ARG C 146 Details of bonding type rmsd hydrogen bonds : bond 0.15261 ( 685) hydrogen bonds : angle 6.86512 ( 1873) SS BOND : bond 0.00332 ( 1) SS BOND : angle 1.91243 ( 2) covalent geometry : bond 0.00354 (15585) covalent geometry : angle 0.61052 (21321) *********************** 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 : 2.184 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: 0.6037 (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: 0.7718 (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: 0.5396 (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: 0.3058 time to fit residues: 189.2271 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 : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 151 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 0.0770 chunk 91 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 140 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 162 optimal weight: 9.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN A 975 GLN B 397 GLN C 258 HIS C 279 GLN 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 = 0.3966 r_free = 0.3966 target = 0.137996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.124033 restraints weight = 32851.471| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.57 r_work: 0.3674 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15586 Z= 0.206 Angle : 0.677 8.433 21323 Z= 0.354 Chirality : 0.045 0.228 2301 Planarity : 0.005 0.054 2577 Dihedral : 15.472 80.701 2426 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.11 % Allowed : 19.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.20), residues: 1742 helix: 0.52 (0.19), residues: 725 sheet: 0.45 (0.34), residues: 210 loop : -0.52 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 241 HIS 0.007 0.001 HIS A 71 PHE 0.028 0.002 PHE C 242 TYR 0.020 0.002 TYR A 363 ARG 0.006 0.001 ARG B 203 Details of bonding type rmsd hydrogen bonds : bond 0.05193 ( 685) hydrogen bonds : angle 5.13421 ( 1873) SS BOND : bond 0.01903 ( 1) SS BOND : angle 0.93958 ( 2) covalent geometry : bond 0.00466 (15585) covalent geometry : angle 0.67743 (21321) *********************** 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 452 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 389 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 LEU cc_start: 0.6693 (tp) cc_final: 0.6455 (tp) REVERT: A 192 GLU cc_start: 0.7321 (mm-30) cc_final: 0.7107 (mm-30) REVERT: A 197 PHE cc_start: 0.7356 (t80) cc_final: 0.7125 (t80) REVERT: A 220 TRP cc_start: 0.8197 (m100) cc_final: 0.7984 (m100) REVERT: A 438 ASN cc_start: 0.7782 (t0) cc_final: 0.7506 (t0) REVERT: A 461 LYS cc_start: 0.8036 (ttpt) cc_final: 0.7388 (ptpt) REVERT: A 465 ASP cc_start: 0.8096 (m-30) cc_final: 0.7826 (m-30) REVERT: A 776 ASP cc_start: 0.8195 (t0) cc_final: 0.7950 (t0) REVERT: A 875 LYS cc_start: 0.8765 (mtmt) cc_final: 0.8420 (mttp) REVERT: A 877 MET cc_start: 0.8329 (mmm) cc_final: 0.8124 (mmp) REVERT: A 919 MET cc_start: 0.7495 (mtt) cc_final: 0.7246 (mtt) REVERT: A 943 ARG cc_start: 0.5494 (tmt170) cc_final: 0.5253 (ttt-90) REVERT: A 965 LEU cc_start: 0.4762 (OUTLIER) cc_final: 0.4136 (tt) REVERT: A 966 LEU cc_start: 0.7471 (mm) cc_final: 0.7191 (mm) REVERT: A 967 MET cc_start: 0.5599 (mmm) cc_final: 0.4933 (ptt) REVERT: A 986 TYR cc_start: 0.7532 (m-80) cc_final: 0.7168 (m-80) REVERT: A 1136 GLU cc_start: 0.6877 (mp0) cc_final: 0.6634 (mp0) REVERT: A 1167 LYS cc_start: 0.8523 (tptt) cc_final: 0.8291 (tptp) REVERT: A 1196 ASP cc_start: 0.7176 (t0) cc_final: 0.6967 (t0) REVERT: B 301 GLU cc_start: 0.7740 (tt0) cc_final: 0.7441 (tt0) REVERT: B 373 LYS cc_start: 0.9035 (mtmt) cc_final: 0.8678 (mttt) REVERT: B 408 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8191 (mm-30) REVERT: C 107 ARG cc_start: 0.7809 (ttp-170) cc_final: 0.7447 (ttp-170) REVERT: C 118 VAL cc_start: 0.9305 (p) cc_final: 0.9090 (t) REVERT: C 325 ARG cc_start: 0.6752 (mtt-85) cc_final: 0.6348 (mtt90) REVERT: C 385 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8160 (tt) outliers start: 63 outliers final: 42 residues processed: 421 average time/residue: 0.2771 time to fit residues: 168.4765 Evaluate side-chains 407 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 363 time to evaluate : 1.599 ------------------------------------------------------------------------------- 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 240 SER 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 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 813 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 893 SER 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 1095 SER Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 346 MET 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 385 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 476 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 33 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN A 733 HIS A1175 GLN B 132 HIS B 279 GLN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.133306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.119811 restraints weight = 33025.171| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.50 r_work: 0.3613 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 15586 Z= 0.315 Angle : 0.806 11.115 21323 Z= 0.422 Chirality : 0.049 0.232 2301 Planarity : 0.007 0.064 2577 Dihedral : 15.959 77.803 2426 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 6.00 % Allowed : 20.87 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.19), residues: 1742 helix: -0.06 (0.19), residues: 731 sheet: 0.18 (0.34), residues: 206 loop : -1.08 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 175 HIS 0.008 0.002 HIS A 298 PHE 0.039 0.003 PHE C 242 TYR 0.027 0.003 TYR C 206 ARG 0.007 0.001 ARG C 182 Details of bonding type rmsd hydrogen bonds : bond 0.06328 ( 685) hydrogen bonds : angle 5.43015 ( 1873) SS BOND : bond 0.01494 ( 1) SS BOND : angle 2.07112 ( 2) covalent geometry : bond 0.00713 (15585) covalent geometry : angle 0.80622 (21321) *********************** 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 468 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 376 time to evaluate : 1.503 Fit side-chains revert: symmetry clash REVERT: A 438 ASN cc_start: 0.7910 (t0) cc_final: 0.7619 (t0) REVERT: A 461 LYS cc_start: 0.8088 (ttpt) cc_final: 0.7660 (ptpt) REVERT: A 564 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.7087 (mt0) REVERT: A 875 LYS cc_start: 0.8827 (mtmt) cc_final: 0.8519 (mttp) REVERT: A 919 MET cc_start: 0.7615 (mtt) cc_final: 0.7260 (mtt) REVERT: A 963 GLU cc_start: 0.6828 (tm-30) cc_final: 0.6268 (tm-30) REVERT: A 966 LEU cc_start: 0.7553 (mm) cc_final: 0.7347 (mm) REVERT: A 967 MET cc_start: 0.5385 (mmm) cc_final: 0.4931 (ptt) REVERT: A 986 TYR cc_start: 0.7640 (m-80) cc_final: 0.7429 (m-80) REVERT: A 1091 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.5979 (mp0) REVERT: A 1117 LYS cc_start: 0.8227 (ttmm) cc_final: 0.7952 (ttmm) REVERT: A 1196 ASP cc_start: 0.7364 (t0) cc_final: 0.7147 (t0) REVERT: B 145 PHE cc_start: 0.7434 (OUTLIER) cc_final: 0.7087 (m-80) REVERT: B 373 LYS cc_start: 0.9002 (mtmt) cc_final: 0.8638 (mttt) REVERT: B 400 GLN cc_start: 0.7630 (tp40) cc_final: 0.7168 (mt0) REVERT: C 107 ARG cc_start: 0.7784 (ttp-170) cc_final: 0.7396 (ttp-170) REVERT: C 118 VAL cc_start: 0.9357 (p) cc_final: 0.9129 (t) REVERT: C 167 LEU cc_start: 0.6243 (tt) cc_final: 0.6022 (tp) REVERT: C 258 HIS cc_start: 0.8743 (OUTLIER) cc_final: 0.8540 (m170) REVERT: C 325 ARG cc_start: 0.6735 (mtt-85) cc_final: 0.6502 (mtt-85) REVERT: C 385 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8226 (tt) outliers start: 92 outliers final: 61 residues processed: 432 average time/residue: 0.2667 time to fit residues: 167.3953 Evaluate side-chains 423 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 357 time to evaluate : 1.486 ------------------------------------------------------------------------------- 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 201 VAL 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 284 ILE Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 416 GLU 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 553 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 586 THR 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 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 1091 GLU Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1175 GLN Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 162 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 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 102 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 171 LEU 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 258 HIS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 124 optimal weight: 10.0000 chunk 52 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 733 HIS A1175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.138325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.124536 restraints weight = 32616.649| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.58 r_work: 0.3679 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2596 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= 0.132 Angle : 0.631 11.984 21323 Z= 0.326 Chirality : 0.042 0.212 2301 Planarity : 0.005 0.054 2577 Dihedral : 15.689 76.737 2426 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.70 % Allowed : 22.37 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.20), residues: 1742 helix: 0.48 (0.19), residues: 735 sheet: 0.34 (0.35), residues: 212 loop : -0.65 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 175 HIS 0.007 0.001 HIS A 298 PHE 0.034 0.001 PHE B 403 TYR 0.014 0.001 TYR C 432 ARG 0.005 0.000 ARG A1148 Details of bonding type rmsd hydrogen bonds : bond 0.04423 ( 685) hydrogen bonds : angle 4.92635 ( 1873) SS BOND : bond 0.00633 ( 1) SS BOND : angle 1.64967 ( 2) covalent geometry : bond 0.00284 (15585) covalent geometry : angle 0.63049 (21321) *********************** 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 449 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 377 time to evaluate : 1.593 Fit side-chains revert: symmetry clash REVERT: A 197 PHE cc_start: 0.7344 (t80) cc_final: 0.7105 (t80) REVERT: A 264 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8233 (mm-40) REVERT: A 438 ASN cc_start: 0.7720 (t0) cc_final: 0.7453 (t0) REVERT: A 461 LYS cc_start: 0.8017 (ttpt) cc_final: 0.7431 (ptpt) REVERT: A 875 LYS cc_start: 0.8792 (mtmt) cc_final: 0.8478 (mttp) REVERT: A 877 MET cc_start: 0.8321 (mmm) cc_final: 0.8104 (mmp) REVERT: A 919 MET cc_start: 0.7619 (mtt) cc_final: 0.7309 (mtt) REVERT: A 966 LEU cc_start: 0.7526 (mm) cc_final: 0.7324 (mm) REVERT: A 967 MET cc_start: 0.5253 (mmm) cc_final: 0.4675 (ptt) REVERT: A 986 TYR cc_start: 0.7498 (m-80) cc_final: 0.7032 (m-80) REVERT: A 1117 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7906 (ttmm) REVERT: A 1136 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6477 (mp0) REVERT: A 1196 ASP cc_start: 0.7186 (t0) cc_final: 0.6985 (t0) REVERT: B 204 LEU cc_start: 0.6480 (tp) cc_final: 0.6181 (tp) REVERT: B 301 GLU cc_start: 0.7786 (tt0) cc_final: 0.7453 (tt0) REVERT: B 373 LYS cc_start: 0.8983 (mtmt) cc_final: 0.8614 (mttt) REVERT: B 396 ARG cc_start: 0.7959 (tpt170) cc_final: 0.7498 (tpt90) REVERT: B 400 GLN cc_start: 0.7483 (tp40) cc_final: 0.7242 (mt0) REVERT: C 107 ARG cc_start: 0.7788 (ttp-170) cc_final: 0.7394 (ttp-170) REVERT: C 118 VAL cc_start: 0.9300 (p) cc_final: 0.9097 (t) REVERT: C 325 ARG cc_start: 0.6704 (mtt-85) cc_final: 0.6428 (mtt-85) REVERT: C 385 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8191 (tt) outliers start: 72 outliers final: 44 residues processed: 416 average time/residue: 0.2873 time to fit residues: 174.6333 Evaluate side-chains 410 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 362 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU 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 264 GLN Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 416 GLU 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 965 LEU Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1117 LYS 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 162 LEU Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 312 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 463 LYS 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 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 60 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 92 optimal weight: 0.1980 chunk 129 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 85 optimal weight: 0.0970 chunk 42 optimal weight: 0.6980 chunk 121 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A1098 ASN A1175 GLN C 279 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.140321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.126244 restraints weight = 33354.394| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.64 r_work: 0.3706 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 15586 Z= 0.116 Angle : 0.594 11.953 21323 Z= 0.306 Chirality : 0.041 0.193 2301 Planarity : 0.004 0.046 2577 Dihedral : 15.511 76.380 2426 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.10 % Favored : 96.84 % Rotamer: Outliers : 4.44 % Allowed : 23.03 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.20), residues: 1742 helix: 0.70 (0.19), residues: 737 sheet: 0.52 (0.35), residues: 215 loop : -0.42 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 175 HIS 0.004 0.001 HIS A 138 PHE 0.030 0.001 PHE B 403 TYR 0.015 0.001 TYR C 432 ARG 0.005 0.000 ARG A1187 Details of bonding type rmsd hydrogen bonds : bond 0.03930 ( 685) hydrogen bonds : angle 4.64526 ( 1873) SS BOND : bond 0.01244 ( 1) SS BOND : angle 1.71766 ( 2) covalent geometry : bond 0.00250 (15585) covalent geometry : angle 0.59392 (21321) *********************** 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 445 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 377 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 GLN cc_start: 0.6824 (mm110) cc_final: 0.6565 (mt0) REVERT: A 195 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8484 (mp) REVERT: A 264 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8178 (mm-40) REVERT: A 438 ASN cc_start: 0.7631 (t0) cc_final: 0.7328 (t0) REVERT: A 461 LYS cc_start: 0.7946 (ttpt) cc_final: 0.7568 (ptpt) REVERT: A 875 LYS cc_start: 0.8762 (mtmt) cc_final: 0.8441 (mttp) REVERT: A 877 MET cc_start: 0.8297 (mmm) cc_final: 0.8095 (mmp) REVERT: A 919 MET cc_start: 0.7734 (mtt) cc_final: 0.7417 (mtt) REVERT: A 965 LEU cc_start: 0.4830 (OUTLIER) cc_final: 0.4161 (tt) REVERT: A 966 LEU cc_start: 0.7426 (mm) cc_final: 0.7124 (mm) REVERT: A 967 MET cc_start: 0.5102 (mmm) cc_final: 0.4599 (ptt) REVERT: A 1117 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7893 (ttmm) REVERT: A 1136 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6572 (mp0) REVERT: A 1186 ASP cc_start: 0.6977 (t0) cc_final: 0.6754 (t0) REVERT: A 1196 ASP cc_start: 0.7222 (t0) cc_final: 0.6958 (t0) REVERT: A 1224 ILE cc_start: 0.5745 (OUTLIER) cc_final: 0.5513 (pt) REVERT: B 204 LEU cc_start: 0.6243 (tp) cc_final: 0.5940 (tp) REVERT: B 373 LYS cc_start: 0.8955 (mtmt) cc_final: 0.8585 (mttt) REVERT: B 396 ARG cc_start: 0.7998 (tpt170) cc_final: 0.7729 (tpt90) REVERT: B 400 GLN cc_start: 0.7431 (tp40) cc_final: 0.7117 (mt0) REVERT: C 107 ARG cc_start: 0.7699 (ttp-170) cc_final: 0.7317 (ttp-170) REVERT: C 325 ARG cc_start: 0.6662 (mtt-85) cc_final: 0.6410 (mtt-85) REVERT: C 453 ILE cc_start: 0.8317 (pt) cc_final: 0.7976 (mt) outliers start: 68 outliers final: 35 residues processed: 416 average time/residue: 0.2817 time to fit residues: 170.1839 Evaluate side-chains 403 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 362 time to evaluate : 1.500 ------------------------------------------------------------------------------- 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 264 GLN Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 305 SER 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 826 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1117 LYS Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1224 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 256 LEU 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 463 LYS 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 386 ASP Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 167 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 153 optimal weight: 0.0030 chunk 14 optimal weight: 0.9980 chunk 134 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 overall best weight: 1.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A1175 GLN B 454 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.138977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.124980 restraints weight = 32921.218| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.61 r_work: 0.3686 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2770 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 : 0.610 11.436 21323 Z= 0.315 Chirality : 0.041 0.194 2301 Planarity : 0.004 0.049 2577 Dihedral : 15.508 75.657 2426 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.33 % Favored : 96.61 % Rotamer: Outliers : 4.76 % Allowed : 23.09 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.20), residues: 1742 helix: 0.74 (0.19), residues: 736 sheet: 0.40 (0.34), residues: 224 loop : -0.42 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 175 HIS 0.005 0.001 HIS A 298 PHE 0.028 0.001 PHE B 403 TYR 0.018 0.001 TYR A 622 ARG 0.005 0.000 ARG A1187 Details of bonding type rmsd hydrogen bonds : bond 0.04129 ( 685) hydrogen bonds : angle 4.62133 ( 1873) SS BOND : bond 0.00605 ( 1) SS BOND : angle 1.44820 ( 2) covalent geometry : bond 0.00306 (15585) covalent geometry : angle 0.60996 (21321) *********************** 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 439 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 366 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 GLN cc_start: 0.6863 (mm110) cc_final: 0.6602 (mt0) REVERT: A 195 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8480 (mp) REVERT: A 438 ASN cc_start: 0.7754 (t0) cc_final: 0.7438 (t0) REVERT: A 461 LYS cc_start: 0.7917 (ttpt) cc_final: 0.7400 (ptpt) REVERT: A 792 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7659 (tt) REVERT: A 875 LYS cc_start: 0.8765 (mtmt) cc_final: 0.8408 (mttp) REVERT: A 919 MET cc_start: 0.7782 (mtt) cc_final: 0.7454 (mtt) REVERT: A 965 LEU cc_start: 0.4814 (OUTLIER) cc_final: 0.4096 (tt) REVERT: A 966 LEU cc_start: 0.7442 (mm) cc_final: 0.7180 (mm) REVERT: A 1117 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7891 (ttmm) REVERT: A 1133 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.6602 (mt) REVERT: A 1136 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6267 (mp0) REVERT: A 1186 ASP cc_start: 0.6941 (t0) cc_final: 0.6708 (t0) REVERT: A 1196 ASP cc_start: 0.7220 (t0) cc_final: 0.6956 (t0) REVERT: B 373 LYS cc_start: 0.8966 (mtmt) cc_final: 0.8597 (mttt) REVERT: B 396 ARG cc_start: 0.7979 (tpt170) cc_final: 0.7681 (tpt90) REVERT: B 400 GLN cc_start: 0.7515 (tp40) cc_final: 0.7173 (mt0) REVERT: C 107 ARG cc_start: 0.7789 (ttp-170) cc_final: 0.7407 (ttp-170) REVERT: C 325 ARG cc_start: 0.6632 (mtt-85) cc_final: 0.6224 (mtt90) REVERT: C 425 LEU cc_start: 0.7883 (mt) cc_final: 0.7498 (mt) REVERT: C 453 ILE cc_start: 0.8276 (pt) cc_final: 0.7978 (mt) outliers start: 73 outliers final: 51 residues processed: 407 average time/residue: 0.2790 time to fit residues: 165.8164 Evaluate side-chains 414 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 357 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU 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 264 GLN Chi-restraints excluded: chain A residue 266 VAL 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 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 792 LEU 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 826 ILE 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 965 LEU Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1117 LYS Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 312 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 393 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 127 optimal weight: 8.9990 chunk 117 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 151 optimal weight: 0.1980 chunk 41 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN B 366 ASN B 454 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.139696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.125688 restraints weight = 32977.528| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.62 r_work: 0.3695 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2840 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= 0.126 Angle : 0.610 11.399 21323 Z= 0.313 Chirality : 0.041 0.194 2301 Planarity : 0.004 0.048 2577 Dihedral : 15.475 74.897 2426 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.16 % Favored : 96.79 % Rotamer: Outliers : 4.76 % Allowed : 23.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.20), residues: 1742 helix: 0.78 (0.19), residues: 737 sheet: 0.47 (0.34), residues: 224 loop : -0.40 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 175 HIS 0.020 0.001 HIS B 454 PHE 0.027 0.001 PHE B 403 TYR 0.017 0.001 TYR C 432 ARG 0.005 0.000 ARG A1187 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 685) hydrogen bonds : angle 4.56566 ( 1873) SS BOND : bond 0.00523 ( 1) SS BOND : angle 1.45640 ( 2) covalent geometry : bond 0.00276 (15585) covalent geometry : angle 0.61007 (21321) *********************** 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 439 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 366 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 GLN cc_start: 0.6831 (mm110) cc_final: 0.6574 (mt0) REVERT: A 178 TYR cc_start: 0.7690 (m-80) cc_final: 0.7390 (m-10) REVERT: A 195 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8419 (mp) REVERT: A 438 ASN cc_start: 0.7711 (t0) cc_final: 0.7405 (t0) REVERT: A 461 LYS cc_start: 0.7889 (ttpt) cc_final: 0.7426 (ptpt) REVERT: A 792 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7642 (tt) REVERT: A 826 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7846 (tt) REVERT: A 875 LYS cc_start: 0.8752 (mtmt) cc_final: 0.8398 (mttp) REVERT: A 919 MET cc_start: 0.7795 (mtt) cc_final: 0.7475 (mtt) REVERT: A 965 LEU cc_start: 0.4819 (OUTLIER) cc_final: 0.4162 (tt) REVERT: A 966 LEU cc_start: 0.7399 (mm) cc_final: 0.7149 (mm) REVERT: A 1091 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.6056 (mp0) REVERT: A 1117 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7852 (ttmm) REVERT: A 1133 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.6766 (mt) REVERT: A 1136 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6616 (mp0) REVERT: A 1186 ASP cc_start: 0.6947 (t0) cc_final: 0.6708 (t0) REVERT: A 1196 ASP cc_start: 0.7176 (t0) cc_final: 0.6926 (t0) REVERT: B 373 LYS cc_start: 0.8950 (mtmt) cc_final: 0.8572 (mttt) REVERT: B 396 ARG cc_start: 0.7976 (tpt170) cc_final: 0.7687 (tpt90) REVERT: B 400 GLN cc_start: 0.7530 (tp40) cc_final: 0.7203 (mt0) REVERT: C 107 ARG cc_start: 0.7779 (ttp-170) cc_final: 0.7389 (ttp-170) REVERT: C 325 ARG cc_start: 0.6623 (mtt-85) cc_final: 0.6362 (mtt-85) REVERT: C 385 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8181 (tt) REVERT: C 425 LEU cc_start: 0.7823 (mt) cc_final: 0.7439 (mt) REVERT: C 453 ILE cc_start: 0.8266 (pt) cc_final: 0.7969 (mt) outliers start: 73 outliers final: 46 residues processed: 408 average time/residue: 0.2814 time to fit residues: 168.4875 Evaluate side-chains 411 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 356 time to evaluate : 1.644 ------------------------------------------------------------------------------- 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 195 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 305 SER 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 792 LEU 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 826 ILE 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 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 1117 LYS Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 312 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 463 LYS Chi-restraints excluded: chain C residue 70 LEU 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 350 LEU Chi-restraints excluded: chain C residue 385 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 60 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 51 optimal weight: 0.0030 chunk 36 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 173 optimal weight: 10.0000 overall best weight: 2.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN B 366 ASN ** B 454 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 = 0.3958 r_free = 0.3958 target = 0.137082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.123253 restraints weight = 32771.552| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.56 r_work: 0.3661 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15586 Z= 0.184 Angle : 0.667 11.038 21323 Z= 0.345 Chirality : 0.043 0.205 2301 Planarity : 0.005 0.052 2577 Dihedral : 15.657 73.962 2426 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.90 % Favored : 96.04 % Rotamer: Outliers : 4.76 % Allowed : 23.61 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.20), residues: 1742 helix: 0.54 (0.19), residues: 736 sheet: 0.26 (0.35), residues: 215 loop : -0.57 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 175 HIS 0.008 0.001 HIS B 454 PHE 0.024 0.002 PHE B 403 TYR 0.019 0.002 TYR A1108 ARG 0.009 0.001 ARG C 146 Details of bonding type rmsd hydrogen bonds : bond 0.04789 ( 685) hydrogen bonds : angle 4.78850 ( 1873) SS BOND : bond 0.00642 ( 1) SS BOND : angle 1.64495 ( 2) covalent geometry : bond 0.00415 (15585) covalent geometry : angle 0.66730 (21321) *********************** 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 439 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 366 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 GLN cc_start: 0.6869 (mm110) cc_final: 0.6560 (mt0) REVERT: A 178 TYR cc_start: 0.7739 (m-80) cc_final: 0.7385 (m-10) REVERT: A 195 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8423 (mp) REVERT: A 197 PHE cc_start: 0.7236 (t80) cc_final: 0.6999 (t80) REVERT: A 438 ASN cc_start: 0.7837 (t0) cc_final: 0.7522 (t0) REVERT: A 461 LYS cc_start: 0.7925 (ttpt) cc_final: 0.7490 (ptpt) REVERT: A 564 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.7101 (mt0) REVERT: A 792 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7746 (tt) REVERT: A 875 LYS cc_start: 0.8795 (mtmt) cc_final: 0.8454 (mttp) REVERT: A 919 MET cc_start: 0.7845 (mtt) cc_final: 0.7550 (mtt) REVERT: A 953 ARG cc_start: 0.6967 (OUTLIER) cc_final: 0.6746 (ptp-170) REVERT: A 1091 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6131 (mp0) REVERT: A 1117 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7880 (ttmm) REVERT: A 1136 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6549 (mp0) REVERT: A 1186 ASP cc_start: 0.6953 (t0) cc_final: 0.6709 (t0) REVERT: A 1196 ASP cc_start: 0.7333 (t0) cc_final: 0.7091 (t0) REVERT: B 373 LYS cc_start: 0.8983 (mtmt) cc_final: 0.8611 (mttt) REVERT: B 396 ARG cc_start: 0.8014 (tpt170) cc_final: 0.7642 (tpt90) REVERT: B 400 GLN cc_start: 0.7615 (tp40) cc_final: 0.7112 (mt0) REVERT: C 107 ARG cc_start: 0.7754 (ttp-170) cc_final: 0.7343 (ttp-170) REVERT: C 325 ARG cc_start: 0.6682 (mtt-85) cc_final: 0.6400 (mtt-85) REVERT: C 385 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8221 (tt) REVERT: C 425 LEU cc_start: 0.7837 (mt) cc_final: 0.7497 (mt) outliers start: 73 outliers final: 52 residues processed: 409 average time/residue: 0.2740 time to fit residues: 163.5819 Evaluate side-chains 415 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 355 time to evaluate : 1.745 ------------------------------------------------------------------------------- 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 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 564 GLN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 792 LEU 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 826 ILE 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 953 ARG 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 1117 LYS Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 256 LEU 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 393 LEU Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 70 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 147 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 171 optimal weight: 6.9990 chunk 177 optimal weight: 8.9990 chunk 72 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 175 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 ASN B 454 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.138505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.124511 restraints weight = 32788.637| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.59 r_work: 0.3680 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15586 Z= 0.140 Angle : 0.641 11.146 21323 Z= 0.328 Chirality : 0.042 0.203 2301 Planarity : 0.005 0.061 2577 Dihedral : 15.576 72.944 2426 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.21 % Favored : 96.73 % Rotamer: Outliers : 4.24 % Allowed : 24.46 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.20), residues: 1742 helix: 0.64 (0.19), residues: 738 sheet: 0.36 (0.34), residues: 224 loop : -0.56 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 175 HIS 0.005 0.001 HIS A 298 PHE 0.026 0.001 PHE B 403 TYR 0.023 0.002 TYR C 432 ARG 0.012 0.000 ARG C 122 Details of bonding type rmsd hydrogen bonds : bond 0.04303 ( 685) hydrogen bonds : angle 4.68522 ( 1873) SS BOND : bond 0.00323 ( 1) SS BOND : angle 2.79510 ( 2) covalent geometry : bond 0.00311 (15585) covalent geometry : angle 0.64032 (21321) *********************** 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 435 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 370 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 GLN cc_start: 0.6847 (mm110) cc_final: 0.6549 (mt0) REVERT: A 175 TRP cc_start: 0.7938 (m100) cc_final: 0.7659 (m100) REVERT: A 178 TYR cc_start: 0.7718 (m-80) cc_final: 0.7367 (m-10) REVERT: A 195 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8386 (mp) REVERT: A 197 PHE cc_start: 0.7232 (t80) cc_final: 0.6996 (t80) REVERT: A 438 ASN cc_start: 0.7798 (t0) cc_final: 0.7483 (t0) REVERT: A 461 LYS cc_start: 0.7958 (ttpt) cc_final: 0.7405 (ptpt) REVERT: A 564 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.7077 (mt0) REVERT: A 792 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7708 (tt) REVERT: A 826 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7908 (tt) REVERT: A 875 LYS cc_start: 0.8772 (mtmt) cc_final: 0.8404 (mttp) REVERT: A 919 MET cc_start: 0.7810 (mtt) cc_final: 0.7509 (mtt) REVERT: A 953 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.6546 (ptp-170) REVERT: A 1081 ARG cc_start: 0.7278 (mtm-85) cc_final: 0.7017 (mtm-85) REVERT: A 1091 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6084 (mp0) REVERT: A 1136 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6222 (mp0) REVERT: A 1186 ASP cc_start: 0.6980 (t0) cc_final: 0.6740 (t0) REVERT: A 1196 ASP cc_start: 0.7253 (t0) cc_final: 0.7017 (t0) REVERT: B 373 LYS cc_start: 0.8962 (mtmt) cc_final: 0.8596 (mttt) REVERT: B 396 ARG cc_start: 0.8027 (tpt170) cc_final: 0.7690 (tpt90) REVERT: B 400 GLN cc_start: 0.7581 (tp40) cc_final: 0.7126 (mt0) REVERT: C 107 ARG cc_start: 0.7753 (ttp-170) cc_final: 0.7348 (ttp-170) REVERT: C 325 ARG cc_start: 0.6660 (mtt-85) cc_final: 0.6388 (mtt-85) REVERT: C 385 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8190 (tt) REVERT: C 425 LEU cc_start: 0.7774 (mt) cc_final: 0.7499 (mt) outliers start: 65 outliers final: 50 residues processed: 409 average time/residue: 0.3207 time to fit residues: 196.5995 Evaluate side-chains 422 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 364 time to evaluate : 1.665 ------------------------------------------------------------------------------- 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 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 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 564 GLN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 792 LEU 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 826 ILE 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 953 ARG 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 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 213 VAL Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 256 LEU 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 393 LEU Chi-restraints excluded: chain B residue 454 HIS 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 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 437 ILE 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 57 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 159 optimal weight: 9.9990 chunk 161 optimal weight: 0.2980 chunk 131 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 24 optimal weight: 0.0170 chunk 150 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 170 optimal weight: 0.9990 overall best weight: 0.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.140374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.126245 restraints weight = 33016.070| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.63 r_work: 0.3705 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15586 Z= 0.121 Angle : 0.633 11.540 21323 Z= 0.323 Chirality : 0.042 0.207 2301 Planarity : 0.004 0.072 2577 Dihedral : 15.431 75.517 2426 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.16 % Favored : 96.79 % Rotamer: Outliers : 3.59 % Allowed : 25.57 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.20), residues: 1742 helix: 0.75 (0.19), residues: 737 sheet: 0.41 (0.34), residues: 228 loop : -0.49 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 175 HIS 0.026 0.001 HIS B 454 PHE 0.027 0.001 PHE B 403 TYR 0.023 0.001 TYR C 432 ARG 0.011 0.000 ARG C 122 Details of bonding type rmsd hydrogen bonds : bond 0.03963 ( 685) hydrogen bonds : angle 4.58187 ( 1873) SS BOND : bond 0.01007 ( 1) SS BOND : angle 2.29718 ( 2) covalent geometry : bond 0.00260 (15585) covalent geometry : angle 0.63306 (21321) ********************** 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 428 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 373 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 GLN cc_start: 0.6841 (mm110) cc_final: 0.6557 (mt0) REVERT: A 178 TYR cc_start: 0.7672 (m-80) cc_final: 0.7356 (m-10) REVERT: A 195 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8354 (mp) REVERT: A 438 ASN cc_start: 0.7715 (t0) cc_final: 0.7421 (t0) REVERT: A 564 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.7145 (mt0) REVERT: A 792 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7619 (tt) REVERT: A 826 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7916 (tt) REVERT: A 875 LYS cc_start: 0.8733 (mtmt) cc_final: 0.8377 (mttp) REVERT: A 919 MET cc_start: 0.7794 (mtt) cc_final: 0.7492 (mtt) REVERT: A 953 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.6566 (ptp-170) REVERT: A 1081 ARG cc_start: 0.7218 (mtm-85) cc_final: 0.6981 (mtm-85) REVERT: A 1091 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.6044 (mp0) REVERT: A 1093 MET cc_start: 0.3474 (pmm) cc_final: 0.3268 (pmm) REVERT: A 1136 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6630 (mp0) REVERT: A 1186 ASP cc_start: 0.6948 (t0) cc_final: 0.6693 (t0) REVERT: A 1196 ASP cc_start: 0.7204 (t0) cc_final: 0.6971 (t0) REVERT: B 301 GLU cc_start: 0.7754 (tt0) cc_final: 0.7404 (tt0) REVERT: B 373 LYS cc_start: 0.8943 (mtmt) cc_final: 0.8572 (mttt) REVERT: B 396 ARG cc_start: 0.7996 (tpt170) cc_final: 0.7694 (tpt90) REVERT: B 400 GLN cc_start: 0.7574 (tp40) cc_final: 0.7142 (mt0) REVERT: C 107 ARG cc_start: 0.7731 (ttp-170) cc_final: 0.7351 (ttp-170) REVERT: C 325 ARG cc_start: 0.6622 (mtt-85) cc_final: 0.6363 (mtt-85) REVERT: C 385 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8182 (tt) outliers start: 55 outliers final: 38 residues processed: 403 average time/residue: 0.2694 time to fit residues: 158.9664 Evaluate side-chains 415 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 369 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU 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 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 564 GLN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 792 LEU 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 826 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 953 ARG 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 1136 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 229 LYS 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 350 LEU Chi-restraints excluded: chain C residue 385 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 86 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 176 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.134685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.121014 restraints weight = 33020.411| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.52 r_work: 0.3631 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 15586 Z= 0.274 Angle : 0.788 12.649 21323 Z= 0.407 Chirality : 0.047 0.219 2301 Planarity : 0.006 0.074 2577 Dihedral : 15.857 74.858 2426 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.54 % Favored : 95.41 % Rotamer: Outliers : 4.17 % Allowed : 25.51 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.20), residues: 1742 helix: 0.21 (0.19), residues: 738 sheet: 0.05 (0.35), residues: 218 loop : -0.88 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 175 HIS 0.009 0.002 HIS C 258 PHE 0.039 0.003 PHE B 403 TYR 0.030 0.003 TYR C 432 ARG 0.011 0.001 ARG C 146 Details of bonding type rmsd hydrogen bonds : bond 0.05698 ( 685) hydrogen bonds : angle 5.12768 ( 1873) SS BOND : bond 0.00761 ( 1) SS BOND : angle 3.28259 ( 2) covalent geometry : bond 0.00622 (15585) covalent geometry : angle 0.78777 (21321) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7122.75 seconds wall clock time: 123 minutes 41.63 seconds (7421.63 seconds total)