Starting phenix.real_space_refine on Fri Aug 7 02:00:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fok_29352/08_2026/8fok_29352.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fok_29352/08_2026/8fok_29352.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fok_29352/08_2026/8fok_29352.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fok_29352/08_2026/8fok_29352.map" model { file = "/net/cci-nas-00/data/ceres_data/8fok_29352/08_2026/8fok_29352.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fok_29352/08_2026/8fok_29352.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8fok_29352/08_2026/8fok_29352.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fok_29352/08_2026/8fok_29352.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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 Fe 4 7.16 5 P 34 5.49 5 S 94 5.16 5 C 11854 2.51 5 N 3234 2.21 5 O 3607 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18827 Number of models: 1 Model: "" Number of chains: 7 Chain: "1" Number of atoms: 8250 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1046, 8242 Classifications: {'peptide': 1046} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 50, 'TRANS': 995} Chain breaks: 5 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ARG:plan': 6, 'GLN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 69 Conformer: "B" Number of residues, atoms: 1046, 8242 Classifications: {'peptide': 1046} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 50, 'TRANS': 995} Chain breaks: 5 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ARG:plan': 6, 'GLN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 69 bond proxies already assigned to first conformer: 8385 Chain: "A" Number of atoms: 2866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2866 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 333} Chain breaks: 3 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ASN:plan1': 3, 'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 3555 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 430, 3532 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 13, 'TRANS': 416} Chain breaks: 5 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 39 Conformer: "B" Number of residues, atoms: 430, 3532 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 13, 'TRANS': 416} Chain breaks: 5 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 39 bond proxies already assigned to first conformer: 3581 Chain: "C" Number of atoms: 3428 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 433, 3414 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 5, 'PTRANS': 24, 'TRANS': 403} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 433, 3414 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 5, 'PTRANS': 24, 'TRANS': 403} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3476 Chain: "T" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 415 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "P" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 305 Classifications: {'DNA': 4, 'RNAv2': 10} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna3p': 13} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13324 SG CYS B 336 56.588 105.469 67.146 1.00 50.15 S ATOM 14113 SG CYS B 434 61.539 104.824 63.164 1.00 54.17 S ATOM 13981 SG CYS B 417 62.615 105.241 69.680 1.00 45.11 S ATOM 14430 SG CYS B 474 60.780 110.248 66.747 1.00 62.10 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AASP 11414 " occ=0.25 ... (14 atoms not shown) pdb=" OD2BASP 11414 " occ=0.75 residue: pdb=" N AASP C 263 " occ=0.30 ... (14 atoms not shown) pdb=" OD2BASP C 263 " occ=0.70 residue: pdb=" N ACYS C 399 " occ=0.95 ... (10 atoms not shown) pdb=" SG BCYS C 399 " occ=0.05 Time building chain proxies: 4.80, per 1000 atoms: 0.25 Number of scatterers: 18827 At special positions: 0 Unit cell: (95.22, 160.632, 163.944, 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) Fe 4 26.01 S 94 16.00 P 34 15.00 O 3607 8.00 N 3234 7.00 C 11854 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 996.7 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 601 " pdb="FE1 SF4 B 601 " - pdb=" SG CYS B 336 " pdb="FE4 SF4 B 601 " - pdb=" SG CYS B 474 " pdb="FE3 SF4 B 601 " - pdb=" SG CYS B 417 " pdb="FE2 SF4 B 601 " - pdb=" SG CYS B 434 " Number of angles added : 12 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4344 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 19 sheets defined 50.3% alpha, 14.0% beta 5 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain '1' and resid 402 through 419 Proline residue: 1 412 - end of helix Processing helix chain '1' and resid 480 through 489 Processing helix chain '1' and resid 597 through 606 Processing helix chain '1' and resid 615 through 631 Processing helix chain '1' and resid 643 through 656 Processing helix chain '1' and resid 659 through 664 Processing helix chain '1' and resid 682 through 691 Processing helix chain '1' and resid 701 through 708 Processing helix chain '1' and resid 715 through 724 Processing helix chain '1' and resid 738 through 743 Processing helix chain '1' and resid 744 through 768 Processing helix chain '1' and resid 769 through 782 Processing helix chain '1' and resid 784 through 790 Processing helix chain '1' and resid 793 through 807 Processing helix chain '1' and resid 867 through 877 Processing helix chain '1' and resid 904 through 925 removed outlier: 3.517A pdb=" N ARG 1 908 " --> pdb=" O GLY 1 904 " (cutoff:3.500A) Processing helix chain '1' and resid 933 through 953 removed outlier: 3.516A pdb=" N TYR 1 951 " --> pdb=" O ALA 1 947 " (cutoff:3.500A) Processing helix chain '1' and resid 963 through 988 Processing helix chain '1' and resid 1008 through 1025 removed outlier: 3.835A pdb=" N ALA 11012 " --> pdb=" O ASN 11008 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE 11015 " --> pdb=" O ASP 11011 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU 11025 " --> pdb=" O ARG 11021 " (cutoff:3.500A) Processing helix chain '1' and resid 1079 through 1095 Processing helix chain '1' and resid 1098 through 1119 Processing helix chain '1' and resid 1123 through 1128 removed outlier: 3.573A pdb=" N LYS 11128 " --> pdb=" O ASP 11125 " (cutoff:3.500A) Processing helix chain '1' and resid 1146 through 1159 removed outlier: 4.084A pdb=" N GLN 11150 " --> pdb=" O MET 11146 " (cutoff:3.500A) Processing helix chain '1' and resid 1189 through 1191 No H-bonds generated for 'chain '1' and resid 1189 through 1191' Processing helix chain '1' and resid 1195 through 1200 Processing helix chain '1' and resid 1201 through 1205 Processing helix chain '1' and resid 1209 through 1217 removed outlier: 3.530A pdb=" N TYR 11213 " --> pdb=" O ASP 11209 " (cutoff:3.500A) Processing helix chain '1' and resid 1218 through 1226 Processing helix chain '1' and resid 1233 through 1242 Processing helix chain '1' and resid 1244 through 1254 removed outlier: 4.125A pdb=" N TYR 11248 " --> pdb=" O ASP 11244 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG 11250 " --> pdb=" O LYS 11246 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ARG 11251 " --> pdb=" O LYS 11247 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU 11252 " --> pdb=" O TYR 11248 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY 11253 " --> pdb=" O PHE 11249 " (cutoff:3.500A) Processing helix chain '1' and resid 1266 through 1271 removed outlier: 3.534A pdb=" N ILE 11271 " --> pdb=" O LEU 11267 " (cutoff:3.500A) Processing helix chain '1' and resid 1272 through 1279 removed outlier: 4.533A pdb=" N ASP 11279 " --> pdb=" O GLU 11275 " (cutoff:3.500A) Processing helix chain '1' and resid 1322 through 1343 removed outlier: 4.305A pdb=" N GLN 11329 " --> pdb=" O GLN 11325 " (cutoff:3.500A) Processing helix chain '1' and resid 1381 through 1396 removed outlier: 3.710A pdb=" N PHE 11396 " --> pdb=" O PHE 11392 " (cutoff:3.500A) Processing helix chain '1' and resid 1397 through 1403 Processing helix chain '1' and resid 1423 through 1434 Processing helix chain '1' and resid 1434 through 1450 removed outlier: 3.663A pdb=" N VAL 11445 " --> pdb=" O GLY 11441 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR 11448 " --> pdb=" O VAL 11444 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 22 Processing helix chain 'A' and resid 24 through 34 Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 89 through 96 removed outlier: 4.958A pdb=" N ASP A 94 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 121 removed outlier: 4.800A pdb=" N ALA A 119 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG A 121 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 151 removed outlier: 4.179A pdb=" N ILE A 137 " --> pdb=" O CYS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 Processing helix chain 'A' and resid 180 through 192 Processing helix chain 'A' and resid 210 through 229 Proline residue: A 222 - end of helix removed outlier: 4.128A pdb=" N VAL A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 236 removed outlier: 3.768A pdb=" N GLU A 236 " --> pdb=" O ASN A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 236' Processing helix chain 'A' and resid 237 through 245 Processing helix chain 'A' and resid 246 through 249 Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 269 through 285 removed outlier: 3.631A pdb=" N ASP A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 310 Processing helix chain 'A' and resid 314 through 320 removed outlier: 4.326A pdb=" N THR A 318 " --> pdb=" O ASP A 314 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 314 through 320' Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 376 through 394 Processing helix chain 'B' and resid 43 through 55 Processing helix chain 'B' and resid 71 through 95 Processing helix chain 'B' and resid 98 through 113 Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 120 through 138 removed outlier: 3.521A pdb=" N ARG B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 163 Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 184 through 191 Processing helix chain 'B' and resid 191 through 207 removed outlier: 4.728A pdb=" N ALA B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N SER B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 222 Processing helix chain 'B' and resid 232 through 239 removed outlier: 3.673A pdb=" N ASN B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 278 Processing helix chain 'B' and resid 279 through 284 removed outlier: 3.719A pdb=" N GLU B 283 " --> pdb=" O ARG B 280 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP B 284 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 299 removed outlier: 4.290A pdb=" N ILE B 290 " --> pdb=" O ARG B 286 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR B 299 " --> pdb=" O SER B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 334 through 348 Processing helix chain 'B' and resid 351 through 365 Processing helix chain 'B' and resid 368 through 380 Processing helix chain 'B' and resid 388 through 395 Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 434 through 439 Processing helix chain 'B' and resid 440 through 450 Processing helix chain 'B' and resid 454 through 467 Processing helix chain 'B' and resid 469 through 482 Processing helix chain 'B' and resid 499 through 511 Processing helix chain 'C' and resid 253 through 277 removed outlier: 3.660A pdb=" N ILE C 265 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 283 Processing helix chain 'C' and resid 321 through 326 Processing helix chain 'C' and resid 378 through 389 Processing helix chain 'C' and resid 410 through 423 Processing helix chain 'C' and resid 440 through 446 Processing helix chain 'C' and resid 460 through 469 Processing helix chain 'C' and resid 469 through 475 removed outlier: 3.580A pdb=" N THR C 475 " --> pdb=" O PRO C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 542 removed outlier: 3.560A pdb=" N ASP C 541 " --> pdb=" O ASP C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 554 Processing helix chain 'C' and resid 555 through 568 Processing helix chain 'C' and resid 613 through 621 removed outlier: 3.790A pdb=" N LEU C 617 " --> pdb=" O VAL C 614 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLY C 618 " --> pdb=" O SER C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 626 removed outlier: 3.616A pdb=" N PHE C 626 " --> pdb=" O VAL C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 697 Processing sheet with id=AA1, first strand: chain '1' and resid 515 through 519 removed outlier: 3.626A pdb=" N LEU 1 366 " --> pdb=" O ILE 1 386 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR 1 365 " --> pdb=" O GLU 1 361 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLU 1 361 " --> pdb=" O THR 1 365 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE 1 367 " --> pdb=" O TYR 1 359 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR 1 359 " --> pdb=" O ILE 1 367 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE 1 369 " --> pdb=" O LEU 1 357 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS 1 373 " --> pdb=" O GLN 1 353 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLN 1 353 " --> pdb=" O LYS 1 373 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 425 through 431 removed outlier: 7.583A pdb=" N ASP 1 444 " --> pdb=" O PRO 1 397 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS 1 473 " --> pdb=" O LEU 1 396 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 609 through 612 removed outlier: 6.624A pdb=" N LEU 1 582 " --> pdb=" O ARG 1 609 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ARG 1 611 " --> pdb=" O LEU 1 582 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N THR 1 584 " --> pdb=" O ARG 1 611 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP 1 581 " --> pdb=" O ALA 1 563 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLN 1 554 " --> pdb=" O ASN 1 548 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASN 1 548 " --> pdb=" O GLN 1 554 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ILE 1 556 " --> pdb=" O LEU 1 546 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU 1 546 " --> pdb=" O ILE 1 556 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER 1 558 " --> pdb=" O GLN 1 544 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN 1 566 " --> pdb=" O LEU 1 536 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LEU 1 536 " --> pdb=" O ASN 1 566 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '1' and resid 854 through 856 removed outlier: 5.432A pdb=" N ILE 11034 " --> pdb=" O ASP 1 864 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASP 1 864 " --> pdb=" O ILE 11034 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN 11036 " --> pdb=" O VAL 1 862 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N SER 1 999 " --> pdb=" O GLY 1 995 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLY 1 995 " --> pdb=" O SER 1 999 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N MET 11001 " --> pdb=" O VAL 1 993 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU 1 991 " --> pdb=" O ASP 11003 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 854 through 856 removed outlier: 13.566A pdb=" N ASP 11035 " --> pdb=" O LEU 11056 " (cutoff:3.500A) removed outlier: 9.314A pdb=" N LEU 11056 " --> pdb=" O ASP 11035 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N VAL 11037 " --> pdb=" O VAL 11054 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU 11052 " --> pdb=" O LYS 11039 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LEU 11041 " --> pdb=" O ALA 11050 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA 11050 " --> pdb=" O LEU 11041 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LEU 11043 " --> pdb=" O LYS 11048 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LYS 11048 " --> pdb=" O LEU 11043 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 1129 through 1132 Processing sheet with id=AA7, first strand: chain '1' and resid 1283 through 1286 removed outlier: 4.436A pdb=" N LEU 11283 " --> pdb=" O PHE 11296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '1' and resid 1305 through 1307 Processing sheet with id=AA9, first strand: chain '1' and resid 1356 through 1357 Processing sheet with id=AB1, first strand: chain 'A' and resid 57 through 60 removed outlier: 5.752A pdb=" N PHE A 47 " --> pdb=" O TYR A 59 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLU A 46 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A 79 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 105 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 57 through 60 removed outlier: 5.752A pdb=" N PHE A 47 " --> pdb=" O TYR A 59 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLU A 46 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A 79 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 108 through 112 removed outlier: 4.635A pdb=" N TRP A 159 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 181 through 182 removed outlier: 3.979A pdb=" N GLN B 181 " --> pdb=" O LYS B 226 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE B 242 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 294 through 302 removed outlier: 5.679A pdb=" N LEU C 316 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N PHE C 360 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG C 331 " --> pdb=" O PHE C 360 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL C 362 " --> pdb=" O ARG C 331 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ASP C 333 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N SER C 364 " --> pdb=" O ASP C 333 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N VAL C 362 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LYS C 353 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA C 349 " --> pdb=" O LEU C 366 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 340 through 342 Processing sheet with id=AB7, first strand: chain 'C' and resid 375 through 377 removed outlier: 4.291A pdb=" N VAL C 689 " --> pdb=" O VAL C 683 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR C 681 " --> pdb=" O LEU C 691 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 515 through 517 removed outlier: 5.937A pdb=" N THR C 482 " --> pdb=" O LYS C 516 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LYS C 394 " --> pdb=" O VAL C 428 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ILE C 430 " --> pdb=" O LYS C 394 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE C 396 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N PHE C 432 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR C 398 " --> pdb=" O PHE C 432 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 531 through 533 removed outlier: 6.263A pdb=" N GLY C 532 " --> pdb=" O ILE C 632 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 578 through 579 removed outlier: 3.655A pdb=" N SER C 608 " --> pdb=" O ARG C 579 " (cutoff:3.500A) 897 hydrogen bonds defined for protein. 2551 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 4.09 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.33: 3616 1.33 - 1.57: 15474 1.57 - 1.80: 164 1.80 - 2.04: 35 2.04 - 2.28: 13 Bond restraints: 19302 Sorted by residual: bond pdb=" CB PRO 1 894 " pdb=" CG PRO 1 894 " ideal model delta sigma weight residual 1.492 2.278 -0.786 5.00e-02 4.00e+02 2.47e+02 bond pdb=" C LEU 1 954 " pdb=" N GLY 1 955 " ideal model delta sigma weight residual 1.331 1.518 -0.187 1.46e-02 4.69e+03 1.64e+02 bond pdb=" CG PRO 1 894 " pdb=" CD PRO 1 894 " ideal model delta sigma weight residual 1.503 1.114 0.389 3.40e-02 8.65e+02 1.31e+02 bond pdb=" CG PRO 11266 " pdb=" CD PRO 11266 " ideal model delta sigma weight residual 1.503 1.181 0.322 3.40e-02 8.65e+02 8.98e+01 bond pdb=" CB PRO 11266 " pdb=" CG PRO 11266 " ideal model delta sigma weight residual 1.492 1.089 0.403 5.00e-02 4.00e+02 6.50e+01 ... (remaining 19297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 16.46: 26274 16.46 - 32.92: 5 32.92 - 49.38: 1 49.38 - 65.84: 0 65.84 - 82.30: 1 Bond angle restraints: 26281 Sorted by residual: angle pdb=" CB PRO 1 894 " pdb=" CG PRO 1 894 " pdb=" CD PRO 1 894 " ideal model delta sigma weight residual 106.10 23.80 82.30 3.20e+00 9.77e-02 6.62e+02 angle pdb=" CA PRO 1 894 " pdb=" N PRO 1 894 " pdb=" CD PRO 1 894 " ideal model delta sigma weight residual 112.00 78.26 33.74 1.40e+00 5.10e-01 5.81e+02 angle pdb=" N PRO 11266 " pdb=" CD PRO 11266 " pdb=" CG PRO 11266 " ideal model delta sigma weight residual 103.20 75.01 28.19 1.50e+00 4.44e-01 3.53e+02 angle pdb=" CA PRO 11266 " pdb=" CB PRO 11266 " pdb=" CG PRO 11266 " ideal model delta sigma weight residual 104.50 73.13 31.37 1.90e+00 2.77e-01 2.73e+02 angle pdb=" N PRO 1 894 " pdb=" CD PRO 1 894 " pdb=" CG PRO 1 894 " ideal model delta sigma weight residual 103.20 122.16 -18.96 1.50e+00 4.44e-01 1.60e+02 ... (remaining 26276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.27: 11000 28.27 - 56.54: 587 56.54 - 84.81: 57 84.81 - 113.07: 9 113.07 - 141.34: 1 Dihedral angle restraints: 11654 sinusoidal: 4959 harmonic: 6695 Sorted by residual: dihedral pdb=" N PRO 1 894 " pdb=" CG PRO 1 894 " pdb=" CD PRO 1 894 " pdb=" CB PRO 1 894 " ideal model delta sinusoidal sigma weight residual 30.00 171.34 -141.34 1 1.50e+01 4.44e-03 7.60e+01 dihedral pdb=" N PRO 11266 " pdb=" CG PRO 11266 " pdb=" CD PRO 11266 " pdb=" CB PRO 11266 " ideal model delta sinusoidal sigma weight residual 30.00 97.28 -67.28 1 1.50e+01 4.44e-03 2.62e+01 dihedral pdb=" CA ALA C 349 " pdb=" C ALA C 349 " pdb=" N PHE C 350 " pdb=" CA PHE C 350 " ideal model delta harmonic sigma weight residual -180.00 -159.00 -21.00 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 11651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2287 0.049 - 0.098: 490 0.098 - 0.147: 132 0.147 - 0.196: 6 0.196 - 0.245: 12 Chirality restraints: 2927 Sorted by residual: chirality pdb=" P A P 1 " pdb=" OP1 A P 1 " pdb=" OP2 A P 1 " pdb=" O5' A P 1 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" P G P 5 " pdb=" OP1 G P 5 " pdb=" OP2 G P 5 " pdb=" O5' G P 5 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" P G P 2 " pdb=" OP1 G P 2 " pdb=" OP2 G P 2 " pdb=" O5' G P 2 " both_signs ideal model delta sigma weight residual True 2.17 -2.41 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 2924 not shown) Planarity restraints: 3278 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU 1 954 " -0.034 2.00e-02 2.50e+03 6.34e-02 4.02e+01 pdb=" C LEU 1 954 " 0.110 2.00e-02 2.50e+03 pdb=" O LEU 1 954 " -0.043 2.00e-02 2.50e+03 pdb=" N GLY 1 955 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP 1 902 " 0.023 2.00e-02 2.50e+03 5.49e-02 3.02e+01 pdb=" C ASP 1 902 " -0.095 2.00e-02 2.50e+03 pdb=" O ASP 1 902 " 0.040 2.00e-02 2.50e+03 pdb=" N GLN 1 903 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 633 " -0.085 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO C 634 " 0.207 5.00e-02 4.00e+02 pdb=" CA PRO C 634 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO C 634 " -0.064 5.00e-02 4.00e+02 ... (remaining 3275 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 431 2.69 - 3.24: 18537 3.24 - 3.80: 30370 3.80 - 4.35: 40086 4.35 - 4.90: 65493 Nonbonded interactions: 154917 Sorted by model distance: nonbonded pdb=" O THR 1 774 " pdb=" OG1 THR 1 778 " model vdw 2.141 3.040 nonbonded pdb=" OH TYR A 18 " pdb=" O PHE A 329 " model vdw 2.152 3.040 nonbonded pdb=" OH TYR B 51 " pdb=" OH TYR B 129 " model vdw 2.184 3.040 nonbonded pdb=" O TYR 1 859 " pdb=" OG1 THR 11004 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR A 209 " pdb=" OD1 ASP A 303 " model vdw 2.243 3.040 ... (remaining 154912 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 22.600 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 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 : 0.008 0.786 19306 Z= 0.275 Angle : 0.942 82.304 26293 Z= 0.504 Chirality : 0.046 0.245 2927 Planarity : 0.006 0.120 3278 Dihedral : 16.339 141.343 7310 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.15 % Allowed : 17.14 % Favored : 82.71 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.18), residues: 2239 helix: 1.26 (0.16), residues: 1032 sheet: -0.23 (0.30), residues: 265 loop : 0.23 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 1 587 TYR 0.017 0.001 TYR 1 766 PHE 0.021 0.002 PHE C 350 TRP 0.029 0.002 TRP B 376 HIS 0.009 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00823 / 0.28 (19302) covalent geometry : angle 0.93848 / 0.50 (26281) hydrogen bonds : bond 0.15733 / 10.56 ( 899) hydrogen bonds : angle 6.69525 / 4.74 ( 2573) metal coordination : bond 0.00284 / 0.15 ( 4) metal coordination : angle 4.11255 / 2.58 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 102 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 771 LEU cc_start: 0.7815 (mt) cc_final: 0.7553 (mt) outliers start: 3 outliers final: 1 residues processed: 105 average time/residue: 0.1266 time to fit residues: 20.4078 Evaluate side-chains 69 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 1244 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 20.0000 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 40.0000 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 385 GLN 1 523 GLN B 238 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.039431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.029958 restraints weight = 298300.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.031400 restraints weight = 115823.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.031853 restraints weight = 58219.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.031912 restraints weight = 49622.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.031998 restraints weight = 42296.905| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.792 19306 Z= 0.306 Angle : 0.884 80.809 26293 Z= 0.419 Chirality : 0.046 0.344 2927 Planarity : 0.006 0.094 3278 Dihedral : 8.818 81.998 2839 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.41 % Allowed : 16.34 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.18), residues: 2239 helix: 1.50 (0.16), residues: 1026 sheet: -0.22 (0.30), residues: 263 loop : 0.36 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 11076 TYR 0.020 0.002 TYR B 503 PHE 0.018 0.002 PHE B 399 TRP 0.018 0.002 TRP B 376 HIS 0.007 0.001 HIS 1 684 Details of bonding type rmsd/Z covalent geometry : bond 0.00864 / 0.31 (19302) covalent geometry : angle 0.88073 / 0.42 (26281) hydrogen bonds : bond 0.04961 / 3.30 ( 899) hydrogen bonds : angle 5.51280 / 3.87 ( 2573) metal coordination : bond 0.00452 / 0.22 ( 4) metal coordination : angle 3.89342 / 2.48 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 72 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 771 LEU cc_start: 0.8765 (mt) cc_final: 0.8493 (mt) REVERT: 1 855 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8200 (tp) REVERT: 1 883 VAL cc_start: 0.9140 (OUTLIER) cc_final: 0.8835 (m) REVERT: 1 1001 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.7793 (mmt) REVERT: A 49 MET cc_start: 0.8353 (ttm) cc_final: 0.8113 (ttm) REVERT: B 221 GLN cc_start: 0.8911 (mt0) cc_final: 0.8588 (mp10) outliers start: 48 outliers final: 25 residues processed: 118 average time/residue: 0.1054 time to fit residues: 20.1917 Evaluate side-chains 95 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 67 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 357 LEU Chi-restraints excluded: chain 1 residue 404 THR Chi-restraints excluded: chain 1 residue 407 HIS Chi-restraints excluded: chain 1 residue 467 SER Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 553 LYS Chi-restraints excluded: chain 1 residue 614 ASN Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 883 VAL Chi-restraints excluded: chain 1 residue 893 LEU Chi-restraints excluded: chain 1 residue 957 VAL Chi-restraints excluded: chain 1 residue 991 LEU Chi-restraints excluded: chain 1 residue 1000 VAL Chi-restraints excluded: chain 1 residue 1001 MET Chi-restraints excluded: chain 1 residue 1032 ILE Chi-restraints excluded: chain 1 residue 1068 VAL Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1334 ILE Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain 1 residue 1425 SER Chi-restraints excluded: chain 1 residue 1440 THR Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 144 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 chunk 107 optimal weight: 40.0000 chunk 16 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 181 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 844 GLN ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11433 GLN A 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.039392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.029884 restraints weight = 335349.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.031329 restraints weight = 124682.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.031959 restraints weight = 64206.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.031946 restraints weight = 54974.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.032046 restraints weight = 43733.369| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 19306 Z= 0.228 Angle : 0.641 17.888 26293 Z= 0.335 Chirality : 0.045 0.231 2927 Planarity : 0.005 0.113 3278 Dihedral : 8.768 81.944 2837 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.16 % Allowed : 15.74 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.18), residues: 2239 helix: 1.52 (0.16), residues: 1031 sheet: -0.28 (0.31), residues: 268 loop : 0.29 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 11076 TYR 0.019 0.001 TYR B 503 PHE 0.016 0.002 PHE B 399 TRP 0.011 0.001 TRP B 376 HIS 0.005 0.001 HIS 1 684 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.23 (19302) covalent geometry : angle 0.63564 / 0.33 (26281) hydrogen bonds : bond 0.04617 / 3.08 ( 899) hydrogen bonds : angle 5.33994 / 3.74 ( 2573) metal coordination : bond 0.00414 / 0.20 ( 4) metal coordination : angle 4.02173 / 2.54 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 68 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 617 LYS cc_start: 0.9322 (tttt) cc_final: 0.9111 (tppt) REVERT: 1 771 LEU cc_start: 0.8806 (mt) cc_final: 0.8534 (mt) REVERT: 1 883 VAL cc_start: 0.9137 (OUTLIER) cc_final: 0.8833 (m) REVERT: 1 1001 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7726 (mmt) REVERT: 1 1330 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8300 (tp) REVERT: A 49 MET cc_start: 0.8414 (ttm) cc_final: 0.8105 (ttm) REVERT: B 221 GLN cc_start: 0.8894 (mt0) cc_final: 0.8585 (mp10) outliers start: 43 outliers final: 29 residues processed: 110 average time/residue: 0.1205 time to fit residues: 21.7178 Evaluate side-chains 99 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 67 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 362 VAL Chi-restraints excluded: chain 1 residue 407 HIS Chi-restraints excluded: chain 1 residue 467 SER Chi-restraints excluded: chain 1 residue 481 ILE Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 614 ASN Chi-restraints excluded: chain 1 residue 844 GLN Chi-restraints excluded: chain 1 residue 883 VAL Chi-restraints excluded: chain 1 residue 896 VAL Chi-restraints excluded: chain 1 residue 957 VAL Chi-restraints excluded: chain 1 residue 991 LEU Chi-restraints excluded: chain 1 residue 1000 VAL Chi-restraints excluded: chain 1 residue 1001 MET Chi-restraints excluded: chain 1 residue 1032 ILE Chi-restraints excluded: chain 1 residue 1068 VAL Chi-restraints excluded: chain 1 residue 1111 GLU Chi-restraints excluded: chain 1 residue 1134 SER Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1330 ILE Chi-restraints excluded: chain 1 residue 1334 ILE Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain 1 residue 1425 SER Chi-restraints excluded: chain 1 residue 1440 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 89 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 139 optimal weight: 0.6980 chunk 162 optimal weight: 7.9990 chunk 177 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.039726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.030172 restraints weight = 339155.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.031661 restraints weight = 129369.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.032151 restraints weight = 64532.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.032227 restraints weight = 51010.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.032322 restraints weight = 43818.597| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 19306 Z= 0.155 Angle : 0.573 11.119 26293 Z= 0.295 Chirality : 0.043 0.220 2927 Planarity : 0.005 0.072 3278 Dihedral : 8.669 81.259 2837 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.95 % Allowed : 16.49 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.18), residues: 2239 helix: 1.70 (0.16), residues: 1018 sheet: -0.22 (0.31), residues: 264 loop : 0.39 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 11076 TYR 0.020 0.001 TYR 1 843 PHE 0.014 0.001 PHE B 399 TRP 0.011 0.001 TRP 1 671 HIS 0.005 0.001 HIS 1 684 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (19302) covalent geometry : angle 0.56666 / 0.30 (26281) hydrogen bonds : bond 0.04113 / 2.74 ( 899) hydrogen bonds : angle 5.13115 / 3.59 ( 2573) metal coordination : bond 0.00386 / 0.19 ( 4) metal coordination : angle 3.97227 / 2.48 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 70 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 617 LYS cc_start: 0.9349 (tttt) cc_final: 0.9126 (tppt) REVERT: 1 771 LEU cc_start: 0.8789 (mt) cc_final: 0.8479 (mt) REVERT: 1 1330 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8260 (tp) REVERT: A 49 MET cc_start: 0.8405 (ttm) cc_final: 0.7908 (ttm) REVERT: B 221 GLN cc_start: 0.8912 (mt0) cc_final: 0.8544 (mp10) outliers start: 39 outliers final: 30 residues processed: 107 average time/residue: 0.1101 time to fit residues: 19.2252 Evaluate side-chains 98 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 404 THR Chi-restraints excluded: chain 1 residue 407 HIS Chi-restraints excluded: chain 1 residue 481 ILE Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 553 LYS Chi-restraints excluded: chain 1 residue 614 ASN Chi-restraints excluded: chain 1 residue 641 GLN Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 896 VAL Chi-restraints excluded: chain 1 residue 957 VAL Chi-restraints excluded: chain 1 residue 991 LEU Chi-restraints excluded: chain 1 residue 1007 ASP Chi-restraints excluded: chain 1 residue 1032 ILE Chi-restraints excluded: chain 1 residue 1068 VAL Chi-restraints excluded: chain 1 residue 1111 GLU Chi-restraints excluded: chain 1 residue 1134 SER Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1274 VAL Chi-restraints excluded: chain 1 residue 1330 ILE Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain 1 residue 1425 SER Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 7 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 170 optimal weight: 30.0000 chunk 13 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 428 GLN 1 754 ASN 1 844 GLN ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.040343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.030738 restraints weight = 351887.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.032293 restraints weight = 129248.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.032898 restraints weight = 63623.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.032946 restraints weight = 49085.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.033047 restraints weight = 43332.398| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19306 Z= 0.115 Angle : 0.534 8.438 26293 Z= 0.276 Chirality : 0.043 0.191 2927 Planarity : 0.004 0.064 3278 Dihedral : 8.515 79.780 2837 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.50 % Allowed : 16.74 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.18), residues: 2239 helix: 1.84 (0.17), residues: 1018 sheet: -0.07 (0.31), residues: 270 loop : 0.53 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 1 975 TYR 0.014 0.001 TYR B 503 PHE 0.011 0.001 PHE C 268 TRP 0.013 0.001 TRP 1 671 HIS 0.004 0.001 HIS 1 684 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (19302) covalent geometry : angle 0.52807 / 0.28 (26281) hydrogen bonds : bond 0.03641 / 2.41 ( 899) hydrogen bonds : angle 4.88879 / 3.42 ( 2573) metal coordination : bond 0.00305 / 0.15 ( 4) metal coordination : angle 3.87959 / 2.40 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 70 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 771 LEU cc_start: 0.8763 (mt) cc_final: 0.8461 (mt) REVERT: A 49 MET cc_start: 0.8312 (mtm) cc_final: 0.7862 (ttm) outliers start: 30 outliers final: 18 residues processed: 100 average time/residue: 0.1155 time to fit residues: 19.0673 Evaluate side-chains 82 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 404 THR Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 614 ASN Chi-restraints excluded: chain 1 residue 641 GLN Chi-restraints excluded: chain 1 residue 670 THR Chi-restraints excluded: chain 1 residue 861 LEU Chi-restraints excluded: chain 1 residue 951 TYR Chi-restraints excluded: chain 1 residue 957 VAL Chi-restraints excluded: chain 1 residue 1111 GLU Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1274 VAL Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 15 optimal weight: 30.0000 chunk 102 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 24 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 407 HIS 1 728 HIS ** 1 874 GLN ** 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 = 0.3188 r_free = 0.3188 target = 0.038756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.029170 restraints weight = 340613.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.030621 restraints weight = 133125.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.031219 restraints weight = 61032.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.031091 restraints weight = 58873.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.031201 restraints weight = 49421.259| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.136 19306 Z= 0.274 Angle : 0.636 9.511 26293 Z= 0.328 Chirality : 0.044 0.184 2927 Planarity : 0.005 0.060 3278 Dihedral : 8.705 80.564 2837 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.26 % Allowed : 16.34 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.18), residues: 2239 helix: 1.58 (0.16), residues: 1027 sheet: -0.35 (0.31), residues: 267 loop : 0.39 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 1 793 TYR 0.020 0.002 TYR B 503 PHE 0.018 0.002 PHE B 399 TRP 0.009 0.001 TRP A 274 HIS 0.007 0.001 HIS B 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.27 (19302) covalent geometry : angle 0.62987 / 0.33 (26281) hydrogen bonds : bond 0.04511 / 3.00 ( 899) hydrogen bonds : angle 5.16476 / 3.61 ( 2573) metal coordination : bond 0.00499 / 0.24 ( 4) metal coordination : angle 4.12071 / 2.61 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 64 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 617 LYS cc_start: 0.9203 (mmmm) cc_final: 0.8944 (mmmm) REVERT: 1 1001 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.7888 (mmt) REVERT: 1 1330 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8477 (tp) REVERT: A 49 MET cc_start: 0.8381 (mtm) cc_final: 0.7858 (ttm) outliers start: 45 outliers final: 34 residues processed: 105 average time/residue: 0.1234 time to fit residues: 21.2193 Evaluate side-chains 101 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 65 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 404 THR Chi-restraints excluded: chain 1 residue 407 HIS Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 614 ASN Chi-restraints excluded: chain 1 residue 641 GLN Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 860 VAL Chi-restraints excluded: chain 1 residue 861 LEU Chi-restraints excluded: chain 1 residue 893 LEU Chi-restraints excluded: chain 1 residue 896 VAL Chi-restraints excluded: chain 1 residue 951 TYR Chi-restraints excluded: chain 1 residue 957 VAL Chi-restraints excluded: chain 1 residue 991 LEU Chi-restraints excluded: chain 1 residue 1001 MET Chi-restraints excluded: chain 1 residue 1007 ASP Chi-restraints excluded: chain 1 residue 1032 ILE Chi-restraints excluded: chain 1 residue 1068 VAL Chi-restraints excluded: chain 1 residue 1134 SER Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1274 VAL Chi-restraints excluded: chain 1 residue 1330 ILE Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain 1 residue 1425 SER Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 9.9990 chunk 150 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 146 optimal weight: 0.5980 chunk 105 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 215 optimal weight: 0.6980 chunk 174 optimal weight: 7.9990 overall best weight: 2.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 407 HIS ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.039537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.030328 restraints weight = 357257.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.031668 restraints weight = 140116.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.031915 restraints weight = 76675.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.031846 restraints weight = 66073.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.032039 restraints weight = 62958.849| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19306 Z= 0.135 Angle : 0.557 11.058 26293 Z= 0.286 Chirality : 0.043 0.184 2927 Planarity : 0.004 0.058 3278 Dihedral : 8.620 79.958 2837 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.74 % Favored : 97.21 % Rotamer: Outliers : 1.55 % Allowed : 17.19 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.18), residues: 2239 helix: 1.71 (0.17), residues: 1027 sheet: -0.19 (0.31), residues: 269 loop : 0.47 (0.21), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 1 975 TYR 0.016 0.001 TYR B 503 PHE 0.013 0.001 PHE C 515 TRP 0.009 0.001 TRP 1 671 HIS 0.022 0.001 HIS 1 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (19302) covalent geometry : angle 0.55053 / 0.29 (26281) hydrogen bonds : bond 0.03874 / 2.57 ( 899) hydrogen bonds : angle 4.96076 / 3.46 ( 2573) metal coordination : bond 0.00370 / 0.18 ( 4) metal coordination : angle 3.99276 / 2.50 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 64 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 619 MET cc_start: 0.7931 (tpp) cc_final: 0.7693 (ttm) REVERT: 1 1330 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8271 (tp) REVERT: A 49 MET cc_start: 0.8274 (mtm) cc_final: 0.8026 (mtp) REVERT: B 74 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.7986 (mt0) outliers start: 31 outliers final: 25 residues processed: 93 average time/residue: 0.1213 time to fit residues: 18.6075 Evaluate side-chains 89 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 62 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 407 HIS Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 614 ASN Chi-restraints excluded: chain 1 residue 641 GLN Chi-restraints excluded: chain 1 residue 670 THR Chi-restraints excluded: chain 1 residue 861 LEU Chi-restraints excluded: chain 1 residue 896 VAL Chi-restraints excluded: chain 1 residue 951 TYR Chi-restraints excluded: chain 1 residue 957 VAL Chi-restraints excluded: chain 1 residue 991 LEU Chi-restraints excluded: chain 1 residue 1203 SER Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1274 VAL Chi-restraints excluded: chain 1 residue 1330 ILE Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 79 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 45 optimal weight: 20.0000 chunk 183 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 154 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 85 optimal weight: 0.0070 chunk 144 optimal weight: 6.9990 chunk 169 optimal weight: 9.9990 overall best weight: 4.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 407 HIS ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.039349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.030016 restraints weight = 390482.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.031410 restraints weight = 147671.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.031526 restraints weight = 79495.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.031593 restraints weight = 65395.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.031900 restraints weight = 57125.631| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 19306 Z= 0.167 Angle : 0.561 11.528 26293 Z= 0.287 Chirality : 0.043 0.174 2927 Planarity : 0.004 0.057 3278 Dihedral : 8.610 79.866 2837 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.70 % Favored : 97.26 % Rotamer: Outliers : 1.75 % Allowed : 17.14 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.18), residues: 2239 helix: 1.69 (0.16), residues: 1029 sheet: -0.22 (0.31), residues: 265 loop : 0.47 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 1 975 TYR 0.016 0.001 TYR B 503 PHE 0.013 0.001 PHE B 399 TRP 0.008 0.001 TRP 1 671 HIS 0.015 0.001 HIS 1 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (19302) covalent geometry : angle 0.55447 / 0.29 (26281) hydrogen bonds : bond 0.03878 / 2.56 ( 899) hydrogen bonds : angle 4.94951 / 3.45 ( 2573) metal coordination : bond 0.00390 / 0.19 ( 4) metal coordination : angle 3.98234 / 2.51 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 64 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 1001 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.7757 (mmt) REVERT: 1 1330 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8250 (tp) outliers start: 35 outliers final: 28 residues processed: 97 average time/residue: 0.1224 time to fit residues: 19.6712 Evaluate side-chains 93 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 63 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 407 HIS Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 614 ASN Chi-restraints excluded: chain 1 residue 641 GLN Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 860 VAL Chi-restraints excluded: chain 1 residue 896 VAL Chi-restraints excluded: chain 1 residue 951 TYR Chi-restraints excluded: chain 1 residue 957 VAL Chi-restraints excluded: chain 1 residue 991 LEU Chi-restraints excluded: chain 1 residue 1001 MET Chi-restraints excluded: chain 1 residue 1007 ASP Chi-restraints excluded: chain 1 residue 1203 SER Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1274 VAL Chi-restraints excluded: chain 1 residue 1330 ILE Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain 1 residue 1425 SER Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 176 optimal weight: 3.9990 chunk 178 optimal weight: 6.9990 chunk 209 optimal weight: 7.9990 chunk 192 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 15 optimal weight: 30.0000 chunk 62 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 205 optimal weight: 0.2980 chunk 75 optimal weight: 6.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 407 HIS ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.039278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.029967 restraints weight = 370511.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.031341 restraints weight = 142588.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.031489 restraints weight = 75911.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.031540 restraints weight = 63525.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.031801 restraints weight = 55088.708| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 19306 Z= 0.172 Angle : 0.563 11.782 26293 Z= 0.288 Chirality : 0.043 0.174 2927 Planarity : 0.004 0.057 3278 Dihedral : 8.624 79.894 2837 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.88 % Favored : 97.08 % Rotamer: Outliers : 1.85 % Allowed : 17.19 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.18), residues: 2239 helix: 1.70 (0.16), residues: 1029 sheet: -0.23 (0.31), residues: 265 loop : 0.47 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 1 975 TYR 0.017 0.001 TYR B 503 PHE 0.013 0.001 PHE B 399 TRP 0.008 0.001 TRP A 274 HIS 0.013 0.001 HIS 1 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (19302) covalent geometry : angle 0.55615 / 0.29 (26281) hydrogen bonds : bond 0.03882 / 2.57 ( 899) hydrogen bonds : angle 4.94818 / 3.45 ( 2573) metal coordination : bond 0.00384 / 0.19 ( 4) metal coordination : angle 3.98477 / 2.51 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 62 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: 1 1001 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7791 (mmt) REVERT: A 49 MET cc_start: 0.8112 (mtp) cc_final: 0.7162 (ttm) outliers start: 37 outliers final: 34 residues processed: 97 average time/residue: 0.1204 time to fit residues: 19.6182 Evaluate side-chains 97 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 62 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 404 THR Chi-restraints excluded: chain 1 residue 407 HIS Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 614 ASN Chi-restraints excluded: chain 1 residue 641 GLN Chi-restraints excluded: chain 1 residue 670 THR Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 860 VAL Chi-restraints excluded: chain 1 residue 861 LEU Chi-restraints excluded: chain 1 residue 893 LEU Chi-restraints excluded: chain 1 residue 896 VAL Chi-restraints excluded: chain 1 residue 951 TYR Chi-restraints excluded: chain 1 residue 957 VAL Chi-restraints excluded: chain 1 residue 991 LEU Chi-restraints excluded: chain 1 residue 1001 MET Chi-restraints excluded: chain 1 residue 1007 ASP Chi-restraints excluded: chain 1 residue 1068 VAL Chi-restraints excluded: chain 1 residue 1111 GLU Chi-restraints excluded: chain 1 residue 1203 SER Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1274 VAL Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain 1 residue 1425 SER Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 10 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 211 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 164 optimal weight: 8.9990 chunk 33 optimal weight: 20.0000 chunk 212 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 407 HIS 1 736 GLN ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.039064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.029829 restraints weight = 362502.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.031164 restraints weight = 140456.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.031261 restraints weight = 77049.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.031212 restraints weight = 75077.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.031468 restraints weight = 60390.740| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 19306 Z= 0.197 Angle : 0.574 11.948 26293 Z= 0.294 Chirality : 0.043 0.174 2927 Planarity : 0.004 0.057 3278 Dihedral : 8.644 79.991 2837 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.83 % Favored : 97.12 % Rotamer: Outliers : 1.80 % Allowed : 17.29 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.18), residues: 2239 helix: 1.68 (0.16), residues: 1029 sheet: -0.30 (0.31), residues: 263 loop : 0.46 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 11076 TYR 0.017 0.001 TYR B 503 PHE 0.014 0.001 PHE C 515 TRP 0.008 0.001 TRP A 274 HIS 0.010 0.001 HIS 1 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.20 (19302) covalent geometry : angle 0.56721 / 0.29 (26281) hydrogen bonds : bond 0.03976 / 2.63 ( 899) hydrogen bonds : angle 4.98496 / 3.47 ( 2573) metal coordination : bond 0.00408 / 0.20 ( 4) metal coordination : angle 4.03166 / 2.55 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 62 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: 1 1001 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.7799 (mmt) REVERT: A 49 MET cc_start: 0.8063 (mtp) cc_final: 0.7207 (ttm) outliers start: 36 outliers final: 33 residues processed: 96 average time/residue: 0.1261 time to fit residues: 20.5399 Evaluate side-chains 96 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 62 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 614 ASN Chi-restraints excluded: chain 1 residue 641 GLN Chi-restraints excluded: chain 1 residue 670 THR Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 860 VAL Chi-restraints excluded: chain 1 residue 861 LEU Chi-restraints excluded: chain 1 residue 893 LEU Chi-restraints excluded: chain 1 residue 896 VAL Chi-restraints excluded: chain 1 residue 951 TYR Chi-restraints excluded: chain 1 residue 957 VAL Chi-restraints excluded: chain 1 residue 991 LEU Chi-restraints excluded: chain 1 residue 1001 MET Chi-restraints excluded: chain 1 residue 1007 ASP Chi-restraints excluded: chain 1 residue 1068 VAL Chi-restraints excluded: chain 1 residue 1111 GLU Chi-restraints excluded: chain 1 residue 1203 SER Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1274 VAL Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain 1 residue 1425 SER Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 23 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 202 optimal weight: 9.9990 chunk 142 optimal weight: 8.9990 chunk 133 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 214 optimal weight: 0.9980 chunk 170 optimal weight: 20.0000 chunk 176 optimal weight: 9.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 407 HIS ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.039809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.030565 restraints weight = 346102.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.031823 restraints weight = 139860.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.032029 restraints weight = 76035.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.032086 restraints weight = 64716.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.032426 restraints weight = 54974.514| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19306 Z= 0.117 Angle : 0.540 11.438 26293 Z= 0.276 Chirality : 0.042 0.166 2927 Planarity : 0.004 0.057 3278 Dihedral : 8.554 79.235 2837 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.34 % Favored : 97.62 % Rotamer: Outliers : 1.50 % Allowed : 17.64 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.18), residues: 2239 helix: 1.82 (0.17), residues: 1029 sheet: -0.17 (0.32), residues: 263 loop : 0.55 (0.22), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 11076 TYR 0.015 0.001 TYR B 55 PHE 0.011 0.001 PHE C 515 TRP 0.010 0.001 TRP 1 671 HIS 0.005 0.001 HIS 1 684 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (19302) covalent geometry : angle 0.53319 / 0.28 (26281) hydrogen bonds : bond 0.03614 / 2.38 ( 899) hydrogen bonds : angle 4.82506 / 3.36 ( 2573) metal coordination : bond 0.00326 / 0.16 ( 4) metal coordination : angle 3.98023 / 2.48 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2690.93 seconds wall clock time: 47 minutes 45.71 seconds (2865.71 seconds total)