Starting phenix.real_space_refine on Sat Jul 4 05:40:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fok_29352/07_2026/8fok_29352.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fok_29352/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8fok_29352/07_2026/8fok_29352.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fok_29352/07_2026/8fok_29352.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fok_29352/07_2026/8fok_29352.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fok_29352/07_2026/8fok_29352.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8fok_29352/07_2026/8fok_29352.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fok_29352/07_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-dev-6108/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, 'RNA': 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: 6.68, per 1000 atoms: 0.35 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: 1.61 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 2.70 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: 4.29 Time building geometry restraints manager: 2.16 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: 26277 16.46 - 32.92: 5 32.92 - 49.38: 1 49.38 - 65.84: 0 65.84 - 82.30: 1 Bond angle restraints: 26284 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 26279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.27: 11012 28.27 - 56.54: 579 56.54 - 84.81: 55 84.81 - 113.07: 9 113.07 - 141.34: 1 Dihedral angle restraints: 11656 sinusoidal: 4961 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 11653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2239 0.046 - 0.092: 507 0.092 - 0.138: 171 0.138 - 0.184: 6 0.184 - 0.230: 4 Chirality restraints: 2927 Sorted by residual: chirality pdb=" CG LEU C 510 " pdb=" CB LEU C 510 " pdb=" CD1 LEU C 510 " pdb=" CD2 LEU C 510 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CG LEU 1 449 " pdb=" CB LEU 1 449 " pdb=" CD1 LEU 1 449 " pdb=" CD2 LEU 1 449 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILE 1 462 " pdb=" N ILE 1 462 " pdb=" C ILE 1 462 " pdb=" CB ILE 1 462 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.28e-01 ... (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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 26.530 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.310 ------------------------------------------------------------------------------- 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 : 0.939 82.304 26296 Z= 0.503 Chirality : 0.043 0.230 2927 Planarity : 0.006 0.120 3278 Dihedral : 16.240 141.343 7312 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 0.93488 / 0.50 (26284) 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 : 0.752 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: 0.1562 time to fit residues: 25.4822 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 : 0.723 ------------------------------------------------------------------------------- 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 = 0.3203 r_free = 0.3203 target = 0.039352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.029820 restraints weight = 296638.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.031350 restraints weight = 114881.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.031910 restraints weight = 55579.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.031949 restraints weight = 45650.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.032013 restraints weight = 39263.770| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- 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: 0.8332 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.790 19306 Z= 0.305 Angle : 0.893 80.996 26296 Z= 0.422 Chirality : 0.046 0.358 2927 Planarity : 0.006 0.094 3278 Dihedral : 8.445 83.522 2841 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.41 % Allowed : 16.29 % Favored : 81.30 % 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: 1.06 (0.18), residues: 2239 helix: 1.43 (0.16), residues: 1030 sheet: -0.21 (0.31), residues: 258 loop : 0.30 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 11076 TYR 0.021 0.002 TYR B 503 PHE 0.020 0.002 PHE B 399 TRP 0.019 0.002 TRP B 376 HIS 0.007 0.002 HIS B 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00859 / 0.30 (19302) covalent geometry : angle 0.88922 / 0.42 (26284) hydrogen bonds : bond 0.04990 / 3.32 ( 899) hydrogen bonds : angle 5.49544 / 3.86 ( 2573) metal coordination : bond 0.00451 / 0.22 ( 4) metal coordination : angle 3.93853 / 2.50 ( 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 119 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 71 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 771 LEU cc_start: 0.8762 (mt) cc_final: 0.8489 (mt) REVERT: 1 855 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8175 (tp) REVERT: 1 883 VAL cc_start: 0.9125 (OUTLIER) cc_final: 0.8819 (m) REVERT: 1 1001 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7794 (mmt) REVERT: A 49 MET cc_start: 0.8307 (ttm) cc_final: 0.8044 (ttm) REVERT: B 221 GLN cc_start: 0.8901 (mt0) cc_final: 0.8588 (mp10) outliers start: 48 outliers final: 26 residues processed: 116 average time/residue: 0.1350 time to fit residues: 25.1533 Evaluate side-chains 97 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 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 B residue 230 GLU Chi-restraints excluded: chain B residue 258 LEU 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: 2.9990 chunk 148 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 16 optimal weight: 0.0670 chunk 17 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 181 optimal weight: 8.9990 chunk 113 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- 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** 11433 GLN A 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.040299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.030750 restraints weight = 337466.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.032309 restraints weight = 125274.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.032719 restraints weight = 62901.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.032800 restraints weight = 49882.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.032918 restraints weight = 45428.554| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 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 = 0.2944 r_free = 0.2944 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: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 19306 Z= 0.134 Angle : 0.597 16.810 26296 Z= 0.313 Chirality : 0.043 0.224 2927 Planarity : 0.005 0.115 3278 Dihedral : 8.263 82.897 2839 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.25 % Allowed : 16.19 % Favored : 82.56 % 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: 1.33 (0.18), residues: 2239 helix: 1.74 (0.17), residues: 1018 sheet: -0.17 (0.31), residues: 256 loop : 0.38 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 11076 TYR 0.016 0.001 TYR B 503 PHE 0.013 0.001 PHE B 399 TRP 0.013 0.001 TRP 1 671 HIS 0.005 0.001 HIS 1 684 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (19302) covalent geometry : angle 0.59145 / 0.31 (26284) hydrogen bonds : bond 0.04205 / 2.80 ( 899) hydrogen bonds : angle 5.16082 / 3.62 ( 2573) metal coordination : bond 0.00366 / 0.19 ( 4) metal coordination : angle 3.88434 / 2.41 ( 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 93 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 771 LEU cc_start: 0.8743 (mt) cc_final: 0.8468 (mt) REVERT: 1 883 VAL cc_start: 0.9086 (OUTLIER) cc_final: 0.8777 (m) REVERT: 1 1330 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8206 (tp) REVERT: A 49 MET cc_start: 0.8525 (ttm) cc_final: 0.8156 (ttm) REVERT: B 221 GLN cc_start: 0.8918 (mt0) cc_final: 0.8604 (mp10) outliers start: 25 outliers final: 13 residues processed: 93 average time/residue: 0.1386 time to fit residues: 21.1398 Evaluate side-chains 80 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 844 GLN Chi-restraints excluded: chain 1 residue 883 VAL Chi-restraints excluded: chain 1 residue 957 VAL 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 1330 ILE Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain A residue 338 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 89 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 135 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 192 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 chunk 162 optimal weight: 8.9990 chunk 177 optimal weight: 0.0870 chunk 138 optimal weight: 7.9990 overall best weight: 1.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.040542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.030957 restraints weight = 339642.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.032505 restraints weight = 127255.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.033084 restraints weight = 63004.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.033155 restraints weight = 49277.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.033213 restraints weight = 43077.475| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 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 = 0.2957 r_free = 0.2957 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: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 19306 Z= 0.117 Angle : 0.549 10.622 26296 Z= 0.284 Chirality : 0.042 0.203 2927 Planarity : 0.005 0.069 3278 Dihedral : 8.141 82.064 2839 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.65 % Allowed : 16.29 % Favored : 82.06 % 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 (0.16), residues: 1018 sheet: -0.06 (0.30), residues: 270 loop : 0.52 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 11076 TYR 0.021 0.001 TYR 1 843 PHE 0.011 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 0.00248 / 0.12 (19302) covalent geometry : angle 0.54270 / 0.28 (26284) hydrogen bonds : bond 0.03775 / 2.51 ( 899) hydrogen bonds : angle 4.97540 / 3.48 ( 2573) metal coordination : bond 0.00302 / 0.15 ( 4) metal coordination : angle 3.86031 / 2.38 ( 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 104 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 71 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 771 LEU cc_start: 0.8754 (mt) cc_final: 0.8481 (mt) REVERT: 1 1330 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8179 (tp) REVERT: A 49 MET cc_start: 0.8458 (ttm) cc_final: 0.8038 (ttm) REVERT: B 49 LYS cc_start: 0.9176 (mtmm) cc_final: 0.8941 (mtmm) REVERT: B 221 GLN cc_start: 0.8885 (mt0) cc_final: 0.8526 (mp10) outliers start: 33 outliers final: 19 residues processed: 103 average time/residue: 0.1247 time to fit residues: 21.2606 Evaluate side-chains 87 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 641 GLN Chi-restraints excluded: chain 1 residue 957 VAL Chi-restraints excluded: chain 1 residue 991 LEU Chi-restraints excluded: chain 1 residue 1068 VAL 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 338 VAL Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 258 LEU 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: 4.9990 chunk 82 optimal weight: 10.0000 chunk 136 optimal weight: 0.0670 chunk 102 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 170 optimal weight: 30.0000 chunk 13 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 overall best weight: 2.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 844 GLN ** 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 = 0.3243 r_free = 0.3243 target = 0.040331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.030667 restraints weight = 351553.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.032267 restraints weight = 129224.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.032719 restraints weight = 62710.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.032793 restraints weight = 49876.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.032898 restraints weight = 44794.827| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 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 = 0.2944 r_free = 0.2944 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: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19306 Z= 0.132 Angle : 0.527 8.207 26296 Z= 0.273 Chirality : 0.042 0.181 2927 Planarity : 0.004 0.063 3278 Dihedral : 8.076 81.164 2839 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.70 % Allowed : 16.39 % Favored : 81.90 % 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: 1.55 (0.18), residues: 2239 helix: 1.90 (0.17), residues: 1018 sheet: -0.03 (0.31), residues: 265 loop : 0.52 (0.21), residues: 956 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 0.012 0.001 PHE C 268 TRP 0.010 0.001 TRP 1 671 HIS 0.004 0.001 HIS 1 684 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (19302) covalent geometry : angle 0.52062 / 0.27 (26284) hydrogen bonds : bond 0.03697 / 2.45 ( 899) hydrogen bonds : angle 4.88511 / 3.42 ( 2573) metal coordination : bond 0.00271 / 0.13 ( 4) metal coordination : angle 3.77210 / 2.35 ( 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 102 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 68 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 771 LEU cc_start: 0.8745 (mt) cc_final: 0.8447 (mt) REVERT: 1 1330 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8231 (tp) REVERT: A 49 MET cc_start: 0.8394 (mtm) cc_final: 0.7898 (ttm) outliers start: 34 outliers final: 24 residues processed: 101 average time/residue: 0.1243 time to fit residues: 21.0198 Evaluate side-chains 92 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 861 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 1032 ILE Chi-restraints excluded: chain 1 residue 1068 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 15 optimal weight: 20.0000 chunk 102 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 180 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 = 0.3198 r_free = 0.3198 target = 0.039014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.029848 restraints weight = 341711.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.031106 restraints weight = 140913.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.031223 restraints weight = 78044.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.031273 restraints weight = 66999.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.031580 restraints weight = 57179.449| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 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 = 0.2890 r_free = 0.2890 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: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 19306 Z= 0.248 Angle : 0.611 9.568 26296 Z= 0.316 Chirality : 0.043 0.197 2927 Planarity : 0.005 0.059 3278 Dihedral : 8.270 80.924 2839 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.16 % Allowed : 16.49 % Favored : 81.35 % 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: 1.28 (0.18), residues: 2239 helix: 1.68 (0.16), residues: 1027 sheet: -0.28 (0.31), residues: 267 loop : 0.41 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 11076 TYR 0.019 0.002 TYR B 503 PHE 0.017 0.002 PHE B 399 TRP 0.009 0.001 TRP 1 356 HIS 0.006 0.001 HIS B 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.25 (19302) covalent geometry : angle 0.60505 / 0.32 (26284) hydrogen bonds : bond 0.04381 / 2.91 ( 899) hydrogen bonds : angle 5.10577 / 3.56 ( 2573) metal coordination : bond 0.00414 / 0.20 ( 4) metal coordination : angle 4.03084 / 2.55 ( 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 107 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 64 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 1001 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.7877 (mmt) REVERT: 1 1330 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8558 (tp) REVERT: A 49 MET cc_start: 0.8303 (mtm) cc_final: 0.8037 (mtp) outliers start: 43 outliers final: 29 residues processed: 103 average time/residue: 0.1143 time to fit residues: 19.8811 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 : 0.737 ------------------------------------------------------------------------------- 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 492 MET Chi-restraints excluded: chain 1 residue 528 THR 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 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 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 258 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 10.0000 chunk 150 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 215 optimal weight: 0.0060 chunk 174 optimal weight: 3.9990 overall best weight: 2.5602 ------------------------------------------------------------------------------- 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 = 0.3226 r_free = 0.3226 target = 0.039739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.030539 restraints weight = 357658.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.031887 restraints weight = 142531.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.032015 restraints weight = 76611.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.032172 restraints weight = 61538.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.032276 restraints weight = 56085.463| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 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 = 0.2920 r_free = 0.2920 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: 0.2920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19306 Z= 0.132 Angle : 0.541 10.989 26296 Z= 0.279 Chirality : 0.042 0.178 2927 Planarity : 0.004 0.058 3278 Dihedral : 8.214 80.661 2839 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.79 % Favored : 97.17 % Rotamer: Outliers : 1.70 % Allowed : 17.04 % 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: 1.43 (0.18), residues: 2239 helix: 1.80 (0.16), residues: 1027 sheet: -0.12 (0.31), residues: 264 loop : 0.46 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 11076 TYR 0.016 0.001 TYR B 503 PHE 0.013 0.001 PHE B 399 TRP 0.009 0.001 TRP 1 671 HIS 0.017 0.001 HIS 1 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (19302) covalent geometry : angle 0.53492 / 0.28 (26284) hydrogen bonds : bond 0.03794 / 2.51 ( 899) hydrogen bonds : angle 4.91002 / 3.42 ( 2573) metal coordination : bond 0.00338 / 0.17 ( 4) metal coordination : angle 3.90416 / 2.44 ( 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 98 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 64 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 1330 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8354 (tp) outliers start: 34 outliers final: 29 residues processed: 95 average time/residue: 0.1263 time to fit residues: 20.3234 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 : 0.772 ------------------------------------------------------------------------------- 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 682 MET 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 1032 ILE Chi-restraints excluded: chain 1 residue 1068 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 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 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: 5.9990 chunk 151 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 154 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 169 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3220 r_free = 0.3220 target = 0.039578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.030160 restraints weight = 391354.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.031476 restraints weight = 148688.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.031708 restraints weight = 79113.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.031766 restraints weight = 65270.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.032030 restraints weight = 56412.687| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 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 = 0.2909 r_free = 0.2909 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: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 19306 Z= 0.159 Angle : 0.543 11.718 26296 Z= 0.280 Chirality : 0.042 0.171 2927 Planarity : 0.004 0.057 3278 Dihedral : 8.215 80.259 2839 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.88 % Favored : 97.08 % Rotamer: Outliers : 1.65 % Allowed : 17.09 % 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: 1.44 (0.18), residues: 2239 helix: 1.80 (0.16), residues: 1029 sheet: -0.16 (0.31), residues: 265 loop : 0.49 (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 0.007 0.001 HIS 1 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (19302) covalent geometry : angle 0.53714 / 0.28 (26284) hydrogen bonds : bond 0.03790 / 2.51 ( 899) hydrogen bonds : angle 4.91027 / 3.42 ( 2573) metal coordination : bond 0.00365 / 0.18 ( 4) metal coordination : angle 3.90489 / 2.46 ( 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 96 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 63 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: 1 1001 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.7822 (mmt) REVERT: A 49 MET cc_start: 0.8116 (mtp) cc_final: 0.7131 (ttm) outliers start: 33 outliers final: 27 residues processed: 93 average time/residue: 0.1311 time to fit residues: 20.3567 Evaluate side-chains 90 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 62 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 682 MET 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 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 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 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: 0.0370 chunk 178 optimal weight: 0.7980 chunk 209 optimal weight: 0.0050 chunk 192 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 15 optimal weight: 30.0000 chunk 62 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 205 optimal weight: 0.0570 chunk 75 optimal weight: 4.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.040448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.030723 restraints weight = 369901.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.032215 restraints weight = 138477.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.033209 restraints weight = 63048.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.032937 restraints weight = 56903.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.033066 restraints weight = 49818.138| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- 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: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 19306 Z= 0.109 Angle : 0.536 16.260 26296 Z= 0.273 Chirality : 0.041 0.157 2927 Planarity : 0.004 0.057 3278 Dihedral : 8.142 78.533 2839 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.29 % Favored : 97.66 % Rotamer: Outliers : 1.20 % Allowed : 17.39 % 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: 1.64 (0.18), residues: 2239 helix: 1.94 (0.16), residues: 1021 sheet: 0.04 (0.31), residues: 269 loop : 0.61 (0.21), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 1 975 TYR 0.013 0.001 TYR B 503 PHE 0.010 0.001 PHE C 268 TRP 0.012 0.001 TRP 1 671 HIS 0.005 0.001 HIS 1 684 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (19302) covalent geometry : angle 0.52932 / 0.27 (26284) hydrogen bonds : bond 0.03484 / 2.32 ( 899) hydrogen bonds : angle 4.77435 / 3.32 ( 2573) metal coordination : bond 0.00299 / 0.15 ( 4) metal coordination : angle 3.86827 / 2.40 ( 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 89 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: 1 771 LEU cc_start: 0.8786 (mt) cc_final: 0.8517 (mt) REVERT: A 49 MET cc_start: 0.8075 (mtp) cc_final: 0.7355 (ttm) outliers start: 24 outliers final: 20 residues processed: 88 average time/residue: 0.1229 time to fit residues: 18.1983 Evaluate side-chains 81 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 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 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 93 LEU Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 199 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: 9.9990 chunk 67 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 164 optimal weight: 8.9990 chunk 33 optimal weight: 20.0000 chunk 212 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 117 optimal weight: 30.0000 chunk 104 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 736 GLN ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.038878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.029148 restraints weight = 357892.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.030622 restraints weight = 136952.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.031770 restraints weight = 62102.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.031472 restraints weight = 57816.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.031550 restraints weight = 46356.494| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.129 19306 Z= 0.264 Angle : 0.620 12.367 26296 Z= 0.318 Chirality : 0.043 0.170 2927 Planarity : 0.005 0.055 3278 Dihedral : 8.317 79.235 2839 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.01 % Favored : 96.94 % Rotamer: Outliers : 1.20 % Allowed : 17.59 % Favored : 81.20 % 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: 1.36 (0.18), residues: 2239 helix: 1.74 (0.16), residues: 1029 sheet: -0.33 (0.31), residues: 263 loop : 0.50 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 11076 TYR 0.019 0.002 TYR B 503 PHE 0.016 0.002 PHE B 399 TRP 0.009 0.001 TRP 1 356 HIS 0.006 0.001 HIS B 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.26 (19302) covalent geometry : angle 0.61453 / 0.32 (26284) hydrogen bonds : bond 0.04279 / 2.83 ( 899) hydrogen bonds : angle 5.05691 / 3.51 ( 2573) metal coordination : bond 0.00469 / 0.23 ( 4) metal coordination : angle 4.00576 / 2.54 ( 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 87 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: 1 1001 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.7837 (mmt) REVERT: A 49 MET cc_start: 0.8169 (mtp) cc_final: 0.7271 (ttm) outliers start: 24 outliers final: 22 residues processed: 85 average time/residue: 0.1334 time to fit residues: 18.8488 Evaluate side-chains 85 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 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 1001 MET Chi-restraints excluded: chain 1 residue 1007 ASP Chi-restraints excluded: chain 1 residue 1111 GLU Chi-restraints excluded: chain 1 residue 1230 ASP 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 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 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: 4.9990 chunk 146 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 214 optimal weight: 4.9990 chunk 170 optimal weight: 20.0000 chunk 176 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3216 r_free = 0.3216 target = 0.039379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.029792 restraints weight = 345786.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.031261 restraints weight = 134609.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.031917 restraints weight = 61603.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.031756 restraints weight = 58808.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.031875 restraints weight = 51770.277| |-----------------------------------------------------------------------------| 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: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | 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: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 19306 Z= 0.162 Angle : 0.560 11.750 26296 Z= 0.286 Chirality : 0.042 0.167 2927 Planarity : 0.004 0.056 3278 Dihedral : 8.310 78.845 2839 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.79 % Favored : 97.17 % Rotamer: Outliers : 1.15 % Allowed : 17.64 % Favored : 81.20 % 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: 1.45 (0.18), residues: 2239 helix: 1.79 (0.17), residues: 1029 sheet: -0.25 (0.31), residues: 265 loop : 0.56 (0.22), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 11076 TYR 0.016 0.001 TYR B 503 PHE 0.015 0.001 PHE C 515 TRP 0.008 0.001 TRP 1 671 HIS 0.004 0.001 HIS 1 684 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (19302) covalent geometry : angle 0.55363 / 0.29 (26284) hydrogen bonds : bond 0.03860 / 2.55 ( 899) hydrogen bonds : angle 4.92048 / 3.42 ( 2573) metal coordination : bond 0.00346 / 0.17 ( 4) metal coordination : angle 3.98296 / 2.50 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3022.84 seconds wall clock time: 53 minutes 29.67 seconds (3209.67 seconds total)