Starting phenix.real_space_refine on Mon Jun 16 14:10:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fok_29352/06_2025/8fok_29352.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fok_29352/06_2025/8fok_29352.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fok_29352/06_2025/8fok_29352.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fok_29352/06_2025/8fok_29352.map" model { file = "/net/cci-nas-00/data/ceres_data/8fok_29352/06_2025/8fok_29352.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fok_29352/06_2025/8fok_29352.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 6} 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: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 6} 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: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 2} 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: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 4} 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: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 4} 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, 'GLU:plan': 1, 'ASN:plan1': 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, 'GLU:plan': 1, 'ASN:plan1': 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: 17.82, per 1000 atoms: 0.95 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: 4.90 Conformation dependent library (CDL) restraints added in 3.9 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: 6.45 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: 7.25 Time building geometry restraints manager: 5.77 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: 11026 28.27 - 56.54: 593 56.54 - 84.81: 71 84.81 - 113.07: 9 113.07 - 141.34: 1 Dihedral angle restraints: 11700 sinusoidal: 5005 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 11697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2267 0.046 - 0.092: 495 0.092 - 0.138: 156 0.138 - 0.184: 5 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 61.690 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 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= 0.247 Angle : 0.928 82.304 26296 Z= 0.471 Chirality : 0.042 0.230 2927 Planarity : 0.006 0.120 3278 Dihedral : 16.601 141.343 7356 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.65 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (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 TRP 0.029 0.002 TRP B 376 HIS 0.009 0.001 HIS A 27 PHE 0.021 0.002 PHE C 350 TYR 0.017 0.001 TYR 1 766 ARG 0.009 0.001 ARG 1 587 Details of bonding type rmsd hydrogen bonds : bond 0.15733 ( 899) hydrogen bonds : angle 6.69525 ( 2573) metal coordination : bond 0.00284 ( 4) metal coordination : angle 4.11255 ( 12) covalent geometry : bond 0.00814 (19302) covalent geometry : angle 0.92443 (26284) *********************** 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 : 2.235 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: 0.3611 time to fit residues: 58.7148 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 : 2.170 ------------------------------------------------------------------------------- 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 192 optimal weight: 10.0000 chunk 172 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 chunk 59 optimal weight: 7.9990 chunk 116 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 178 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 108 optimal weight: 30.0000 chunk 133 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 385 GLN 1 523 GLN ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11433 GLN B 238 ASN B 401 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.039036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.029538 restraints weight = 323507.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.031036 restraints weight = 121728.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.031608 restraints weight = 60787.333| |-----------------------------------------------------------------------------| r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 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 = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.2886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.798 19306 Z= 0.322 Angle : 0.887 81.262 26296 Z= 0.417 Chirality : 0.045 0.325 2927 Planarity : 0.005 0.094 3278 Dihedral : 10.122 84.260 2885 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.56 % Allowed : 16.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.18), residues: 2239 helix: 1.43 (0.16), residues: 1030 sheet: -0.26 (0.31), residues: 256 loop : 0.28 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 376 HIS 0.008 0.001 HIS 1 684 PHE 0.020 0.002 PHE B 399 TYR 0.023 0.002 TYR B 503 ARG 0.008 0.001 ARG 11076 Details of bonding type rmsd hydrogen bonds : bond 0.04998 ( 899) hydrogen bonds : angle 5.45188 ( 2573) metal coordination : bond 0.00488 ( 4) metal coordination : angle 4.08492 ( 12) covalent geometry : bond 0.00894 (19302) covalent geometry : angle 0.88331 (26284) *********************** 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 122 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 71 time to evaluate : 2.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 617 LYS cc_start: 0.9333 (tttt) cc_final: 0.9106 (tppt) REVERT: 1 771 LEU cc_start: 0.8810 (mt) cc_final: 0.8501 (mt) REVERT: 1 883 VAL cc_start: 0.9117 (OUTLIER) cc_final: 0.8806 (m) REVERT: 1 1001 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.7849 (mmt) REVERT: A 49 MET cc_start: 0.8330 (ttm) cc_final: 0.8078 (ttm) REVERT: B 221 GLN cc_start: 0.8896 (mt0) cc_final: 0.8578 (mp10) outliers start: 51 outliers final: 27 residues processed: 118 average time/residue: 0.2988 time to fit residues: 57.0216 Evaluate side-chains 96 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 67 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 614 ASN Chi-restraints excluded: chain 1 residue 641 GLN Chi-restraints excluded: chain 1 residue 883 VAL Chi-restraints excluded: chain 1 residue 893 LEU Chi-restraints excluded: chain 1 residue 957 VAL Chi-restraints excluded: chain 1 residue 991 LEU Chi-restraints excluded: chain 1 residue 1000 VAL Chi-restraints excluded: chain 1 residue 1001 MET Chi-restraints excluded: chain 1 residue 1032 ILE Chi-restraints excluded: chain 1 residue 1068 VAL Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1334 ILE Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain 1 residue 1425 SER Chi-restraints excluded: chain 1 residue 1440 THR Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 320 GLN 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 482 THR 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 35 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 129 optimal weight: 20.0000 chunk 185 optimal weight: 0.4980 chunk 120 optimal weight: 40.0000 chunk 40 optimal weight: 10.0000 chunk 181 optimal weight: 20.0000 chunk 83 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 428 GLN 1 844 GLN ** 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 = 0.3211 r_free = 0.3211 target = 0.039456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.029988 restraints weight = 396644.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.031432 restraints weight = 140769.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.031499 restraints weight = 78007.267| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 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 = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.2884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 19306 Z= 0.183 Angle : 0.596 18.227 26296 Z= 0.306 Chirality : 0.042 0.188 2927 Planarity : 0.005 0.108 3278 Dihedral : 9.983 83.407 2883 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.06 % Allowed : 16.14 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.18), residues: 2239 helix: 1.61 (0.16), residues: 1025 sheet: -0.21 (0.31), residues: 269 loop : 0.33 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 376 HIS 0.005 0.001 HIS 1 684 PHE 0.015 0.001 PHE B 399 TYR 0.016 0.001 TYR B 503 ARG 0.009 0.000 ARG 1 975 Details of bonding type rmsd hydrogen bonds : bond 0.04241 ( 899) hydrogen bonds : angle 5.19845 ( 2573) metal coordination : bond 0.00406 ( 4) metal coordination : angle 4.15672 ( 12) covalent geometry : bond 0.00404 (19302) covalent geometry : angle 0.58993 (26284) *********************** 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 110 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 69 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 617 LYS cc_start: 0.9357 (tttt) cc_final: 0.9134 (tppt) REVERT: 1 771 LEU cc_start: 0.8765 (mt) cc_final: 0.8481 (mt) REVERT: 1 883 VAL cc_start: 0.9074 (OUTLIER) cc_final: 0.8755 (m) REVERT: 1 1330 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8335 (tp) REVERT: A 49 MET cc_start: 0.8373 (ttm) cc_final: 0.7862 (ttm) REVERT: B 221 GLN cc_start: 0.8964 (mt0) cc_final: 0.8579 (mp10) outliers start: 41 outliers final: 28 residues processed: 109 average time/residue: 0.2961 time to fit residues: 52.5019 Evaluate side-chains 97 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 67 time to evaluate : 2.260 ------------------------------------------------------------------------------- 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 614 ASN Chi-restraints excluded: chain 1 residue 670 THR Chi-restraints excluded: chain 1 residue 844 GLN Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 860 VAL Chi-restraints excluded: chain 1 residue 883 VAL Chi-restraints excluded: chain 1 residue 893 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 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 59 LEU Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 176 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 121 optimal weight: 30.0000 chunk 1 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 157 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 754 ASN ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.039323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.030059 restraints weight = 327967.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.031307 restraints weight = 130919.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.031456 restraints weight = 72400.188| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 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 = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 19306 Z= 0.180 Angle : 0.561 10.865 26296 Z= 0.285 Chirality : 0.041 0.174 2927 Planarity : 0.005 0.072 3278 Dihedral : 9.934 81.836 2883 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.16 % Allowed : 16.39 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.18), residues: 2239 helix: 1.64 (0.16), residues: 1026 sheet: -0.15 (0.31), residues: 271 loop : 0.38 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 1 671 HIS 0.005 0.001 HIS 1 684 PHE 0.014 0.001 PHE B 399 TYR 0.017 0.001 TYR B 503 ARG 0.006 0.000 ARG 11076 Details of bonding type rmsd hydrogen bonds : bond 0.04065 ( 899) hydrogen bonds : angle 5.07831 ( 2573) metal coordination : bond 0.00370 ( 4) metal coordination : angle 4.12725 ( 12) covalent geometry : bond 0.00399 (19302) covalent geometry : angle 0.55418 (26284) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 66 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 617 LYS cc_start: 0.9409 (tttt) cc_final: 0.9163 (tppt) REVERT: 1 771 LEU cc_start: 0.8843 (mt) cc_final: 0.8527 (mt) REVERT: 1 1001 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7809 (mmt) REVERT: 1 1330 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8356 (tp) REVERT: A 49 MET cc_start: 0.8275 (ttm) cc_final: 0.7778 (ttm) outliers start: 43 outliers final: 29 residues processed: 107 average time/residue: 0.3638 time to fit residues: 66.1102 Evaluate side-chains 98 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 2.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 362 VAL Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 614 ASN Chi-restraints excluded: chain 1 residue 670 THR Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 860 VAL Chi-restraints excluded: chain 1 residue 861 LEU Chi-restraints excluded: chain 1 residue 896 VAL 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 1002 ILE Chi-restraints excluded: chain 1 residue 1007 ASP Chi-restraints excluded: chain 1 residue 1032 ILE Chi-restraints excluded: chain 1 residue 1068 VAL Chi-restraints excluded: chain 1 residue 1111 GLU Chi-restraints excluded: chain 1 residue 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 223 optimal weight: 0.2980 chunk 220 optimal weight: 20.0000 chunk 193 optimal weight: 20.0000 chunk 198 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 8 optimal weight: 0.0040 chunk 226 optimal weight: 10.0000 chunk 182 optimal weight: 8.9990 chunk 126 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 407 HIS ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.040333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.031084 restraints weight = 354453.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.032420 restraints weight = 141342.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.032591 restraints weight = 75413.353| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19306 Z= 0.105 Angle : 0.516 10.845 26296 Z= 0.261 Chirality : 0.040 0.152 2927 Planarity : 0.004 0.065 3278 Dihedral : 9.769 78.915 2883 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.45 % Allowed : 17.04 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.18), residues: 2239 helix: 1.90 (0.17), residues: 1018 sheet: -0.02 (0.30), residues: 276 loop : 0.53 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 1 671 HIS 0.004 0.001 HIS 1 684 PHE 0.011 0.001 PHE C 268 TYR 0.014 0.001 TYR B 503 ARG 0.008 0.000 ARG 1 459 Details of bonding type rmsd hydrogen bonds : bond 0.03447 ( 899) hydrogen bonds : angle 4.79630 ( 2573) metal coordination : bond 0.00332 ( 4) metal coordination : angle 4.01408 ( 12) covalent geometry : bond 0.00235 (19302) covalent geometry : angle 0.50936 (26284) *********************** 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 98 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 2.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 617 LYS cc_start: 0.9397 (tttt) cc_final: 0.9156 (tppt) REVERT: 1 771 LEU cc_start: 0.8754 (mt) cc_final: 0.8449 (mt) REVERT: A 49 MET cc_start: 0.8184 (ttm) cc_final: 0.7703 (ttm) outliers start: 29 outliers final: 21 residues processed: 98 average time/residue: 0.3498 time to fit residues: 58.4523 Evaluate side-chains 86 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 402 THR 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 670 THR Chi-restraints excluded: chain 1 residue 860 VAL Chi-restraints excluded: chain 1 residue 861 LEU Chi-restraints excluded: chain 1 residue 893 LEU Chi-restraints excluded: chain 1 residue 896 VAL Chi-restraints excluded: chain 1 residue 1002 ILE Chi-restraints excluded: chain 1 residue 1111 GLU Chi-restraints excluded: chain 1 residue 1274 VAL 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 137 CYS 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 180 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 168 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 156 optimal weight: 20.0000 chunk 211 optimal weight: 8.9990 chunk 217 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 407 HIS 1 844 GLN ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.038787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.029475 restraints weight = 353185.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.030747 restraints weight = 141427.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.030929 restraints weight = 76210.241| |-----------------------------------------------------------------------------| r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 19306 Z= 0.248 Angle : 0.584 11.177 26296 Z= 0.298 Chirality : 0.042 0.160 2927 Planarity : 0.005 0.060 3278 Dihedral : 9.911 78.203 2883 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.31 % Allowed : 16.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.18), residues: 2239 helix: 1.71 (0.16), residues: 1027 sheet: -0.26 (0.32), residues: 265 loop : 0.46 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 274 HIS 0.031 0.001 HIS 1 407 PHE 0.016 0.002 PHE B 399 TYR 0.019 0.002 TYR B 503 ARG 0.006 0.001 ARG 11076 Details of bonding type rmsd hydrogen bonds : bond 0.04233 ( 899) hydrogen bonds : angle 5.03815 ( 2573) metal coordination : bond 0.00409 ( 4) metal coordination : angle 4.04031 ( 12) covalent geometry : bond 0.00539 (19302) covalent geometry : angle 0.57798 (26284) *********************** 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 112 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 66 time to evaluate : 2.458 Fit side-chains revert: symmetry clash REVERT: 1 354 MET cc_start: 0.6484 (ttt) cc_final: 0.6193 (ttt) REVERT: 1 582 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8966 (tt) REVERT: 1 617 LYS cc_start: 0.9414 (tttt) cc_final: 0.9150 (tppt) REVERT: 1 844 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7472 (tm-30) REVERT: 1 1001 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.7789 (mmt) REVERT: B 74 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8286 (mt0) outliers start: 46 outliers final: 34 residues processed: 109 average time/residue: 0.3069 time to fit residues: 55.1542 Evaluate side-chains 103 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 65 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 362 VAL 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 582 LEU Chi-restraints excluded: chain 1 residue 614 ASN Chi-restraints excluded: chain 1 residue 670 THR Chi-restraints excluded: chain 1 residue 844 GLN Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 860 VAL Chi-restraints excluded: chain 1 residue 861 LEU Chi-restraints excluded: chain 1 residue 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 1002 ILE Chi-restraints excluded: chain 1 residue 1007 ASP Chi-restraints excluded: chain 1 residue 1203 SER Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1274 VAL Chi-restraints excluded: chain 1 residue 1334 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 74 GLN Chi-restraints excluded: chain B residue 77 ILE 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 308 ASP Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 173 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 180 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 191 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3211 r_free = 0.3211 target = 0.039263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.029930 restraints weight = 350295.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.031269 restraints weight = 137249.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.031463 restraints weight = 73323.759| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 19306 Z= 0.156 Angle : 0.538 11.013 26296 Z= 0.273 Chirality : 0.041 0.162 2927 Planarity : 0.004 0.057 3278 Dihedral : 9.865 78.615 2883 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.85 % Allowed : 17.24 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.18), residues: 2239 helix: 1.78 (0.16), residues: 1027 sheet: -0.25 (0.31), residues: 270 loop : 0.54 (0.22), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 1 671 HIS 0.008 0.001 HIS 1 407 PHE 0.013 0.001 PHE B 399 TYR 0.016 0.001 TYR B 503 ARG 0.006 0.000 ARG 11076 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 899) hydrogen bonds : angle 4.92784 ( 2573) metal coordination : bond 0.00395 ( 4) metal coordination : angle 4.03450 ( 12) covalent geometry : bond 0.00346 (19302) covalent geometry : angle 0.53092 (26284) *********************** 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 105 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 68 time to evaluate : 2.431 Fit side-chains revert: symmetry clash REVERT: 1 354 MET cc_start: 0.6365 (ttt) cc_final: 0.6071 (ttt) REVERT: 1 582 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8966 (tt) REVERT: 1 617 LYS cc_start: 0.9402 (tttt) cc_final: 0.9176 (tppt) REVERT: 1 1001 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.7825 (mmt) REVERT: B 61 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.6973 (t80) outliers start: 37 outliers final: 32 residues processed: 102 average time/residue: 0.3074 time to fit residues: 51.7899 Evaluate side-chains 100 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 65 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 402 THR 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 582 LEU Chi-restraints excluded: chain 1 residue 641 GLN Chi-restraints excluded: chain 1 residue 670 THR Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 860 VAL Chi-restraints excluded: chain 1 residue 861 LEU Chi-restraints excluded: chain 1 residue 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 1002 ILE Chi-restraints excluded: chain 1 residue 1007 ASP Chi-restraints excluded: chain 1 residue 1032 ILE Chi-restraints excluded: chain 1 residue 1203 SER Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1274 VAL Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain 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 61 PHE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 49 optimal weight: 8.9990 chunk 226 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 107 optimal weight: 40.0000 chunk 156 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 chunk 28 optimal weight: 0.3980 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 407 HIS 1 736 GLN ** 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 = 0.3207 r_free = 0.3207 target = 0.039133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.030071 restraints weight = 311451.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.030879 restraints weight = 133463.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.031218 restraints weight = 75552.268| |-----------------------------------------------------------------------------| r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 19306 Z= 0.172 Angle : 0.542 10.598 26296 Z= 0.274 Chirality : 0.041 0.167 2927 Planarity : 0.004 0.058 3278 Dihedral : 9.864 77.688 2883 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.01 % Allowed : 17.34 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.18), residues: 2239 helix: 1.78 (0.16), residues: 1027 sheet: -0.33 (0.31), residues: 268 loop : 0.54 (0.22), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 274 HIS 0.005 0.001 HIS 1 684 PHE 0.014 0.001 PHE B 399 TYR 0.017 0.001 TYR B 503 ARG 0.005 0.000 ARG 11076 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 899) hydrogen bonds : angle 4.92516 ( 2573) metal coordination : bond 0.00399 ( 4) metal coordination : angle 4.03901 ( 12) covalent geometry : bond 0.00380 (19302) covalent geometry : angle 0.53510 (26284) *********************** 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 105 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 65 time to evaluate : 2.250 Fit side-chains revert: symmetry clash REVERT: 1 354 MET cc_start: 0.6559 (ttt) cc_final: 0.6290 (ttt) REVERT: 1 582 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8941 (tt) REVERT: 1 617 LYS cc_start: 0.9433 (tttt) cc_final: 0.9167 (tppt) REVERT: 1 1001 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7901 (mmt) REVERT: B 61 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7004 (t80) outliers start: 40 outliers final: 35 residues processed: 103 average time/residue: 0.2798 time to fit residues: 48.3283 Evaluate side-chains 101 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 63 time to evaluate : 2.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 362 VAL Chi-restraints excluded: chain 1 residue 402 THR Chi-restraints excluded: chain 1 residue 404 THR Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 582 LEU Chi-restraints excluded: chain 1 residue 641 GLN Chi-restraints excluded: chain 1 residue 670 THR Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 860 VAL Chi-restraints excluded: chain 1 residue 861 LEU Chi-restraints excluded: chain 1 residue 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 1002 ILE Chi-restraints excluded: chain 1 residue 1007 ASP Chi-restraints excluded: chain 1 residue 1032 ILE Chi-restraints excluded: chain 1 residue 1068 VAL Chi-restraints excluded: chain 1 residue 1203 SER Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1274 VAL Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain 1 residue 1425 SER Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 154 optimal weight: 20.0000 chunk 191 optimal weight: 20.0000 chunk 73 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 192 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 128 optimal weight: 30.0000 chunk 195 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 chunk 144 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3209 r_free = 0.3209 target = 0.039149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.030005 restraints weight = 304763.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.031174 restraints weight = 121719.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.031413 restraints weight = 69344.197| |-----------------------------------------------------------------------------| r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 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 = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 19306 Z= 0.164 Angle : 0.539 10.304 26296 Z= 0.272 Chirality : 0.041 0.171 2927 Planarity : 0.004 0.057 3278 Dihedral : 9.859 76.527 2883 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.16 % Allowed : 17.44 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.18), residues: 2239 helix: 1.80 (0.16), residues: 1027 sheet: -0.34 (0.31), residues: 268 loop : 0.57 (0.22), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 1 671 HIS 0.005 0.001 HIS 1 684 PHE 0.013 0.001 PHE B 399 TYR 0.017 0.001 TYR B 503 ARG 0.006 0.000 ARG 11076 Details of bonding type rmsd hydrogen bonds : bond 0.03791 ( 899) hydrogen bonds : angle 4.90162 ( 2573) metal coordination : bond 0.00416 ( 4) metal coordination : angle 4.01263 ( 12) covalent geometry : bond 0.00363 (19302) covalent geometry : angle 0.53236 (26284) *********************** 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 107 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 64 time to evaluate : 2.218 Fit side-chains revert: symmetry clash REVERT: 1 354 MET cc_start: 0.6571 (ttt) cc_final: 0.6290 (ttt) REVERT: 1 582 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8960 (tt) REVERT: 1 617 LYS cc_start: 0.9413 (tttt) cc_final: 0.9073 (tppt) REVERT: 1 844 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7352 (tm-30) REVERT: 1 1001 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.7880 (mmt) REVERT: B 61 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7028 (t80) outliers start: 43 outliers final: 36 residues processed: 105 average time/residue: 0.2792 time to fit residues: 49.4701 Evaluate side-chains 103 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 63 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 362 VAL Chi-restraints excluded: chain 1 residue 402 THR Chi-restraints excluded: chain 1 residue 404 THR Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 582 LEU 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 844 GLN Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 860 VAL Chi-restraints excluded: chain 1 residue 861 LEU Chi-restraints excluded: chain 1 residue 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 1002 ILE Chi-restraints excluded: chain 1 residue 1007 ASP Chi-restraints excluded: chain 1 residue 1032 ILE Chi-restraints excluded: chain 1 residue 1068 VAL Chi-restraints excluded: chain 1 residue 1203 SER Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1274 VAL Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain 1 residue 1425 SER Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 142 optimal weight: 6.9990 chunk 162 optimal weight: 0.7980 chunk 120 optimal weight: 40.0000 chunk 96 optimal weight: 7.9990 chunk 15 optimal weight: 30.0000 chunk 189 optimal weight: 20.0000 chunk 118 optimal weight: 30.0000 chunk 54 optimal weight: 30.0000 chunk 47 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 overall best weight: 6.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3187 r_free = 0.3187 target = 0.038559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.029271 restraints weight = 366367.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.030552 restraints weight = 147378.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.030749 restraints weight = 78025.267| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 19306 Z= 0.241 Angle : 0.589 10.528 26296 Z= 0.300 Chirality : 0.042 0.177 2927 Planarity : 0.005 0.057 3278 Dihedral : 9.978 76.052 2883 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.06 % Allowed : 17.44 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.18), residues: 2239 helix: 1.68 (0.16), residues: 1029 sheet: -0.42 (0.31), residues: 268 loop : 0.49 (0.22), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 274 HIS 0.004 0.001 HIS 1 684 PHE 0.016 0.002 PHE B 399 TYR 0.019 0.001 TYR B 503 ARG 0.007 0.001 ARG 11076 Details of bonding type rmsd hydrogen bonds : bond 0.04192 ( 899) hydrogen bonds : angle 5.05489 ( 2573) metal coordination : bond 0.00489 ( 4) metal coordination : angle 4.19768 ( 12) covalent geometry : bond 0.00523 (19302) covalent geometry : angle 0.58244 (26284) ********************** 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 103 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 62 time to evaluate : 2.249 Fit side-chains revert: symmetry clash REVERT: 1 354 MET cc_start: 0.6485 (ttt) cc_final: 0.6144 (ttt) REVERT: 1 582 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8982 (tt) REVERT: 1 617 LYS cc_start: 0.9409 (tttt) cc_final: 0.9087 (tppt) REVERT: 1 1001 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.7862 (mmt) REVERT: A 49 MET cc_start: 0.7815 (mtp) cc_final: 0.7409 (ttm) REVERT: B 61 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7127 (t80) outliers start: 41 outliers final: 34 residues processed: 100 average time/residue: 0.2876 time to fit residues: 48.1819 Evaluate side-chains 99 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 62 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 402 THR Chi-restraints excluded: chain 1 residue 404 THR Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 582 LEU Chi-restraints excluded: chain 1 residue 614 ASN Chi-restraints excluded: chain 1 residue 641 GLN Chi-restraints excluded: chain 1 residue 670 THR Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 860 VAL Chi-restraints excluded: chain 1 residue 861 LEU Chi-restraints excluded: chain 1 residue 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 1002 ILE Chi-restraints excluded: chain 1 residue 1007 ASP Chi-restraints excluded: chain 1 residue 1032 ILE Chi-restraints excluded: chain 1 residue 1068 VAL Chi-restraints excluded: chain 1 residue 1203 SER Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1274 VAL Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain 1 residue 1425 SER Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 144 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 158 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 188 optimal weight: 6.9990 chunk 203 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 133 optimal weight: 30.0000 chunk 220 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3196 r_free = 0.3196 target = 0.038778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.029474 restraints weight = 359817.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.030940 restraints weight = 139084.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.031025 restraints weight = 72117.301| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 19306 Z= 0.193 Angle : 0.565 13.990 26296 Z= 0.285 Chirality : 0.042 0.177 2927 Planarity : 0.004 0.057 3278 Dihedral : 9.987 75.814 2883 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.88 % Favored : 97.08 % Rotamer: Outliers : 2.06 % Allowed : 17.59 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.18), residues: 2239 helix: 1.73 (0.17), residues: 1029 sheet: -0.40 (0.31), residues: 273 loop : 0.54 (0.22), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 274 HIS 0.003 0.001 HIS C 639 PHE 0.015 0.001 PHE B 399 TYR 0.017 0.001 TYR B 503 ARG 0.006 0.000 ARG 11076 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 899) hydrogen bonds : angle 4.97934 ( 2573) metal coordination : bond 0.00487 ( 4) metal coordination : angle 4.27655 ( 12) covalent geometry : bond 0.00425 (19302) covalent geometry : angle 0.55791 (26284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6455.94 seconds wall clock time: 115 minutes 19.61 seconds (6919.61 seconds total)