Starting phenix.real_space_refine on Sun Aug 24 05:17:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fod_29346/08_2025/8fod_29346.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fod_29346/08_2025/8fod_29346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fod_29346/08_2025/8fod_29346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fod_29346/08_2025/8fod_29346.map" model { file = "/net/cci-nas-00/data/ceres_data/8fod_29346/08_2025/8fod_29346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fod_29346/08_2025/8fod_29346.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 79 5.16 5 C 11110 2.51 5 N 2971 2.21 5 O 3325 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17489 Number of models: 1 Model: "" Number of chains: 5 Chain: "1" Number of atoms: 7607 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 983, 7552 Classifications: {'peptide': 983} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 50, 'TRANS': 932} Chain breaks: 7 Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 417 Unresolved non-hydrogen dihedrals: 315 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 16, 'PHE:plan': 3, 'ASN:plan1': 7, 'HIS:plan': 2, 'GLN:plan1': 5, 'TRP:plan': 1, 'GLU:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 191 Conformer: "B" Number of residues, atoms: 983, 7552 Classifications: {'peptide': 983} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 50, 'TRANS': 932} Chain breaks: 7 Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 417 Unresolved non-hydrogen dihedrals: 315 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 16, 'PHE:plan': 3, 'ASN:plan1': 7, 'HIS:plan': 2, 'GLN:plan1': 5, 'TRP:plan': 1, 'GLU:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 191 bond proxies already assigned to first conformer: 7626 Chain: "A" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3052 Classifications: {'peptide': 380} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 359} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 4, 'ARG:plan': 3, 'GLN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 3507 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 433, 3484 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 13, 'TRANS': 419} Chain breaks: 5 Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 5, 'ASP:plan': 2, 'ARG:plan': 6, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 85 Conformer: "B" Number of residues, atoms: 433, 3484 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 13, 'TRANS': 419} Chain breaks: 5 Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 5, 'ASP:plan': 2, 'ARG:plan': 6, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 85 bond proxies already assigned to first conformer: 3532 Chain: "C" Number of atoms: 3315 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 428, 3291 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 5, 'PTRANS': 24, 'TRANS': 398} Chain breaks: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 59 Conformer: "B" Number of residues, atoms: 428, 3291 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 5, 'PTRANS': 24, 'TRANS': 398} Chain breaks: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 59 bond proxies already assigned to first conformer: 3339 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 12831 SG CYS B 336 35.046 94.020 79.568 1.00 12.48 S ATOM 13601 SG CYS B 434 35.839 88.518 76.597 1.00 8.05 S ATOM 13475 SG CYS B 417 40.736 91.345 79.050 1.00 4.95 S ATOM 13912 SG CYS B 474 38.847 93.635 73.896 1.00 3.46 S Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N AASN 1 745 " occ=0.31 ... (14 atoms not shown) pdb=" ND2BASN 1 745 " occ=0.69 residue: pdb=" N AGLN 1 941 " occ=0.41 ... (16 atoms not shown) pdb=" NE2BGLN 1 941 " occ=0.59 residue: pdb=" N AHIS 11044 " occ=0.39 ... (18 atoms not shown) pdb=" NE2BHIS 11044 " occ=0.61 residue: pdb=" N AASP 11414 " occ=0.45 ... (14 atoms not shown) pdb=" OD2BASP 11414 " occ=0.55 residue: pdb=" N AASP C 263 " occ=0.93 ... (14 atoms not shown) pdb=" OD2BASP C 263 " occ=0.07 residue: pdb=" N ACYS C 399 " occ=0.28 ... (10 atoms not shown) pdb=" SG BCYS C 399 " occ=0.72 Time building chain proxies: 4.96, per 1000 atoms: 0.28 Number of scatterers: 17489 At special positions: 0 Unit cell: (114.264, 130.824, 148.212, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 79 16.00 O 3325 8.00 N 2971 7.00 C 11110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.4 microseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 601 " pdb="FE3 SF4 B 601 " - pdb=" SG CYS B 417 " pdb="FE4 SF4 B 601 " - pdb=" SG CYS B 474 " pdb="FE2 SF4 B 601 " - pdb=" SG CYS B 434 " pdb="FE1 SF4 B 601 " - pdb=" SG CYS B 336 " Number of angles added : 12 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4304 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 19 sheets defined 50.8% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain '1' and resid 402 through 419 removed outlier: 3.590A pdb=" N ILE 1 411 " --> pdb=" O HIS 1 407 " (cutoff:3.500A) Proline residue: 1 412 - end of helix Processing helix chain '1' and resid 480 through 489 Processing helix chain '1' and resid 521 through 523 No H-bonds generated for 'chain '1' and resid 521 through 523' 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 707 Processing helix chain '1' and resid 715 through 725 Processing helix chain '1' and resid 737 through 742 removed outlier: 3.602A pdb=" N ASN 1 742 " --> pdb=" O GLN 1 739 " (cutoff:3.500A) Processing helix chain '1' and resid 743 through 768 removed outlier: 3.572A pdb=" N MET 1 747 " --> pdb=" O ASP 1 743 " (cutoff:3.500A) Processing helix chain '1' and resid 769 through 782 Processing helix chain '1' and resid 784 through 790 removed outlier: 3.543A pdb=" N THR 1 788 " --> pdb=" O ALA 1 784 " (cutoff:3.500A) Processing helix chain '1' and resid 792 through 807 removed outlier: 4.358A pdb=" N ARG 1 796 " --> pdb=" O THR 1 792 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU 1 801 " --> pdb=" O ASN 1 797 " (cutoff:3.500A) Processing helix chain '1' and resid 868 through 876 Processing helix chain '1' and resid 905 through 927 removed outlier: 3.642A pdb=" N THR 1 926 " --> pdb=" O LYS 1 922 " (cutoff:3.500A) Processing helix chain '1' and resid 929 through 950 Processing helix chain '1' and resid 951 through 954 Processing helix chain '1' and resid 963 through 988 Processing helix chain '1' and resid 1008 through 1027 Processing helix chain '1' and resid 1079 through 1094 Processing helix chain '1' and resid 1100 through 1120 Processing helix chain '1' and resid 1123 through 1128 Processing helix chain '1' and resid 1136 through 1140 removed outlier: 3.913A pdb=" N TYR 11140 " --> pdb=" O PRO 11137 " (cutoff:3.500A) Processing helix chain '1' and resid 1146 through 1156 removed outlier: 3.953A pdb=" N GLN 11150 " --> pdb=" O MET 11146 " (cutoff:3.500A) Processing helix chain '1' and resid 1196 through 1201 removed outlier: 3.571A pdb=" N ILE 11201 " --> pdb=" O ASN 11197 " (cutoff:3.500A) Processing helix chain '1' and resid 1202 through 1205 Processing helix chain '1' and resid 1209 through 1216 removed outlier: 3.614A pdb=" N TYR 11213 " --> pdb=" O ASP 11209 " (cutoff:3.500A) Processing helix chain '1' and resid 1218 through 1226 removed outlier: 3.634A pdb=" N VAL 11222 " --> pdb=" O ILE 11218 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG 11224 " --> pdb=" O ALA 11220 " (cutoff:3.500A) Processing helix chain '1' and resid 1275 through 1280 removed outlier: 4.522A pdb=" N ASP 11279 " --> pdb=" O ARG 11276 " (cutoff:3.500A) Processing helix chain '1' and resid 1322 through 1344 removed outlier: 4.064A pdb=" N GLN 11329 " --> pdb=" O GLN 11325 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY 11344 " --> pdb=" O LEU 11340 " (cutoff:3.500A) Processing helix chain '1' and resid 1381 through 1395 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: 4.109A pdb=" N TYR 11448 " --> pdb=" O VAL 11444 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 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: 4.974A pdb=" N ASP A 94 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 121 removed outlier: 4.037A pdb=" N ASP A 116 " --> pdb=" O ASP A 113 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP A 118 " --> pdb=" O ASP A 115 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ALA A 119 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG A 121 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 151 removed outlier: 4.200A pdb=" N ILE A 137 " --> pdb=" O CYS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.582A pdb=" N ALA A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) 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: 4.169A pdb=" N VAL A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 236 removed outlier: 3.872A 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 251 through 265 Processing helix chain 'A' and resid 269 through 285 removed outlier: 3.711A 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 315 through 320 removed outlier: 3.852A pdb=" N LYS A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLN A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 320' Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 353 through 364 removed outlier: 3.654A pdb=" N LYS A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 371 through 391 removed outlier: 4.553A pdb=" N PHE A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) 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: 3.570A 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 208 removed outlier: 4.920A pdb=" N ALA B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 4.805A 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 238 removed outlier: 3.882A 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 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 287 through 297 Processing helix chain 'B' and resid 322 through 325 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 366 Processing helix chain 'B' and resid 368 through 380 Processing helix chain 'B' and resid 387 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 451 Processing helix chain 'B' and resid 454 through 468 removed outlier: 3.885A pdb=" N GLY B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 483 Processing helix chain 'B' and resid 499 through 515 Processing helix chain 'C' and resid 254 through 277 removed outlier: 4.011A pdb=" N ILE C 265 " --> pdb=" O LEU C 261 " (cutoff:3.500A) 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 445 Processing helix chain 'C' and resid 460 through 469 Processing helix chain 'C' and resid 469 through 474 Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 548 through 554 Processing helix chain 'C' and resid 555 through 567 Processing helix chain 'C' and resid 613 through 617 Processing helix chain 'C' and resid 622 through 626 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: 7.131A pdb=" N SER 1 381 " --> pdb=" O VAL 1 515 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N VAL 1 517 " --> pdb=" O SER 1 381 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N MET 1 383 " --> pdb=" O VAL 1 517 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL 1 519 " --> pdb=" O MET 1 383 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLN 1 385 " --> pdb=" O VAL 1 519 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU 1 366 " --> pdb=" O ILE 1 386 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP 1 358 " --> pdb=" O PHE 1 369 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LYS 1 371 " --> pdb=" O TRP 1 356 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N TRP 1 356 " --> pdb=" O LYS 1 371 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 425 through 431 removed outlier: 7.688A pdb=" N ASP 1 444 " --> pdb=" O PRO 1 397 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE 1 395 " --> pdb=" O LEU 1 446 " (cutoff:3.500A) removed outlier: 4.066A 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: 6.778A pdb=" N LEU 1 582 " --> pdb=" O ARG 1 609 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ARG 1 611 " --> pdb=" O LEU 1 582 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR 1 584 " --> pdb=" O ARG 1 611 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP 1 581 " --> pdb=" O ALA 1 563 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLN 1 554 " --> pdb=" O ASN 1 548 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASN 1 548 " --> pdb=" O GLN 1 554 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE 1 556 " --> pdb=" O LEU 1 546 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU 1 546 " --> pdb=" O ILE 1 556 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER 1 558 " --> pdb=" O GLN 1 544 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN 1 544 " --> pdb=" O SER 1 558 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER 1 542 " --> pdb=" O THR 1 560 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN 1 566 " --> pdb=" O LEU 1 536 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU 1 536 " --> pdb=" O ASN 1 566 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG 1 537 " --> pdb=" O VAL 1 634 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE 1 636 " --> pdb=" O ARG 1 537 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU 1 539 " --> pdb=" O ILE 1 636 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE 1 635 " --> pdb=" O CYS 1 697 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '1' and resid 854 through 856 removed outlier: 6.327A pdb=" N VAL 1 862 " --> pdb=" O ASP 11035 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL 11037 " --> pdb=" O VAL 1 860 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL 1 860 " --> pdb=" O VAL 11037 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASP 11003 " --> pdb=" O VAL 1 992 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL 1 992 " --> pdb=" O ASP 11003 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 854 through 856 removed outlier: 6.563A pdb=" N PHE 11038 " --> pdb=" O VAL 11054 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N VAL 11054 " --> pdb=" O PHE 11038 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS 11040 " --> pdb=" O LEU 11052 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LYS 11048 " --> pdb=" O AHIS 11044 " (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: 4.559A 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 56 through 60 removed outlier: 5.775A pdb=" N ARG A 58 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N MET A 49 " --> pdb=" O ARG A 58 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLU A 46 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE A 85 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 56 through 60 removed outlier: 5.775A pdb=" N ARG A 58 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N MET A 49 " --> pdb=" O ARG A 58 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLU A 46 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 325 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 108 through 112 Processing sheet with id=AB4, first strand: chain 'B' and resid 181 through 182 removed outlier: 3.775A 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: 3.890A pdb=" N VAL C 301 " --> pdb=" O SER C 317 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LEU C 316 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL C 330 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL C 362 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LYS C 353 " --> pdb=" O VAL C 362 " (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: 4.240A pdb=" N VAL C 689 " --> pdb=" O VAL C 683 " (cutoff:3.500A) removed outlier: 3.664A 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: 6.716A pdb=" N LYS C 394 " --> pdb=" O VAL C 428 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE C 430 " --> pdb=" O LYS C 394 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ILE C 396 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N PHE C 432 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR C 398 " --> pdb=" O PHE C 432 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 522 through 526 removed outlier: 6.632A pdb=" N TYR C 530 " --> pdb=" O ILE C 630 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ILE C 632 " --> pdb=" O TYR C 530 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLY C 532 " --> pdb=" O ILE C 632 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N MET C 631 " --> pdb=" O ILE C 650 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 578 through 579 889 hydrogen bonds defined for protein. 2508 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.89 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.39: 7227 1.39 - 1.61: 10531 1.61 - 1.84: 103 1.84 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 17873 Sorted by residual: bond pdb=" N PRO A 247 " pdb=" CD PRO A 247 " ideal model delta sigma weight residual 1.473 1.579 -0.106 1.40e-02 5.10e+03 5.73e+01 bond pdb=" CD GLN 1 544 " pdb=" NE2 GLN 1 544 " ideal model delta sigma weight residual 1.328 1.192 0.136 2.10e-02 2.27e+03 4.19e+01 bond pdb=" CA ALA 1 649 " pdb=" CB ALA 1 649 " ideal model delta sigma weight residual 1.528 1.463 0.065 1.56e-02 4.11e+03 1.74e+01 bond pdb=" C HIS A 210 " pdb=" O HIS A 210 " ideal model delta sigma weight residual 1.237 1.288 -0.051 1.36e-02 5.41e+03 1.39e+01 bond pdb=" CA PRO A 247 " pdb=" C PRO A 247 " ideal model delta sigma weight residual 1.520 1.571 -0.052 1.42e-02 4.96e+03 1.34e+01 ... (remaining 17868 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.78: 24254 5.78 - 11.55: 25 11.55 - 17.33: 3 17.33 - 23.11: 1 23.11 - 28.88: 1 Bond angle restraints: 24284 Sorted by residual: angle pdb=" CA PRO A 247 " pdb=" N PRO A 247 " pdb=" CD PRO A 247 " ideal model delta sigma weight residual 112.00 83.12 28.88 1.40e+00 5.10e-01 4.26e+02 angle pdb=" CA HIS A 210 " pdb=" C HIS A 210 " pdb=" O HIS A 210 " ideal model delta sigma weight residual 119.80 114.12 5.68 1.00e+00 1.00e+00 3.22e+01 angle pdb=" CA HIS A 210 " pdb=" C HIS A 210 " pdb=" N PRO A 211 " ideal model delta sigma weight residual 118.85 123.89 -5.04 9.50e-01 1.11e+00 2.81e+01 angle pdb=" C LEU A 246 " pdb=" N PRO A 247 " pdb=" CD PRO A 247 " ideal model delta sigma weight residual 125.00 145.34 -20.34 4.10e+00 5.95e-02 2.46e+01 angle pdb=" C ILE 11409 " pdb=" CA ILE 11409 " pdb=" CB ILE 11409 " ideal model delta sigma weight residual 112.02 105.87 6.15 1.31e+00 5.83e-01 2.21e+01 ... (remaining 24279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 9817 17.67 - 35.34: 833 35.34 - 53.02: 176 53.02 - 70.69: 33 70.69 - 88.36: 20 Dihedral angle restraints: 10879 sinusoidal: 4251 harmonic: 6628 Sorted by residual: dihedral pdb=" CA LEU A 246 " pdb=" C LEU A 246 " pdb=" N PRO A 247 " pdb=" CA PRO A 247 " ideal model delta harmonic sigma weight residual 180.00 156.80 23.20 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA LYS B 393 " pdb=" C LYS B 393 " pdb=" N GLU B 394 " pdb=" CA GLU B 394 " ideal model delta harmonic sigma weight residual 180.00 -158.52 -21.48 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA THR B 71 " pdb=" C THR B 71 " pdb=" N LEU B 72 " pdb=" CA LEU B 72 " ideal model delta harmonic sigma weight residual -180.00 -158.60 -21.40 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 10876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2513 0.087 - 0.173: 214 0.173 - 0.260: 5 0.260 - 0.346: 1 0.346 - 0.433: 2 Chirality restraints: 2735 Sorted by residual: chirality pdb=" CA PRO A 211 " pdb=" N PRO A 211 " pdb=" C PRO A 211 " pdb=" CB PRO A 211 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" CB VAL C 326 " pdb=" CA VAL C 326 " pdb=" CG1 VAL C 326 " pdb=" CG2 VAL C 326 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CB ILE C 632 " pdb=" CA ILE C 632 " pdb=" CG1 ILE C 632 " pdb=" CG2 ILE C 632 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 2732 not shown) Planarity restraints: 3165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 246 " 0.089 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO A 247 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE 1 462 " -0.057 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO 1 463 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO 1 463 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO 1 463 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 35 " -0.057 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO A 36 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 36 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 36 " -0.048 5.00e-02 4.00e+02 ... (remaining 3162 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 658 2.71 - 3.26: 17743 3.26 - 3.81: 27784 3.81 - 4.35: 34547 4.35 - 4.90: 58904 Nonbonded interactions: 139636 Sorted by model distance: nonbonded pdb=" OH TYR A 209 " pdb=" OD1 ASP A 303 " model vdw 2.167 3.040 nonbonded pdb=" OH TYR A 23 " pdb=" O PRO A 328 " model vdw 2.185 3.040 nonbonded pdb=" O ARG 1 537 " pdb=" N ASP 1 633 " model vdw 2.208 3.120 nonbonded pdb=" OD2 ASP C 541 " pdb=" OH TYR C 571 " model vdw 2.248 3.040 nonbonded pdb=" O THR B 166 " pdb=" OG1 THR B 169 " model vdw 2.257 3.040 ... (remaining 139631 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=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 19.410 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6133 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 : 0.006 0.154 17877 Z= 0.263 Angle : 0.857 28.882 24296 Z= 0.470 Chirality : 0.048 0.433 2735 Planarity : 0.006 0.111 3165 Dihedral : 14.421 88.359 6575 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.83 % Favored : 97.08 % Rotamer: Outliers : 0.27 % Allowed : 11.69 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.18), residues: 2221 helix: 0.67 (0.16), residues: 1022 sheet: -0.20 (0.32), residues: 244 loop : -0.02 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG A 45 TYR 0.025 0.002 TYR A 59 PHE 0.029 0.003 PHE C 268 TRP 0.027 0.003 TRP C 695 HIS 0.012 0.002 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00557 (17873) covalent geometry : angle 0.83130 (24284) hydrogen bonds : bond 0.16947 ( 878) hydrogen bonds : angle 7.22186 ( 2508) metal coordination : bond 0.01495 ( 4) metal coordination : angle 9.32977 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 308 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 449 LEU cc_start: 0.7627 (mp) cc_final: 0.7417 (mp) REVERT: 1 482 PHE cc_start: 0.7790 (t80) cc_final: 0.7425 (t80) REVERT: 1 567 ILE cc_start: 0.8432 (mm) cc_final: 0.8128 (mm) REVERT: 1 703 MET cc_start: 0.7040 (tpt) cc_final: 0.6411 (tpt) REVERT: 1 855 LEU cc_start: 0.6916 (tt) cc_final: 0.6689 (tp) REVERT: 1 980 ASN cc_start: 0.5490 (t0) cc_final: 0.5244 (t0) REVERT: 1 1015 ILE cc_start: 0.5503 (mm) cc_final: 0.5085 (tt) REVERT: 1 1436 GLU cc_start: 0.6239 (tt0) cc_final: 0.6004 (tt0) REVERT: 1 1438 MET cc_start: 0.5856 (mmt) cc_final: 0.5210 (mmp) REVERT: A 49 MET cc_start: 0.4492 (mtt) cc_final: 0.4258 (mtm) REVERT: B 96 ASN cc_start: 0.6739 (m-40) cc_final: 0.6180 (m-40) REVERT: B 119 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6895 (tm-30) REVERT: B 224 PHE cc_start: 0.6363 (m-80) cc_final: 0.5977 (m-10) REVERT: B 277 TYR cc_start: 0.5576 (m-80) cc_final: 0.5169 (m-80) REVERT: B 388 MET cc_start: 0.7428 (mmm) cc_final: 0.7044 (mmt) REVERT: B 443 ARG cc_start: 0.6224 (mtp180) cc_final: 0.6010 (mtp180) outliers start: 5 outliers final: 1 residues processed: 311 average time/residue: 0.1213 time to fit residues: 57.3980 Evaluate side-chains 209 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 294 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.4980 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.0770 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 0.9980 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11024 ASN 11088 HIS ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 418 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.180495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.173426 restraints weight = 97966.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.172836 restraints weight = 92697.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.172633 restraints weight = 36494.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.172907 restraints weight = 31712.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.173585 restraints weight = 19239.238| |-----------------------------------------------------------------------------| r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4220 r_free = 0.4220 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4219 r_free = 0.4219 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| r_final: 0.4219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5993 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17877 Z= 0.137 Angle : 0.625 15.831 24296 Z= 0.312 Chirality : 0.043 0.272 2735 Planarity : 0.005 0.071 3165 Dihedral : 4.633 30.415 2421 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.54 % Allowed : 12.38 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.18), residues: 2221 helix: 1.28 (0.16), residues: 1026 sheet: -0.24 (0.32), residues: 249 loop : 0.09 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 699 TYR 0.019 0.002 TYR B 352 PHE 0.020 0.002 PHE B 375 TRP 0.012 0.001 TRP C 695 HIS 0.010 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00309 (17873) covalent geometry : angle 0.60318 (24284) hydrogen bonds : bond 0.03965 ( 878) hydrogen bonds : angle 5.29307 ( 2508) metal coordination : bond 0.00719 ( 4) metal coordination : angle 7.34982 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 231 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 482 PHE cc_start: 0.7826 (t80) cc_final: 0.7466 (t80) REVERT: 1 567 ILE cc_start: 0.8084 (mm) cc_final: 0.7812 (mm) REVERT: 1 703 MET cc_start: 0.6687 (tpt) cc_final: 0.5831 (tpt) REVERT: 1 706 SER cc_start: 0.7830 (OUTLIER) cc_final: 0.7550 (m) REVERT: 1 980 ASN cc_start: 0.5506 (t0) cc_final: 0.5022 (t0) REVERT: 1 1015 ILE cc_start: 0.5443 (mm) cc_final: 0.5128 (tt) REVERT: 1 1100 GLU cc_start: 0.5726 (pm20) cc_final: 0.5159 (pt0) REVERT: 1 1276 ARG cc_start: 0.5905 (tpt170) cc_final: 0.5324 (tpt170) REVERT: 1 1438 MET cc_start: 0.5747 (mmt) cc_final: 0.5083 (mmp) REVERT: A 51 PHE cc_start: 0.4461 (OUTLIER) cc_final: 0.3639 (t80) REVERT: B 119 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6618 (tm-30) REVERT: B 207 LEU cc_start: 0.7053 (mt) cc_final: 0.6616 (mm) REVERT: B 234 GLU cc_start: 0.6468 (OUTLIER) cc_final: 0.6214 (tt0) REVERT: B 277 TYR cc_start: 0.5676 (m-80) cc_final: 0.5283 (m-80) REVERT: B 451 MET cc_start: 0.6957 (mmm) cc_final: 0.6675 (tpp) REVERT: C 392 SER cc_start: 0.4548 (m) cc_final: 0.4133 (p) REVERT: C 402 TYR cc_start: 0.6384 (m-80) cc_final: 0.5788 (m-80) outliers start: 29 outliers final: 11 residues processed: 247 average time/residue: 0.1232 time to fit residues: 46.5726 Evaluate side-chains 214 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 706 SER Chi-restraints excluded: chain 1 residue 954 LEU Chi-restraints excluded: chain 1 residue 1079 CYS Chi-restraints excluded: chain 1 residue 1106 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 672 CYS Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 705 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 108 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 chunk 146 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 121 optimal weight: 0.7980 chunk 129 optimal weight: 30.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 941 GLN A A 60 ASN ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.180897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.168102 restraints weight = 113896.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.170161 restraints weight = 105061.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.171168 restraints weight = 44266.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.171881 restraints weight = 42990.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.171923 restraints weight = 28806.681| |-----------------------------------------------------------------------------| r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4182 r_free = 0.4182 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4182 r_free = 0.4182 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.4182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6058 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17877 Z= 0.124 Angle : 0.587 12.258 24296 Z= 0.291 Chirality : 0.043 0.322 2735 Planarity : 0.005 0.062 3165 Dihedral : 4.396 25.780 2421 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.49 % Allowed : 13.12 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.18), residues: 2221 helix: 1.51 (0.16), residues: 1025 sheet: -0.47 (0.30), residues: 281 loop : 0.14 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 215 TYR 0.022 0.001 TYR B 397 PHE 0.017 0.002 PHE B 375 TRP 0.009 0.001 TRP C 695 HIS 0.013 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00275 (17873) covalent geometry : angle 0.56907 (24284) hydrogen bonds : bond 0.03554 ( 878) hydrogen bonds : angle 4.92135 ( 2508) metal coordination : bond 0.00831 ( 4) metal coordination : angle 6.46096 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 219 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: 1 482 PHE cc_start: 0.7813 (t80) cc_final: 0.7423 (t80) REVERT: 1 567 ILE cc_start: 0.8156 (mm) cc_final: 0.7854 (mm) REVERT: 1 703 MET cc_start: 0.6703 (tpt) cc_final: 0.5883 (tpt) REVERT: 1 706 SER cc_start: 0.7825 (OUTLIER) cc_final: 0.7472 (m) REVERT: 1 1015 ILE cc_start: 0.5506 (mm) cc_final: 0.5038 (tt) REVERT: 1 1040 LYS cc_start: 0.7272 (mtpp) cc_final: 0.6778 (mtpt) REVERT: 1 1100 GLU cc_start: 0.5530 (pm20) cc_final: 0.5271 (pt0) REVERT: 1 1168 ILE cc_start: 0.6681 (OUTLIER) cc_final: 0.6416 (pt) REVERT: 1 1276 ARG cc_start: 0.5751 (tpt170) cc_final: 0.5083 (tpt170) REVERT: 1 1438 MET cc_start: 0.5726 (mmt) cc_final: 0.4812 (mmm) REVERT: B 128 TYR cc_start: 0.5612 (OUTLIER) cc_final: 0.3772 (m-80) REVERT: B 207 LEU cc_start: 0.6961 (mt) cc_final: 0.6598 (mm) REVERT: B 234 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.6153 (tt0) REVERT: B 277 TYR cc_start: 0.5652 (m-80) cc_final: 0.5243 (m-80) REVERT: B 451 MET cc_start: 0.7089 (mmm) cc_final: 0.6772 (tpp) REVERT: C 392 SER cc_start: 0.4585 (m) cc_final: 0.4122 (p) REVERT: C 423 GLU cc_start: 0.6842 (mp0) cc_final: 0.6594 (mt-10) REVERT: C 537 ASP cc_start: 0.6968 (p0) cc_final: 0.6688 (p0) outliers start: 27 outliers final: 15 residues processed: 237 average time/residue: 0.1213 time to fit residues: 44.7909 Evaluate side-chains 219 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 200 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 706 SER Chi-restraints excluded: chain 1 residue 755 ILE Chi-restraints excluded: chain 1 residue 954 LEU Chi-restraints excluded: chain 1 residue 1007 ASP Chi-restraints excluded: chain 1 residue 1079 CYS Chi-restraints excluded: chain 1 residue 1168 ILE Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 672 CYS Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 705 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 185 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 220 optimal weight: 7.9990 chunk 137 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 161 optimal weight: 7.9990 chunk 152 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 524 ASN 11024 ASN 11036 ASN 11194 HIS 11450 ASN A 210 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 385 GLN ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.173476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.161609 restraints weight = 99581.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.163298 restraints weight = 100669.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.164057 restraints weight = 37851.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.164413 restraints weight = 34499.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.164644 restraints weight = 25267.529| |-----------------------------------------------------------------------------| r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4110 r_free = 0.4110 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4110 r_free = 0.4110 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| r_final: 0.4110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 17877 Z= 0.242 Angle : 0.762 15.262 24296 Z= 0.380 Chirality : 0.049 0.361 2735 Planarity : 0.006 0.064 3165 Dihedral : 5.109 25.004 2419 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.34 % Allowed : 12.96 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.18), residues: 2221 helix: 1.01 (0.16), residues: 1010 sheet: -0.77 (0.32), residues: 249 loop : -0.34 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 215 TYR 0.023 0.002 TYR 11391 PHE 0.030 0.003 PHE B 375 TRP 0.018 0.002 TRP C 695 HIS 0.011 0.002 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00551 (17873) covalent geometry : angle 0.74214 (24284) hydrogen bonds : bond 0.04362 ( 878) hydrogen bonds : angle 5.40869 ( 2508) metal coordination : bond 0.01700 ( 4) metal coordination : angle 7.88347 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 215 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: 1 416 ASP cc_start: 0.5977 (m-30) cc_final: 0.5670 (m-30) REVERT: 1 733 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7958 (tp) REVERT: 1 1015 ILE cc_start: 0.5475 (mm) cc_final: 0.4958 (tt) REVERT: 1 1168 ILE cc_start: 0.6928 (OUTLIER) cc_final: 0.6602 (pt) REVERT: 1 1351 SER cc_start: 0.7593 (m) cc_final: 0.7088 (p) REVERT: 1 1438 MET cc_start: 0.5667 (mmt) cc_final: 0.4809 (mmm) REVERT: A 117 TYR cc_start: 0.6497 (m-80) cc_final: 0.6261 (m-80) REVERT: B 87 LEU cc_start: 0.6794 (mp) cc_final: 0.6339 (mp) REVERT: B 121 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7567 (tt) REVERT: B 128 TYR cc_start: 0.6136 (OUTLIER) cc_final: 0.4478 (m-80) REVERT: B 234 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6129 (tt0) REVERT: B 415 TRP cc_start: 0.6718 (OUTLIER) cc_final: 0.6163 (m-10) REVERT: B 451 MET cc_start: 0.7306 (mmm) cc_final: 0.7008 (tpp) REVERT: C 272 ILE cc_start: 0.6043 (OUTLIER) cc_final: 0.5739 (mm) REVERT: C 392 SER cc_start: 0.5015 (m) cc_final: 0.4419 (p) REVERT: C 425 LYS cc_start: 0.7222 (mttt) cc_final: 0.6164 (tptt) outliers start: 43 outliers final: 23 residues processed: 251 average time/residue: 0.1235 time to fit residues: 48.6455 Evaluate side-chains 215 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 469 ASP Chi-restraints excluded: chain 1 residue 661 SER Chi-restraints excluded: chain 1 residue 692 SER Chi-restraints excluded: chain 1 residue 717 SER Chi-restraints excluded: chain 1 residue 733 ILE Chi-restraints excluded: chain 1 residue 954 LEU Chi-restraints excluded: chain 1 residue 1079 CYS Chi-restraints excluded: chain 1 residue 1086 SER Chi-restraints excluded: chain 1 residue 1106 VAL Chi-restraints excluded: chain 1 residue 1168 ILE Chi-restraints excluded: chain 1 residue 1334 ILE Chi-restraints excluded: chain 1 residue 1338 ILE Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain B residue 470 TYR Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 672 CYS Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 705 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 111 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 35 optimal weight: 0.1980 chunk 15 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 418 HIS C 692 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.177689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.166822 restraints weight = 100146.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.168450 restraints weight = 100228.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.169150 restraints weight = 34055.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.169591 restraints weight = 31909.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.170064 restraints weight = 21340.663| |-----------------------------------------------------------------------------| r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4179 r_free = 0.4179 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4179 r_free = 0.4179 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.4179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6081 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17877 Z= 0.120 Angle : 0.592 12.161 24296 Z= 0.297 Chirality : 0.043 0.320 2735 Planarity : 0.005 0.057 3165 Dihedral : 4.534 20.353 2419 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.54 % Allowed : 14.24 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.18), residues: 2221 helix: 1.47 (0.16), residues: 1012 sheet: -0.55 (0.31), residues: 277 loop : -0.21 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 654 TYR 0.025 0.001 TYR A 261 PHE 0.039 0.002 PHE B 375 TRP 0.010 0.001 TRP C 695 HIS 0.008 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00270 (17873) covalent geometry : angle 0.57741 (24284) hydrogen bonds : bond 0.03417 ( 878) hydrogen bonds : angle 4.87757 ( 2508) metal coordination : bond 0.00830 ( 4) metal coordination : angle 6.00317 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: 1 954 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6830 (tp) REVERT: 1 1015 ILE cc_start: 0.5402 (mm) cc_final: 0.4923 (tt) REVERT: 1 1040 LYS cc_start: 0.7151 (mtpp) cc_final: 0.6699 (mtpt) REVERT: 1 1351 SER cc_start: 0.7572 (m) cc_final: 0.7079 (p) REVERT: 1 1438 MET cc_start: 0.5515 (mmt) cc_final: 0.4646 (mmm) REVERT: B 87 LEU cc_start: 0.6688 (mp) cc_final: 0.6348 (mp) REVERT: B 128 TYR cc_start: 0.5977 (OUTLIER) cc_final: 0.4127 (m-80) REVERT: B 234 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.6004 (tt0) REVERT: B 451 MET cc_start: 0.7260 (mmm) cc_final: 0.7039 (tpp) REVERT: C 392 SER cc_start: 0.4897 (m) cc_final: 0.4324 (p) REVERT: C 480 ILE cc_start: 0.7584 (mp) cc_final: 0.7337 (mt) REVERT: C 537 ASP cc_start: 0.7104 (p0) cc_final: 0.6791 (p0) outliers start: 27 outliers final: 20 residues processed: 225 average time/residue: 0.1207 time to fit residues: 42.7764 Evaluate side-chains 217 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 661 SER Chi-restraints excluded: chain 1 residue 692 SER Chi-restraints excluded: chain 1 residue 954 LEU Chi-restraints excluded: chain 1 residue 1079 CYS Chi-restraints excluded: chain 1 residue 1106 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 672 CYS Chi-restraints excluded: chain C residue 689 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 89 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 156 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 162 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 567 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 = 0.4238 r_free = 0.4238 target = 0.174436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.165094 restraints weight = 99159.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.166306 restraints weight = 101514.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.166481 restraints weight = 53468.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.166816 restraints weight = 45448.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.167118 restraints weight = 39512.849| |-----------------------------------------------------------------------------| r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4138 r_free = 0.4138 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4138 r_free = 0.4138 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| r_final: 0.4138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17877 Z= 0.193 Angle : 0.660 12.344 24296 Z= 0.332 Chirality : 0.045 0.375 2735 Planarity : 0.005 0.062 3165 Dihedral : 4.807 22.928 2419 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.86 % Allowed : 13.97 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.18), residues: 2221 helix: 1.24 (0.16), residues: 1013 sheet: -0.71 (0.31), residues: 276 loop : -0.38 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 82 TYR 0.018 0.002 TYR C 530 PHE 0.038 0.002 PHE B 375 TRP 0.015 0.002 TRP B 376 HIS 0.048 0.002 HIS B 418 Details of bonding type rmsd covalent geometry : bond 0.00441 (17873) covalent geometry : angle 0.64470 (24284) hydrogen bonds : bond 0.03846 ( 878) hydrogen bonds : angle 5.06441 ( 2508) metal coordination : bond 0.01305 ( 4) metal coordination : angle 6.44769 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 0.678 Fit side-chains REVERT: 1 988 MET cc_start: 0.5083 (ppp) cc_final: 0.4806 (tmm) REVERT: 1 1015 ILE cc_start: 0.5497 (mm) cc_final: 0.4965 (tt) REVERT: 1 1351 SER cc_start: 0.7723 (m) cc_final: 0.7280 (p) REVERT: 1 1438 MET cc_start: 0.5458 (mmt) cc_final: 0.4579 (mmm) REVERT: B 87 LEU cc_start: 0.7007 (mp) cc_final: 0.6642 (mp) REVERT: B 121 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7619 (tt) REVERT: B 128 TYR cc_start: 0.6166 (OUTLIER) cc_final: 0.4356 (m-80) REVERT: B 215 ARG cc_start: 0.5973 (mpt-90) cc_final: 0.5567 (mpt-90) REVERT: B 234 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.5886 (tt0) REVERT: B 415 TRP cc_start: 0.6543 (OUTLIER) cc_final: 0.5994 (m-10) REVERT: B 451 MET cc_start: 0.7312 (mmm) cc_final: 0.7054 (tpp) REVERT: C 272 ILE cc_start: 0.5943 (OUTLIER) cc_final: 0.5659 (mm) REVERT: C 392 SER cc_start: 0.5005 (m) cc_final: 0.4352 (p) outliers start: 33 outliers final: 23 residues processed: 225 average time/residue: 0.1206 time to fit residues: 42.5875 Evaluate side-chains 220 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 661 SER Chi-restraints excluded: chain 1 residue 692 SER Chi-restraints excluded: chain 1 residue 717 SER Chi-restraints excluded: chain 1 residue 954 LEU Chi-restraints excluded: chain 1 residue 1079 CYS Chi-restraints excluded: chain 1 residue 1106 VAL Chi-restraints excluded: chain 1 residue 1289 SER Chi-restraints excluded: chain 1 residue 1334 ILE Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 672 CYS Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 705 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 109 optimal weight: 8.9990 chunk 193 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 728 HIS 11388 GLN B 185 ASN B 418 HIS ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.173505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.162042 restraints weight = 99664.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.163755 restraints weight = 99610.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.164447 restraints weight = 32934.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.164720 restraints weight = 35907.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.164720 restraints weight = 23500.330| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4108 r_free = 0.4108 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4108 r_free = 0.4108 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| r_final: 0.4108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6229 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 17877 Z= 0.195 Angle : 0.669 13.218 24296 Z= 0.337 Chirality : 0.047 0.594 2735 Planarity : 0.005 0.063 3165 Dihedral : 4.918 22.517 2419 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.23 % Allowed : 14.29 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.18), residues: 2221 helix: 1.10 (0.16), residues: 1018 sheet: -0.79 (0.32), residues: 268 loop : -0.51 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 654 TYR 0.019 0.002 TYR 11391 PHE 0.046 0.002 PHE B 375 TRP 0.016 0.002 TRP B 376 HIS 0.015 0.002 HIS B 418 Details of bonding type rmsd covalent geometry : bond 0.00449 (17873) covalent geometry : angle 0.65311 (24284) hydrogen bonds : bond 0.03891 ( 878) hydrogen bonds : angle 5.12977 ( 2508) metal coordination : bond 0.01429 ( 4) metal coordination : angle 6.62515 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: 1 551 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6712 (pm20) REVERT: 1 733 ILE cc_start: 0.8379 (mt) cc_final: 0.8178 (mm) REVERT: 1 1015 ILE cc_start: 0.5538 (mm) cc_final: 0.4989 (tt) REVERT: 1 1276 ARG cc_start: 0.5807 (tpt170) cc_final: 0.5103 (tpp-160) REVERT: 1 1351 SER cc_start: 0.7808 (m) cc_final: 0.7378 (p) REVERT: 1 1438 MET cc_start: 0.5476 (mmt) cc_final: 0.4532 (mmp) REVERT: A 117 TYR cc_start: 0.6342 (m-80) cc_final: 0.6092 (m-80) REVERT: B 87 LEU cc_start: 0.7099 (mp) cc_final: 0.6752 (mp) REVERT: B 121 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7620 (tt) REVERT: B 128 TYR cc_start: 0.6137 (OUTLIER) cc_final: 0.4354 (m-80) REVERT: B 215 ARG cc_start: 0.6162 (mpt-90) cc_final: 0.5746 (mpt-90) REVERT: B 234 GLU cc_start: 0.6565 (OUTLIER) cc_final: 0.5986 (tt0) REVERT: B 415 TRP cc_start: 0.6593 (OUTLIER) cc_final: 0.6118 (m-10) REVERT: B 451 MET cc_start: 0.7448 (mmm) cc_final: 0.7218 (tpp) REVERT: C 481 GLN cc_start: 0.6091 (tp-100) cc_final: 0.5713 (tp40) REVERT: C 537 ASP cc_start: 0.7113 (p0) cc_final: 0.6851 (p0) REVERT: C 672 CYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7708 (p) outliers start: 39 outliers final: 27 residues processed: 228 average time/residue: 0.1129 time to fit residues: 41.1086 Evaluate side-chains 219 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 551 GLU Chi-restraints excluded: chain 1 residue 692 SER Chi-restraints excluded: chain 1 residue 717 SER Chi-restraints excluded: chain 1 residue 954 LEU Chi-restraints excluded: chain 1 residue 1079 CYS Chi-restraints excluded: chain 1 residue 1106 VAL Chi-restraints excluded: chain 1 residue 1168 ILE Chi-restraints excluded: chain 1 residue 1188 SER Chi-restraints excluded: chain 1 residue 1289 SER Chi-restraints excluded: chain 1 residue 1334 ILE Chi-restraints excluded: chain 1 residue 1338 ILE Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 298 TYR Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 606 HIS Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 672 CYS Chi-restraints excluded: chain C residue 689 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 117 optimal weight: 8.9990 chunk 142 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 175 optimal weight: 1.9990 chunk 116 optimal weight: 0.0040 chunk 62 optimal weight: 2.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11450 ASN B 185 ASN ** C 567 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 = 0.4240 r_free = 0.4240 target = 0.174310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.166935 restraints weight = 93314.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.165979 restraints weight = 88358.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.164641 restraints weight = 38467.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.164953 restraints weight = 32667.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.165365 restraints weight = 20240.824| |-----------------------------------------------------------------------------| r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4116 r_free = 0.4116 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4116 r_free = 0.4116 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| r_final: 0.4116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6217 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 17877 Z= 0.162 Angle : 0.634 12.215 24296 Z= 0.318 Chirality : 0.045 0.446 2735 Planarity : 0.005 0.064 3165 Dihedral : 4.798 22.437 2419 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.02 % Allowed : 14.67 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.18), residues: 2221 helix: 1.21 (0.16), residues: 1017 sheet: -0.86 (0.31), residues: 281 loop : -0.44 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 654 TYR 0.018 0.002 TYR B 62 PHE 0.037 0.002 PHE B 375 TRP 0.013 0.001 TRP B 376 HIS 0.034 0.002 HIS B 418 Details of bonding type rmsd covalent geometry : bond 0.00377 (17873) covalent geometry : angle 0.61974 (24284) hydrogen bonds : bond 0.03641 ( 878) hydrogen bonds : angle 5.04230 ( 2508) metal coordination : bond 0.00679 ( 4) metal coordination : angle 6.11261 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: 1 551 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6592 (pm20) REVERT: 1 1015 ILE cc_start: 0.5442 (mm) cc_final: 0.4986 (tt) REVERT: 1 1276 ARG cc_start: 0.5800 (tpt170) cc_final: 0.5090 (tpp-160) REVERT: 1 1351 SER cc_start: 0.7867 (m) cc_final: 0.7515 (p) REVERT: 1 1438 MET cc_start: 0.5331 (mmt) cc_final: 0.4409 (mmp) REVERT: A 231 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6669 (tm-30) REVERT: B 87 LEU cc_start: 0.7021 (mp) cc_final: 0.6687 (mp) REVERT: B 128 TYR cc_start: 0.6183 (OUTLIER) cc_final: 0.4275 (m-80) REVERT: B 215 ARG cc_start: 0.6103 (mpt-90) cc_final: 0.5748 (mpt-90) REVERT: B 234 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.5921 (tt0) REVERT: B 415 TRP cc_start: 0.6531 (OUTLIER) cc_final: 0.6081 (m-10) REVERT: C 481 GLN cc_start: 0.6019 (tp-100) cc_final: 0.5731 (tp40) REVERT: C 537 ASP cc_start: 0.7110 (p0) cc_final: 0.6853 (p0) outliers start: 35 outliers final: 25 residues processed: 223 average time/residue: 0.1111 time to fit residues: 38.8374 Evaluate side-chains 219 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 551 GLU Chi-restraints excluded: chain 1 residue 692 SER Chi-restraints excluded: chain 1 residue 717 SER Chi-restraints excluded: chain 1 residue 954 LEU Chi-restraints excluded: chain 1 residue 1079 CYS Chi-restraints excluded: chain 1 residue 1106 VAL Chi-restraints excluded: chain 1 residue 1168 ILE Chi-restraints excluded: chain 1 residue 1289 SER Chi-restraints excluded: chain 1 residue 1338 ILE Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 298 TYR Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain B residue 447 GLU Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 606 HIS Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 689 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 70 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 121 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 104 optimal weight: 20.0000 chunk 208 optimal weight: 4.9990 chunk 164 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11024 ASN B 185 ASN C 275 HIS ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.171941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.161712 restraints weight = 99233.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.163098 restraints weight = 102828.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.163401 restraints weight = 53551.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.163607 restraints weight = 46101.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.163868 restraints weight = 37728.393| |-----------------------------------------------------------------------------| r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4097 r_free = 0.4097 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4097 r_free = 0.4097 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| r_final: 0.4097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6264 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 17877 Z= 0.238 Angle : 0.735 14.875 24296 Z= 0.369 Chirality : 0.048 0.474 2735 Planarity : 0.005 0.066 3165 Dihedral : 5.238 27.001 2419 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.13 % Allowed : 14.72 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.18), residues: 2221 helix: 0.85 (0.16), residues: 1009 sheet: -0.94 (0.32), residues: 263 loop : -0.64 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 654 TYR 0.024 0.002 TYR 11391 PHE 0.041 0.003 PHE B 375 TRP 0.019 0.002 TRP B 376 HIS 0.008 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00552 (17873) covalent geometry : angle 0.71741 (24284) hydrogen bonds : bond 0.04240 ( 878) hydrogen bonds : angle 5.37116 ( 2508) metal coordination : bond 0.01264 ( 4) metal coordination : angle 7.29839 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 197 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: 1 522 PRO cc_start: 0.6087 (Cg_endo) cc_final: 0.5792 (Cg_exo) REVERT: 1 551 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6573 (pm20) REVERT: 1 1351 SER cc_start: 0.7933 (m) cc_final: 0.7570 (p) REVERT: 1 1438 MET cc_start: 0.5383 (mmt) cc_final: 0.4483 (mmp) REVERT: A 231 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6858 (tm-30) REVERT: B 121 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7707 (tt) REVERT: B 128 TYR cc_start: 0.6331 (OUTLIER) cc_final: 0.4442 (m-80) REVERT: B 234 GLU cc_start: 0.6531 (OUTLIER) cc_final: 0.5935 (tt0) REVERT: B 415 TRP cc_start: 0.6658 (OUTLIER) cc_final: 0.6346 (m-10) REVERT: C 481 GLN cc_start: 0.6264 (tp-100) cc_final: 0.5946 (tp40) outliers start: 37 outliers final: 27 residues processed: 226 average time/residue: 0.1149 time to fit residues: 40.6214 Evaluate side-chains 220 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 551 GLU Chi-restraints excluded: chain 1 residue 692 SER Chi-restraints excluded: chain 1 residue 717 SER Chi-restraints excluded: chain 1 residue 954 LEU Chi-restraints excluded: chain 1 residue 1079 CYS Chi-restraints excluded: chain 1 residue 1086 SER Chi-restraints excluded: chain 1 residue 1106 VAL Chi-restraints excluded: chain 1 residue 1168 ILE Chi-restraints excluded: chain 1 residue 1289 SER Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 298 TYR Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 470 TYR Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 606 HIS Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 689 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 171 optimal weight: 0.9990 chunk 210 optimal weight: 0.7980 chunk 196 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 177 optimal weight: 0.0270 chunk 50 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 190 optimal weight: 0.0870 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.177012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.164934 restraints weight = 107457.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.166885 restraints weight = 98693.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.167376 restraints weight = 37505.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.167799 restraints weight = 39914.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.167799 restraints weight = 25967.174| |-----------------------------------------------------------------------------| r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4145 r_free = 0.4145 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4145 r_free = 0.4145 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| r_final: 0.4145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6129 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 17877 Z= 0.118 Angle : 0.580 10.630 24296 Z= 0.292 Chirality : 0.043 0.344 2735 Planarity : 0.005 0.061 3165 Dihedral : 4.583 25.229 2419 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.96 % Allowed : 15.78 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.18), residues: 2221 helix: 1.40 (0.16), residues: 1012 sheet: -0.84 (0.31), residues: 280 loop : -0.32 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 654 TYR 0.022 0.001 TYR B 62 PHE 0.027 0.002 PHE B 375 TRP 0.014 0.001 TRP B 376 HIS 0.008 0.001 HIS B 418 Details of bonding type rmsd covalent geometry : bond 0.00260 (17873) covalent geometry : angle 0.56989 (24284) hydrogen bonds : bond 0.03241 ( 878) hydrogen bonds : angle 4.83066 ( 2508) metal coordination : bond 0.00618 ( 4) metal coordination : angle 4.81225 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 213 time to evaluate : 0.462 Fit side-chains REVERT: 1 533 MET cc_start: 0.8531 (pmm) cc_final: 0.8324 (pmm) REVERT: 1 551 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6412 (pm20) REVERT: 1 685 PHE cc_start: 0.6852 (t80) cc_final: 0.6617 (t80) REVERT: 1 1276 ARG cc_start: 0.5587 (tpt170) cc_final: 0.4840 (tpp-160) REVERT: 1 1351 SER cc_start: 0.7972 (m) cc_final: 0.7574 (p) REVERT: 1 1438 MET cc_start: 0.5329 (mmt) cc_final: 0.4483 (mmt) REVERT: A 378 GLN cc_start: 0.5677 (tm-30) cc_final: 0.5393 (tm-30) REVERT: B 128 TYR cc_start: 0.5994 (OUTLIER) cc_final: 0.4052 (m-80) REVERT: B 415 TRP cc_start: 0.6328 (OUTLIER) cc_final: 0.5772 (m-10) REVERT: C 481 GLN cc_start: 0.6103 (tp-100) cc_final: 0.5708 (tp40) outliers start: 15 outliers final: 8 residues processed: 224 average time/residue: 0.1176 time to fit residues: 40.7425 Evaluate side-chains 209 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 198 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 551 GLU Chi-restraints excluded: chain 1 residue 692 SER Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 689 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 168 optimal weight: 4.9990 chunk 179 optimal weight: 0.0980 chunk 78 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 191 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11024 ASN A 233 ASN B 185 ASN ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.173530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.162836 restraints weight = 102994.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.164306 restraints weight = 109013.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.164615 restraints weight = 58367.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.164908 restraints weight = 48718.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.165490 restraints weight = 37050.089| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4114 r_free = 0.4114 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4114 r_free = 0.4114 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| r_final: 0.4114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6223 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 17877 Z= 0.195 Angle : 0.681 12.177 24296 Z= 0.341 Chirality : 0.046 0.362 2735 Planarity : 0.005 0.064 3165 Dihedral : 4.917 26.850 2419 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.38 % Allowed : 15.73 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.18), residues: 2221 helix: 1.13 (0.16), residues: 1016 sheet: -1.01 (0.31), residues: 280 loop : -0.47 (0.21), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 654 TYR 0.019 0.002 TYR 11391 PHE 0.028 0.002 PHE C 403 TRP 0.018 0.002 TRP B 376 HIS 0.010 0.001 HIS B 418 Details of bonding type rmsd covalent geometry : bond 0.00454 (17873) covalent geometry : angle 0.66660 (24284) hydrogen bonds : bond 0.03816 ( 878) hydrogen bonds : angle 5.13805 ( 2508) metal coordination : bond 0.01212 ( 4) metal coordination : angle 6.37025 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2310.67 seconds wall clock time: 41 minutes 6.73 seconds (2466.73 seconds total)