Starting phenix.real_space_refine on Mon Jul 28 15:42:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p92_13258/07_2025/7p92_13258.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p92_13258/07_2025/7p92_13258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p92_13258/07_2025/7p92_13258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p92_13258/07_2025/7p92_13258.map" model { file = "/net/cci-nas-00/data/ceres_data/7p92_13258/07_2025/7p92_13258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p92_13258/07_2025/7p92_13258.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 7 Type Number sf(0) Gaussians Fe 34 7.16 5 Zn 1 6.06 5 P 1 5.49 5 S 114 5.16 5 C 6472 2.51 5 N 1730 2.21 5 O 2084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10436 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4376 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 554, 4365 Classifications: {'peptide': 554} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 532} Conformer: "B" Number of residues, atoms: 554, 4365 Classifications: {'peptide': 554} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 532} bond proxies already assigned to first conformer: 4425 Chain: "B" Number of atoms: 4585 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 612, 4577 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 580} Chain breaks: 1 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 62 Conformer: "B" Number of residues, atoms: 612, 4577 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 580} Chain breaks: 1 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 62 bond proxies already assigned to first conformer: 4653 Chain: "C" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1218 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 148} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Unusual residues: {'FES': 1, 'SF4': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 60 Unusual residues: {' ZN': 1, 'FES': 1, 'FMN': 1, 'SF4': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 132 Classifications: {'water': 132} Link IDs: {None: 131} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2758 SG CYS A 350 76.094 68.056 75.135 1.00 7.59 S ATOM 2316 SG CYS A 295 70.402 70.632 76.629 1.00 15.55 S ATOM 3806 SG CYS A 486 74.752 69.368 81.232 1.00 15.55 S ATOM 3776 SG CYS A 482 71.757 64.495 77.601 1.00 8.52 S ATOM 1222 SG CYS A 153 65.862 60.075 68.302 1.00 15.55 S ATOM 1515 SG CYS A 192 71.900 58.207 69.319 1.00 15.55 S ATOM 1496 SG CYS A 189 69.750 62.975 72.476 1.00 15.55 S ATOM 1475 SG CYS A 186 70.872 63.816 66.223 1.00 15.55 S ATOM 1545 SG CYS A 196 74.895 51.015 69.541 1.00 15.55 S ATOM 1191 SG CYS A 149 69.171 52.733 67.459 1.00 15.55 S ATOM 1173 SG CYS A 146 70.040 47.258 70.514 1.00 15.55 S ATOM 1151 SG CYS A 143 71.821 47.899 64.339 1.00 15.55 S ATOM 825 SG CYS A 105 80.344 44.271 71.706 1.00 15.55 S ATOM 762 SG CYS A 96 85.941 42.905 68.371 1.00 15.55 S ATOM 782 SG CYS A 99 83.223 48.709 68.392 1.00 15.55 S ATOM 377 SG CYS A 48 65.096 33.681 75.979 1.00 7.95 S ATOM 464 SG CYS A 60 62.624 36.306 75.858 1.00 9.17 S ATOM 271 SG CYS A 34 66.250 39.621 73.336 1.00 7.94 S ATOM 352 SG CYS A 45 68.443 36.750 72.900 1.00 15.55 S ATOM 8774 SG CYS B 588 87.917 28.834 25.382 1.00 47.57 S ATOM 8877 SG CYS B 608 84.009 25.515 29.155 1.00 51.02 S ATOM 8908 SG CYS B 614 81.727 27.263 23.766 1.00 52.63 S ATOM 8893 SG CYS B 611 83.209 31.619 28.640 1.00 52.63 S ATOM 8738 SG CYS B 581 84.135 29.198 11.632 1.00 57.57 S ATOM 8753 SG CYS B 584 86.565 26.230 16.586 1.00 54.61 S ATOM 8723 SG CYS B 578 81.923 23.294 13.234 1.00 48.09 S ATOM 8929 SG CYS B 618 80.658 28.677 16.893 1.00 51.77 S ATOM 8030 SG CYS B 485 59.775 40.451 61.575 1.00 8.10 S ATOM 8069 SG CYS B 491 62.595 34.858 59.436 1.00 9.22 S ATOM 8388 SG CYS B 531 56.796 35.119 62.533 1.00 15.46 S ATOM 8049 SG CYS B 488 63.213 35.635 64.600 1.00 15.55 S ATOM 4632 SG CYS B 31 35.161 32.924 35.511 1.00 33.27 S ATOM 4660 SG CYS B 36 37.749 32.402 33.129 1.00 30.10 S ATOM 4895 SG CYS B 78 37.178 29.852 39.546 1.00 33.00 S ATOM 4922 SG CYS B 82 40.030 29.454 37.554 1.00 32.46 S ATOM 7886 SG CYS B 468 67.438 20.304 41.306 1.00 22.67 S ATOM 8612 SG CYS B 560 69.489 19.038 38.306 1.00 27.99 S ATOM 8643 SG CYS B 565 69.963 22.604 39.651 1.00 31.40 S ATOM 9876 SG CYS C 119 48.824 32.667 41.485 1.00 19.72 S ATOM 9899 SG CYS C 123 48.616 29.924 39.489 1.00 21.32 S ATOM 9582 SG CYS C 78 53.316 34.474 39.243 1.00 19.40 S ATOM 9612 SG CYS C 83 53.317 32.227 36.513 1.00 17.79 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 130 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 130 " occ=0.50 Time building chain proxies: 13.26, per 1000 atoms: 1.27 Number of scatterers: 10436 At special positions: 0 Unit cell: (112.888, 106.296, 110.416, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 34 26.01 S 114 16.00 P 1 15.00 O 2084 8.00 N 1730 7.00 C 6472 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: 3.05 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 705 " pdb="FE1 FES A 705 " - pdb=" SG CYS A 48 " pdb="FE2 FES A 705 " - pdb=" SG CYS A 34 " pdb="FE2 FES A 705 " - pdb=" SG CYS A 45 " pdb="FE1 FES A 705 " - pdb=" SG CYS A 60 " pdb=" FES B 704 " pdb="FE2 FES B 704 " - pdb=" SG CYS B 82 " pdb="FE1 FES B 704 " - pdb=" SG CYS B 31 " pdb="FE1 FES B 704 " - pdb=" SG CYS B 36 " pdb="FE2 FES B 704 " - pdb=" SG CYS B 78 " pdb=" FES C 201 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 78 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 83 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 123 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 119 " pdb=" SF4 A 701 " pdb="FE4 SF4 A 701 " - pdb=" SG CYS A 482 " pdb="FE1 SF4 A 701 " - pdb=" SG CYS A 350 " pdb="FE2 SF4 A 701 " - pdb=" SG CYS A 295 " pdb="FE3 SF4 A 701 " - pdb=" SG CYS A 486 " pdb=" SF4 A 702 " pdb="FE4 SF4 A 702 " - pdb=" SG CYS A 186 " pdb="FE2 SF4 A 702 " - pdb=" SG CYS A 192 " pdb="FE1 SF4 A 702 " - pdb=" SG CYS A 153 " pdb="FE3 SF4 A 702 " - pdb=" SG CYS A 189 " pdb=" SF4 A 703 " pdb="FE3 SF4 A 703 " - pdb=" SG CYS A 146 " pdb="FE2 SF4 A 703 " - pdb=" SG CYS A 149 " pdb="FE4 SF4 A 703 " - pdb=" SG CYS A 143 " pdb="FE1 SF4 A 703 " - pdb=" SG CYS A 196 " pdb=" SF4 A 704 " pdb="FE2 SF4 A 704 " - pdb=" NE2 HIS A 92 " pdb="FE4 SF4 A 704 " - pdb=" SG CYS A 99 " pdb="FE3 SF4 A 704 " - pdb=" SG CYS A 96 " pdb="FE1 SF4 A 704 " - pdb=" SG CYS A 105 " pdb=" SF4 B 700 " pdb="FE1 SF4 B 700 " - pdb=" SG CYS B 588 " pdb="FE4 SF4 B 700 " - pdb=" SG CYS B 611 " pdb="FE2 SF4 B 700 " - pdb=" SG CYS B 608 " pdb="FE3 SF4 B 700 " - pdb=" SG CYS B 614 " pdb=" SF4 B 701 " pdb="FE1 SF4 B 701 " - pdb=" SG CYS B 581 " pdb="FE4 SF4 B 701 " - pdb=" SG CYS B 618 " pdb="FE2 SF4 B 701 " - pdb=" SG CYS B 584 " pdb="FE3 SF4 B 701 " - pdb=" SG CYS B 578 " pdb=" SF4 B 702 " pdb="FE1 SF4 B 702 " - pdb=" SG CYS B 485 " pdb="FE3 SF4 B 702 " - pdb=" SG CYS B 531 " pdb="FE4 SF4 B 702 " - pdb=" SG CYS B 488 " pdb="FE2 SF4 B 702 " - pdb=" SG CYS B 491 " Number of angles added : 99 Zn2+ tetrahedral coordination pdb=" ZN B 705 " pdb="ZN ZN B 705 " - pdb=" NE2 HIS B 555 " pdb="ZN ZN B 705 " - pdb=" SG CYS B 565 " pdb="ZN ZN B 705 " - pdb=" SG CYS B 468 " pdb="ZN ZN B 705 " - pdb=" SG CYS B 560 " Number of angles added : 3 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2418 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 11 sheets defined 51.2% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 18 through 26 Processing helix chain 'A' and resid 74 through 91 removed outlier: 3.940A pdb=" N THR A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 105 through 115 Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.642A pdb=" N GLU A 170 " --> pdb=" O ARG A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 179 Processing helix chain 'A' and resid 180 through 184 Processing helix chain 'A' and resid 190 through 196 Processing helix chain 'A' and resid 206 through 216 removed outlier: 3.500A pdb=" N LEU A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 263 through 285 Processing helix chain 'A' and resid 295 through 306 Processing helix chain 'A' and resid 307 through 310 removed outlier: 3.566A pdb=" N LEU A 310 " --> pdb=" O PRO A 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 307 through 310' Processing helix chain 'A' and resid 318 through 330 Processing helix chain 'A' and resid 330 through 335 Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 351 through 358 removed outlier: 3.661A pdb=" N PHE A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 358 " --> pdb=" O LYS A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.554A pdb=" N VAL A 389 " --> pdb=" O ILE A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 408 through 410 No H-bonds generated for 'chain 'A' and resid 408 through 410' Processing helix chain 'A' and resid 412 through 426 Processing helix chain 'A' and resid 462 through 470 removed outlier: 4.718A pdb=" N LYS A 466 " --> pdb=" O GLY A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 489 removed outlier: 4.179A pdb=" N VAL A 487 " --> pdb=" O TYR A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 514 removed outlier: 3.598A pdb=" N ILE A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 522 Processing helix chain 'A' and resid 523 through 534 Processing helix chain 'A' and resid 536 through 545 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 40 through 56 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.710A pdb=" N GLY B 85 " --> pdb=" O CYS B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 113 Processing helix chain 'B' and resid 119 through 123 Processing helix chain 'B' and resid 139 through 145 Processing helix chain 'B' and resid 160 through 167 removed outlier: 3.793A pdb=" N TYR B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 179 Processing helix chain 'B' and resid 181 through 192 Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'B' and resid 233 through 242 Processing helix chain 'B' and resid 242 through 258 removed outlier: 3.798A pdb=" N VAL B 246 " --> pdb=" O ASP B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 287 Processing helix chain 'B' and resid 311 through 315 Processing helix chain 'B' and resid 316 through 325 Processing helix chain 'B' and resid 342 through 346 Processing helix chain 'B' and resid 353 through 365 removed outlier: 3.604A pdb=" N ILE B 359 " --> pdb=" O THR B 355 " (cutoff:3.500A) Proline residue: B 360 - end of helix Processing helix chain 'B' and resid 366 through 373 removed outlier: 4.074A pdb=" N ARG B 373 " --> pdb=" O ASN B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 Processing helix chain 'B' and resid 427 through 431 removed outlier: 3.942A pdb=" N SER B 430 " --> pdb=" O GLY B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 450 removed outlier: 3.547A pdb=" N LYS B 449 " --> pdb=" O TYR B 445 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS B 450 " --> pdb=" O ASP B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 484 Processing helix chain 'B' and resid 488 through 507 removed outlier: 4.105A pdb=" N MET B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 529 Processing helix chain 'B' and resid 531 through 536 Processing helix chain 'B' and resid 538 through 558 removed outlier: 7.323A pdb=" N GLU B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLU B 551 " --> pdb=" O LEU B 547 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR B 552 " --> pdb=" O PHE B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 578 removed outlier: 3.503A pdb=" N CYS B 578 " --> pdb=" O PRO B 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 16 Processing helix chain 'C' and resid 18 through 20 No H-bonds generated for 'chain 'C' and resid 18 through 20' Processing helix chain 'C' and resid 21 through 34 Processing helix chain 'C' and resid 37 through 49 Processing helix chain 'C' and resid 51 through 62 removed outlier: 3.610A pdb=" N ILE C 55 " --> pdb=" O PRO C 51 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 87 Processing helix chain 'C' and resid 87 through 100 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 140 through 157 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 11 removed outlier: 9.013A pdb=" N VAL A 70 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TYR A 4 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 165 Processing sheet with id=AA4, first strand: chain 'A' and resid 259 through 262 removed outlier: 6.769A pdb=" N VAL A 220 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N PHE A 261 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLY A 222 " --> pdb=" O PHE A 261 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A 219 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL A 345 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE A 221 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N PHE A 347 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N MET A 223 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N ILE A 368 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU A 344 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LEU A 370 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N SER A 346 " --> pdb=" O LEU A 370 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 291 removed outlier: 6.402A pdb=" N GLN A 290 " --> pdb=" O ILE A 477 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL A 479 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N THR A 451 " --> pdb=" O LEU A 447 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU A 447 " --> pdb=" O THR A 451 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS A 430 " --> pdb=" O THR A 446 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 72 through 76 Processing sheet with id=AA7, first strand: chain 'B' and resid 124 through 125 removed outlier: 4.068A pdb=" N LEU B 124 " --> pdb=" O VAL B 133 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 302 through 308 Processing sheet with id=AA9, first strand: chain 'B' and resid 374 through 375 Processing sheet with id=AB1, first strand: chain 'B' and resid 394 through 399 removed outlier: 7.543A pdb=" N ILE B 460 " --> pdb=" O MET B 383 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N SER B 385 " --> pdb=" O ILE B 460 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL B 462 " --> pdb=" O SER B 385 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ALA B 387 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N THR B 464 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 112 through 117 481 hydrogen bonds defined for protein. 1345 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: 3.49 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 4102 1.40 - 1.62: 6180 1.62 - 1.84: 110 1.84 - 2.06: 0 2.06 - 2.28: 96 Bond restraints: 10488 Sorted by residual: bond pdb=" C4 FMN B 703 " pdb=" C4A FMN B 703 " ideal model delta sigma weight residual 1.485 1.383 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" C ARG C 149 " pdb=" O ARG C 149 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.15e-02 7.56e+03 2.36e+01 bond pdb=" C4A FMN B 703 " pdb=" N5 FMN B 703 " ideal model delta sigma weight residual 1.300 1.374 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" O5' FMN B 703 " pdb=" P FMN B 703 " ideal model delta sigma weight residual 1.676 1.610 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C10 FMN B 703 " pdb=" N1 FMN B 703 " ideal model delta sigma weight residual 1.317 1.378 -0.061 2.00e-02 2.50e+03 9.20e+00 ... (remaining 10483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 13788 1.45 - 2.89: 325 2.89 - 4.34: 74 4.34 - 5.78: 8 5.78 - 7.23: 6 Bond angle restraints: 14201 Sorted by residual: angle pdb=" N ARG C 149 " pdb=" CA ARG C 149 " pdb=" C ARG C 149 " ideal model delta sigma weight residual 110.97 107.52 3.45 1.09e+00 8.42e-01 1.00e+01 angle pdb=" CA ARG C 149 " pdb=" C ARG C 149 " pdb=" O ARG C 149 " ideal model delta sigma weight residual 121.00 117.98 3.02 1.05e+00 9.07e-01 8.30e+00 angle pdb=" N ARG C 34 " pdb=" CA ARG C 34 " pdb=" CB ARG C 34 " ideal model delta sigma weight residual 110.49 115.25 -4.76 1.69e+00 3.50e-01 7.93e+00 angle pdb=" CA ARG C 149 " pdb=" C ARG C 149 " pdb=" N LYS C 150 " ideal model delta sigma weight residual 116.92 120.07 -3.15 1.16e+00 7.43e-01 7.37e+00 angle pdb=" N GLN B 10 " pdb=" CA GLN B 10 " pdb=" CB GLN B 10 " ideal model delta sigma weight residual 110.12 113.88 -3.76 1.47e+00 4.63e-01 6.56e+00 ... (remaining 14196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 5765 17.80 - 35.59: 477 35.59 - 53.39: 84 53.39 - 71.18: 19 71.18 - 88.98: 9 Dihedral angle restraints: 6354 sinusoidal: 2567 harmonic: 3787 Sorted by residual: dihedral pdb=" N ARG C 34 " pdb=" C ARG C 34 " pdb=" CA ARG C 34 " pdb=" CB ARG C 34 " ideal model delta harmonic sigma weight residual 122.80 133.11 -10.31 0 2.50e+00 1.60e-01 1.70e+01 dihedral pdb=" C ARG C 34 " pdb=" N ARG C 34 " pdb=" CA ARG C 34 " pdb=" CB ARG C 34 " ideal model delta harmonic sigma weight residual -122.60 -131.76 9.16 0 2.50e+00 1.60e-01 1.34e+01 dihedral pdb=" CA ASP A 497 " pdb=" CB ASP A 497 " pdb=" CG ASP A 497 " pdb=" OD1 ASP A 497 " ideal model delta sinusoidal sigma weight residual -30.00 -87.93 57.93 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 6351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1388 0.063 - 0.126: 207 0.126 - 0.189: 5 0.189 - 0.251: 0 0.251 - 0.314: 1 Chirality restraints: 1601 Sorted by residual: chirality pdb=" CA ARG C 34 " pdb=" N ARG C 34 " pdb=" C ARG C 34 " pdb=" CB ARG C 34 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA ILE B 90 " pdb=" N ILE B 90 " pdb=" C ILE B 90 " pdb=" CB ILE B 90 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA GLU A 374 " pdb=" N GLU A 374 " pdb=" C GLU A 374 " pdb=" CB GLU A 374 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 1598 not shown) Planarity restraints: 1811 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 334 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.90e+00 pdb=" N PRO B 335 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 335 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 335 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 101 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.71e+00 pdb=" N PRO B 102 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 102 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 102 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 491 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C CYS B 491 " -0.027 2.00e-02 2.50e+03 pdb=" O CYS B 491 " 0.010 2.00e-02 2.50e+03 pdb=" N ARG B 492 " 0.009 2.00e-02 2.50e+03 ... (remaining 1808 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 101 2.57 - 3.15: 8640 3.15 - 3.73: 16847 3.73 - 4.32: 24259 4.32 - 4.90: 39429 Nonbonded interactions: 89276 Sorted by model distance: nonbonded pdb=" O HOH A 885 " pdb=" O HOH A 910 " model vdw 1.985 3.040 nonbonded pdb=" O HOH A 907 " pdb=" O HOH A 917 " model vdw 1.995 3.040 nonbonded pdb=" O PHE A 169 " pdb=" O HOH A 801 " model vdw 1.999 3.040 nonbonded pdb=" O PHE B 475 " pdb=" O HOH B 801 " model vdw 2.005 3.040 nonbonded pdb=" O HOH A 889 " pdb=" O HOH A 890 " model vdw 2.020 3.040 ... (remaining 89271 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 41.040 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 10532 Z= 0.184 Angle : 0.805 21.960 14303 Z= 0.318 Chirality : 0.043 0.314 1601 Planarity : 0.004 0.046 1811 Dihedral : 13.787 88.977 3936 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.18 % Allowed : 0.18 % Favored : 99.63 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.23), residues: 1318 helix: 1.30 (0.22), residues: 575 sheet: -0.91 (0.43), residues: 124 loop : -0.67 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 344 HIS 0.004 0.001 HIS A 276 PHE 0.011 0.001 PHE B 123 TYR 0.019 0.001 TYR A 459 ARG 0.004 0.001 ARG A 120 Details of bonding type rmsd hydrogen bonds : bond 0.15613 ( 481) hydrogen bonds : angle 6.42092 ( 1345) metal coordination : bond 0.01415 ( 44) metal coordination : angle 6.54393 ( 102) covalent geometry : bond 0.00380 (10488) covalent geometry : angle 0.58762 (14201) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: A 432 ASP cc_start: 0.6630 (m-30) cc_final: 0.6305 (m-30) REVERT: A 435 SER cc_start: 0.8023 (m) cc_final: 0.7802 (p) REVERT: A 506 LYS cc_start: 0.7970 (ttpp) cc_final: 0.7758 (ttpp) REVERT: B 276 MET cc_start: 0.7644 (mmp) cc_final: 0.7427 (mmp) REVERT: C 105 ASN cc_start: 0.7653 (m-40) cc_final: 0.7342 (m-40) REVERT: C 111 MET cc_start: 0.6345 (tpp) cc_final: 0.6143 (tpp) outliers start: 1 outliers final: 0 residues processed: 196 average time/residue: 1.6265 time to fit residues: 337.7040 Evaluate side-chains 167 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 55 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 102 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN A 55 GLN B 4 ASN C 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.168831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.140534 restraints weight = 16791.502| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.24 r_work: 0.2920 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10532 Z= 0.152 Angle : 0.833 22.433 14303 Z= 0.306 Chirality : 0.045 0.157 1601 Planarity : 0.005 0.048 1811 Dihedral : 4.187 20.350 1457 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.66 % Allowed : 8.84 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.23), residues: 1318 helix: 1.24 (0.21), residues: 590 sheet: -0.92 (0.42), residues: 136 loop : -0.55 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 208 HIS 0.004 0.001 HIS A 545 PHE 0.014 0.002 PHE B 301 TYR 0.014 0.001 TYR A 459 ARG 0.005 0.001 ARG B 121 Details of bonding type rmsd hydrogen bonds : bond 0.04851 ( 481) hydrogen bonds : angle 5.31400 ( 1345) metal coordination : bond 0.01307 ( 44) metal coordination : angle 6.94133 ( 102) covalent geometry : bond 0.00350 (10488) covalent geometry : angle 0.59372 (14201) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 1.256 Fit side-chains REVERT: A 333 ARG cc_start: 0.6985 (ttp-110) cc_final: 0.6638 (ttp80) REVERT: A 432 ASP cc_start: 0.7203 (m-30) cc_final: 0.6882 (m-30) REVERT: A 435 SER cc_start: 0.8132 (m) cc_final: 0.7857 (p) REVERT: A 480 MET cc_start: 0.8715 (mmm) cc_final: 0.8449 (mmt) REVERT: A 506 LYS cc_start: 0.8305 (ttpp) cc_final: 0.7969 (ttpp) REVERT: B 206 LEU cc_start: 0.7773 (mm) cc_final: 0.7569 (mp) REVERT: B 276 MET cc_start: 0.8273 (mmp) cc_final: 0.8003 (mmp) REVERT: B 376 GLU cc_start: 0.6545 (mm-30) cc_final: 0.6114 (tm-30) REVERT: C 105 ASN cc_start: 0.7683 (m-40) cc_final: 0.7163 (m-40) REVERT: C 111 MET cc_start: 0.6952 (tpp) cc_final: 0.6481 (tpp) outliers start: 17 outliers final: 6 residues processed: 178 average time/residue: 1.4783 time to fit residues: 280.8741 Evaluate side-chains 166 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 386 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 111 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 34 optimal weight: 0.4980 chunk 52 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN B 4 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.167524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.139393 restraints weight = 20326.139| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.44 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 10532 Z= 0.193 Angle : 0.886 23.033 14303 Z= 0.328 Chirality : 0.046 0.186 1601 Planarity : 0.005 0.061 1811 Dihedral : 4.486 21.723 1457 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.30 % Allowed : 10.59 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.23), residues: 1318 helix: 1.17 (0.21), residues: 584 sheet: -1.01 (0.42), residues: 136 loop : -0.66 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 344 HIS 0.005 0.002 HIS B 520 PHE 0.017 0.002 PHE B 301 TYR 0.014 0.002 TYR C 73 ARG 0.007 0.001 ARG C 149 Details of bonding type rmsd hydrogen bonds : bond 0.05080 ( 481) hydrogen bonds : angle 5.30209 ( 1345) metal coordination : bond 0.01593 ( 44) metal coordination : angle 7.33783 ( 102) covalent geometry : bond 0.00455 (10488) covalent geometry : angle 0.63548 (14201) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 1.479 Fit side-chains REVERT: A 274 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7355 (tp30) REVERT: A 340 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.6341 (mp0) REVERT: A 432 ASP cc_start: 0.6783 (m-30) cc_final: 0.6374 (m-30) REVERT: A 506 LYS cc_start: 0.8034 (ttpp) cc_final: 0.7800 (ttpp) REVERT: B 48 PHE cc_start: 0.7074 (OUTLIER) cc_final: 0.5926 (t80) REVERT: B 276 MET cc_start: 0.7662 (mmp) cc_final: 0.7459 (mmp) REVERT: C 72 LYS cc_start: 0.6344 (OUTLIER) cc_final: 0.5876 (ttmt) REVERT: C 111 MET cc_start: 0.6588 (tpp) cc_final: 0.6361 (tpp) REVERT: C 134 GLU cc_start: 0.5753 (tp30) cc_final: 0.5377 (mm-30) outliers start: 24 outliers final: 10 residues processed: 171 average time/residue: 2.1698 time to fit residues: 394.4254 Evaluate side-chains 165 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 155 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 13 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 11 optimal weight: 0.1980 chunk 83 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN B 4 ASN B 260 GLN C 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.168549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.139176 restraints weight = 22015.172| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.78 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10532 Z= 0.142 Angle : 0.813 22.060 14303 Z= 0.294 Chirality : 0.044 0.160 1601 Planarity : 0.005 0.049 1811 Dihedral : 4.307 20.858 1457 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.03 % Allowed : 12.62 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.23), residues: 1318 helix: 1.27 (0.21), residues: 585 sheet: -0.82 (0.43), residues: 129 loop : -0.59 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 208 HIS 0.003 0.001 HIS B 520 PHE 0.012 0.002 PHE A 467 TYR 0.013 0.001 TYR C 73 ARG 0.006 0.001 ARG C 149 Details of bonding type rmsd hydrogen bonds : bond 0.04357 ( 481) hydrogen bonds : angle 5.11863 ( 1345) metal coordination : bond 0.01242 ( 44) metal coordination : angle 6.83355 ( 102) covalent geometry : bond 0.00329 (10488) covalent geometry : angle 0.57535 (14201) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 1.205 Fit side-chains REVERT: A 274 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7338 (tp30) REVERT: A 374 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6968 (mt-10) REVERT: A 432 ASP cc_start: 0.6719 (m-30) cc_final: 0.6284 (m-30) REVERT: A 506 LYS cc_start: 0.8079 (ttpp) cc_final: 0.7806 (ttpp) REVERT: B 48 PHE cc_start: 0.7020 (OUTLIER) cc_final: 0.5921 (t80) outliers start: 21 outliers final: 7 residues processed: 171 average time/residue: 1.4739 time to fit residues: 268.6114 Evaluate side-chains 165 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain C residue 155 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 76 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 112 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN B 4 ASN B 260 GLN C 116 GLN ** C 132 ASN ** 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 = 0.3786 r_free = 0.3786 target = 0.166869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.132256 restraints weight = 22723.501| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 4.19 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3368 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3368 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 10532 Z= 0.224 Angle : 0.929 25.596 14303 Z= 0.344 Chirality : 0.047 0.187 1601 Planarity : 0.006 0.063 1811 Dihedral : 4.702 22.521 1457 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.49 % Allowed : 13.35 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.23), residues: 1318 helix: 0.98 (0.21), residues: 585 sheet: -0.86 (0.43), residues: 130 loop : -0.68 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 344 HIS 0.005 0.002 HIS B 520 PHE 0.015 0.002 PHE B 301 TYR 0.016 0.002 TYR C 73 ARG 0.007 0.001 ARG C 149 Details of bonding type rmsd hydrogen bonds : bond 0.05239 ( 481) hydrogen bonds : angle 5.30177 ( 1345) metal coordination : bond 0.01779 ( 44) metal coordination : angle 7.67172 ( 102) covalent geometry : bond 0.00533 (10488) covalent geometry : angle 0.66797 (14201) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 1.228 Fit side-chains REVERT: A 274 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7415 (tp30) REVERT: A 341 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7862 (tttp) REVERT: A 374 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7117 (mt-10) REVERT: A 432 ASP cc_start: 0.6813 (m-30) cc_final: 0.6359 (m-30) REVERT: A 506 LYS cc_start: 0.7855 (ttpp) cc_final: 0.7649 (ttpp) REVERT: B 48 PHE cc_start: 0.7218 (OUTLIER) cc_final: 0.5861 (t80) REVERT: B 207 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.6601 (tttt) REVERT: B 466 LYS cc_start: 0.7654 (mptt) cc_final: 0.7107 (pttt) REVERT: C 72 LYS cc_start: 0.6300 (OUTLIER) cc_final: 0.5970 (ttmt) REVERT: C 134 GLU cc_start: 0.5982 (tp30) cc_final: 0.5423 (mm-30) outliers start: 27 outliers final: 8 residues processed: 169 average time/residue: 1.5873 time to fit residues: 285.3823 Evaluate side-chains 162 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 207 LYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 155 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 49 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN B 4 ASN B 260 GLN C 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.168881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.140605 restraints weight = 17820.102| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.30 r_work: 0.2901 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10532 Z= 0.130 Angle : 0.803 22.454 14303 Z= 0.287 Chirality : 0.043 0.161 1601 Planarity : 0.005 0.051 1811 Dihedral : 4.318 20.520 1457 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.66 % Allowed : 14.18 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.23), residues: 1318 helix: 1.25 (0.21), residues: 586 sheet: -0.84 (0.44), residues: 129 loop : -0.59 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 208 HIS 0.003 0.001 HIS B 520 PHE 0.012 0.001 PHE A 394 TYR 0.013 0.001 TYR C 73 ARG 0.009 0.001 ARG C 149 Details of bonding type rmsd hydrogen bonds : bond 0.04159 ( 481) hydrogen bonds : angle 5.06195 ( 1345) metal coordination : bond 0.01157 ( 44) metal coordination : angle 6.77019 ( 102) covalent geometry : bond 0.00300 (10488) covalent geometry : angle 0.56523 (14201) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 1.129 Fit side-chains REVERT: A 274 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7791 (tp30) REVERT: A 432 ASP cc_start: 0.7142 (m-30) cc_final: 0.6727 (m-30) REVERT: A 480 MET cc_start: 0.8762 (mmm) cc_final: 0.8489 (mmt) REVERT: A 506 LYS cc_start: 0.8402 (ttpp) cc_final: 0.8044 (ttpp) REVERT: B 48 PHE cc_start: 0.7126 (OUTLIER) cc_final: 0.5923 (t80) REVERT: B 207 LYS cc_start: 0.7539 (OUTLIER) cc_final: 0.6571 (tttt) REVERT: B 466 LYS cc_start: 0.7846 (mptt) cc_final: 0.7141 (pttt) outliers start: 18 outliers final: 7 residues processed: 171 average time/residue: 1.4755 time to fit residues: 268.7694 Evaluate side-chains 161 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 207 LYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain C residue 155 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 87 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 125 optimal weight: 0.0060 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 62 optimal weight: 0.4980 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN B 4 ASN B 99 ASN B 260 GLN C 116 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.169748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.141568 restraints weight = 21564.871| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.53 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10532 Z= 0.115 Angle : 0.761 22.607 14303 Z= 0.274 Chirality : 0.042 0.154 1601 Planarity : 0.005 0.049 1811 Dihedral : 4.119 19.544 1457 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.66 % Allowed : 14.73 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.23), residues: 1318 helix: 1.38 (0.22), residues: 587 sheet: -0.75 (0.44), residues: 129 loop : -0.49 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 208 HIS 0.002 0.001 HIS B 520 PHE 0.011 0.001 PHE A 394 TYR 0.011 0.001 TYR C 73 ARG 0.011 0.001 ARG C 149 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 481) hydrogen bonds : angle 4.90667 ( 1345) metal coordination : bond 0.00997 ( 44) metal coordination : angle 6.36519 ( 102) covalent geometry : bond 0.00263 (10488) covalent geometry : angle 0.54068 (14201) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 1.360 Fit side-chains REVERT: A 274 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7280 (tp30) REVERT: A 381 MET cc_start: 0.7815 (ttp) cc_final: 0.7566 (ptp) REVERT: A 432 ASP cc_start: 0.6518 (m-30) cc_final: 0.6090 (m-30) REVERT: A 480 MET cc_start: 0.8167 (mmm) cc_final: 0.7840 (mmt) REVERT: A 506 LYS cc_start: 0.8114 (ttpp) cc_final: 0.7855 (ttpp) REVERT: B 48 PHE cc_start: 0.6946 (OUTLIER) cc_final: 0.6061 (t80) REVERT: B 207 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.6626 (tttt) REVERT: B 287 LEU cc_start: 0.6987 (mp) cc_final: 0.6593 (mt) REVERT: B 466 LYS cc_start: 0.7626 (mptt) cc_final: 0.7333 (pttt) REVERT: C 134 GLU cc_start: 0.5548 (tp30) cc_final: 0.5179 (mm-30) outliers start: 18 outliers final: 8 residues processed: 163 average time/residue: 2.0220 time to fit residues: 352.2031 Evaluate side-chains 159 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 207 LYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 155 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 80 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN B 99 ASN B 260 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.169778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.139967 restraints weight = 17854.936| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.51 r_work: 0.2881 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10532 Z= 0.116 Angle : 0.760 22.481 14303 Z= 0.272 Chirality : 0.042 0.155 1601 Planarity : 0.005 0.048 1811 Dihedral : 4.091 19.714 1457 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.57 % Allowed : 15.10 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.23), residues: 1318 helix: 1.43 (0.22), residues: 587 sheet: -0.88 (0.42), residues: 136 loop : -0.43 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 208 HIS 0.002 0.001 HIS B 520 PHE 0.011 0.001 PHE A 394 TYR 0.013 0.001 TYR C 73 ARG 0.012 0.000 ARG C 149 Details of bonding type rmsd hydrogen bonds : bond 0.03857 ( 481) hydrogen bonds : angle 4.86513 ( 1345) metal coordination : bond 0.00963 ( 44) metal coordination : angle 6.41394 ( 102) covalent geometry : bond 0.00264 (10488) covalent geometry : angle 0.53523 (14201) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 2.276 Fit side-chains REVERT: A 274 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7797 (tp30) REVERT: A 374 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7656 (mt-10) REVERT: A 381 MET cc_start: 0.8667 (ttp) cc_final: 0.8380 (ptp) REVERT: A 432 ASP cc_start: 0.7029 (m-30) cc_final: 0.6641 (m-30) REVERT: A 480 MET cc_start: 0.8718 (mmm) cc_final: 0.8415 (mmt) REVERT: A 506 LYS cc_start: 0.8394 (ttpp) cc_final: 0.8013 (ttpp) REVERT: B 48 PHE cc_start: 0.7076 (OUTLIER) cc_final: 0.5997 (t80) REVERT: B 207 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.6509 (tttt) REVERT: B 466 LYS cc_start: 0.7883 (mptt) cc_final: 0.7135 (pttt) REVERT: C 72 LYS cc_start: 0.6342 (OUTLIER) cc_final: 0.6067 (ttmt) REVERT: C 134 GLU cc_start: 0.6246 (tp30) cc_final: 0.5525 (mm-30) outliers start: 17 outliers final: 8 residues processed: 162 average time/residue: 1.7308 time to fit residues: 301.8456 Evaluate side-chains 163 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 207 LYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 155 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 30 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 0.0060 chunk 16 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 102 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN B 99 ASN B 260 GLN C 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.169900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.141207 restraints weight = 18898.684| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.38 r_work: 0.2901 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10532 Z= 0.116 Angle : 0.758 22.551 14303 Z= 0.272 Chirality : 0.042 0.154 1601 Planarity : 0.005 0.048 1811 Dihedral : 4.075 19.629 1457 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.20 % Allowed : 15.56 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.23), residues: 1318 helix: 1.45 (0.22), residues: 587 sheet: -0.89 (0.42), residues: 137 loop : -0.40 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 208 HIS 0.002 0.001 HIS B 520 PHE 0.011 0.001 PHE A 394 TYR 0.012 0.001 TYR C 73 ARG 0.015 0.001 ARG C 149 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 481) hydrogen bonds : angle 4.83042 ( 1345) metal coordination : bond 0.00969 ( 44) metal coordination : angle 6.39619 ( 102) covalent geometry : bond 0.00265 (10488) covalent geometry : angle 0.53409 (14201) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 1.116 Fit side-chains REVERT: A 234 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7470 (mt-10) REVERT: A 274 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7854 (tp30) REVERT: A 381 MET cc_start: 0.8658 (ttp) cc_final: 0.8436 (ptp) REVERT: A 432 ASP cc_start: 0.7014 (m-30) cc_final: 0.6616 (m-30) REVERT: A 480 MET cc_start: 0.8695 (mmm) cc_final: 0.8433 (mmt) REVERT: A 506 LYS cc_start: 0.8404 (ttpp) cc_final: 0.8031 (ttpp) REVERT: B 48 PHE cc_start: 0.7106 (OUTLIER) cc_final: 0.6057 (t80) REVERT: B 207 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.6535 (tttt) REVERT: B 276 MET cc_start: 0.8241 (mmp) cc_final: 0.7973 (mmp) REVERT: B 287 LEU cc_start: 0.6999 (mp) cc_final: 0.6634 (mt) REVERT: C 134 GLU cc_start: 0.6261 (tp30) cc_final: 0.5558 (mm-30) REVERT: C 149 ARG cc_start: 0.5806 (mtm110) cc_final: 0.4678 (mmm160) outliers start: 13 outliers final: 8 residues processed: 158 average time/residue: 1.9523 time to fit residues: 329.4265 Evaluate side-chains 161 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 207 LYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 155 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 42 optimal weight: 0.0040 chunk 130 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN B 99 ASN B 260 GLN C 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.167916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.139271 restraints weight = 19712.925| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.42 r_work: 0.2887 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10532 Z= 0.183 Angle : 0.862 22.665 14303 Z= 0.315 Chirality : 0.045 0.177 1601 Planarity : 0.005 0.059 1811 Dihedral : 4.490 21.650 1457 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.57 % Allowed : 15.38 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.23), residues: 1318 helix: 1.20 (0.21), residues: 587 sheet: -0.78 (0.43), residues: 130 loop : -0.48 (0.26), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 344 HIS 0.005 0.001 HIS B 520 PHE 0.012 0.002 PHE B 123 TYR 0.016 0.002 TYR C 73 ARG 0.011 0.001 ARG C 149 Details of bonding type rmsd hydrogen bonds : bond 0.04699 ( 481) hydrogen bonds : angle 5.06618 ( 1345) metal coordination : bond 0.01422 ( 44) metal coordination : angle 7.23375 ( 102) covalent geometry : bond 0.00434 (10488) covalent geometry : angle 0.61075 (14201) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 1.122 Fit side-chains REVERT: A 20 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8569 (tt) REVERT: A 274 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7893 (tp30) REVERT: A 374 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7632 (mt-10) REVERT: A 432 ASP cc_start: 0.7081 (m-30) cc_final: 0.6674 (m-30) REVERT: A 480 MET cc_start: 0.8742 (mmm) cc_final: 0.8508 (mmt) REVERT: A 506 LYS cc_start: 0.8400 (ttpp) cc_final: 0.8032 (ttpp) REVERT: B 48 PHE cc_start: 0.7174 (OUTLIER) cc_final: 0.5894 (t80) REVERT: B 207 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.6614 (tttt) REVERT: B 276 MET cc_start: 0.8279 (mmp) cc_final: 0.8017 (mmp) REVERT: C 134 GLU cc_start: 0.6444 (tp30) cc_final: 0.5776 (mm-30) REVERT: C 149 ARG cc_start: 0.5872 (mtm110) cc_final: 0.5545 (mtm110) outliers start: 17 outliers final: 9 residues processed: 162 average time/residue: 1.6736 time to fit residues: 289.2703 Evaluate side-chains 162 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 207 LYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 155 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 101 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 71 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 76 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN B 4 ASN B 99 ASN B 235 ASN B 260 GLN C 116 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.168853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.140051 restraints weight = 16707.936| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.22 r_work: 0.2911 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10532 Z= 0.141 Angle : 0.812 22.356 14303 Z= 0.292 Chirality : 0.044 0.161 1601 Planarity : 0.005 0.049 1811 Dihedral : 4.335 20.621 1457 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.57 % Allowed : 15.38 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.23), residues: 1318 helix: 1.29 (0.22), residues: 581 sheet: -0.90 (0.42), residues: 135 loop : -0.46 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 208 HIS 0.003 0.001 HIS B 520 PHE 0.011 0.002 PHE A 467 TYR 0.014 0.001 TYR C 73 ARG 0.011 0.001 ARG C 149 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 481) hydrogen bonds : angle 4.98113 ( 1345) metal coordination : bond 0.01169 ( 44) metal coordination : angle 6.82398 ( 102) covalent geometry : bond 0.00329 (10488) covalent geometry : angle 0.57415 (14201) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9053.31 seconds wall clock time: 164 minutes 9.30 seconds (9849.30 seconds total)