Starting phenix.real_space_refine on Thu Jul 2 21:49:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7p92_13258/07_2026/7p92_13258.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p92_13258/07_2026/7p92_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 { model { file = "/net/cci-nas-00/data/ceres_data/7p92_13258/07_2026/7p92_13258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p92_13258/07_2026/7p92_13258.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7p92_13258/07_2026/7p92_13258.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7p92_13258/07_2026/7p92_13258.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p92_13258/07_2026/7p92_13258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p92_13258/07_2026/7p92_13258.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 3, 'PHE:plan': 1} 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: {'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 3, 'PHE:plan': 1} 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: 3.34, per 1000 atoms: 0.32 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: 0.63 Conformation dependent library (CDL) restraints added in 724.6 milliseconds 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: 0.33 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: 1.48 Time building geometry restraints manager: 0.79 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=" 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=" N ARG C 34 " pdb=" CA ARG C 34 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.77e+00 bond pdb=" CA ARG C 149 " pdb=" C ARG C 149 " ideal model delta sigma weight residual 1.524 1.496 0.028 1.24e-02 6.50e+03 5.28e+00 bond pdb=" C GLU C 153 " pdb=" O GLU C 153 " ideal model delta sigma weight residual 1.237 1.215 0.021 1.16e-02 7.43e+03 3.37e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 ... (remaining 10483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 13666 1.25 - 2.50: 431 2.50 - 3.75: 85 3.75 - 5.01: 15 5.01 - 6.26: 4 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 - 34.79: 6230 34.79 - 69.59: 110 69.59 - 104.38: 11 104.38 - 139.18: 0 139.18 - 173.97: 1 Dihedral angle restraints: 6352 sinusoidal: 2565 harmonic: 3787 Sorted by residual: dihedral pdb=" C10 FMN B 703 " pdb=" C1' FMN B 703 " pdb=" N10 FMN B 703 " pdb=" C2' FMN B 703 " ideal model delta sinusoidal sigma weight residual 257.59 83.62 173.97 1 2.00e+01 2.50e-03 4.79e+01 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 ... (remaining 6349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1390 0.063 - 0.126: 205 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: 1810 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 1807 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 12.540 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.950 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 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 : 0.003 0.072 10532 Z= 0.160 Angle : 0.788 21.960 14303 Z= 0.314 Chirality : 0.043 0.314 1601 Planarity : 0.004 0.046 1810 Dihedral : 14.117 173.970 3934 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.64 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (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 ARG 0.004 0.001 ARG A 120 TYR 0.019 0.001 TYR A 459 PHE 0.011 0.001 PHE B 123 TRP 0.003 0.001 TRP B 344 HIS 0.004 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (10488) covalent geometry : angle 0.56374 / 0.31 (14201) hydrogen bonds : bond 0.15613 / 10.22 ( 481) hydrogen bonds : angle 6.42092 / 4.59 ( 1345) metal coordination : bond 0.01415 / 0.99 ( 44) metal coordination : angle 6.54393 / 4.66 ( 102) *********************** 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 : 0.400 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: 0.7759 (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: 0.6178 time to fit residues: 128.4737 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 : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.0070 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 7.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 ASN A 55 GLN B 4 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.170995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.141855 restraints weight = 23553.149| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.94 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3495 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (13 function evaluations) r_final: 0.3495 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10532 Z= 0.113 Angle : 0.769 23.731 14303 Z= 0.280 Chirality : 0.043 0.157 1601 Planarity : 0.004 0.043 1810 Dihedral : 6.265 173.323 1455 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.20 % Allowed : 8.47 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.24), residues: 1318 helix: 1.41 (0.22), residues: 589 sheet: -0.86 (0.42), residues: 136 loop : -0.50 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 121 TYR 0.012 0.001 TYR A 272 PHE 0.013 0.001 PHE A 394 TRP 0.011 0.002 TRP B 208 HIS 0.002 0.001 HIS A 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (10488) covalent geometry : angle 0.54556 / 0.28 (14201) hydrogen bonds : bond 0.04194 / 2.72 ( 481) hydrogen bonds : angle 5.19107 / 3.77 ( 1345) metal coordination : bond 0.00975 / 0.66 ( 44) metal coordination : angle 6.44560 / 4.75 ( 102) *********************** 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 189 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 177 time to evaluate : 0.290 Fit side-chains REVERT: A 432 ASP cc_start: 0.6700 (m-30) cc_final: 0.6374 (m-30) REVERT: A 506 LYS cc_start: 0.8005 (ttpp) cc_final: 0.7746 (ttpp) REVERT: B 276 MET cc_start: 0.7712 (mmp) cc_final: 0.7457 (mmp) REVERT: C 105 ASN cc_start: 0.7625 (m-40) cc_final: 0.7267 (m-40) REVERT: C 111 MET cc_start: 0.6403 (tpp) cc_final: 0.6187 (tpp) outliers start: 12 outliers final: 3 residues processed: 182 average time/residue: 0.5615 time to fit residues: 108.6457 Evaluate side-chains 167 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 164 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 77 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 1 optimal weight: 0.0000 chunk 126 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 34 optimal weight: 0.0970 chunk 49 optimal weight: 0.7980 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 ASN B 4 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 = 0.3830 r_free = 0.3830 target = 0.170949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.143562 restraints weight = 23038.372| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.61 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3518 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.3518 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10532 Z= 0.104 Angle : 0.730 22.804 14303 Z= 0.264 Chirality : 0.042 0.151 1601 Planarity : 0.004 0.045 1810 Dihedral : 6.133 171.104 1455 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.38 % Allowed : 10.77 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.24), residues: 1318 helix: 1.63 (0.22), residues: 580 sheet: -0.79 (0.42), residues: 136 loop : -0.49 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 149 TYR 0.012 0.001 TYR C 73 PHE 0.011 0.001 PHE A 394 TRP 0.007 0.001 TRP B 208 HIS 0.002 0.001 HIS B 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (10488) covalent geometry : angle 0.51938 / 0.26 (14201) hydrogen bonds : bond 0.03733 / 2.41 ( 481) hydrogen bonds : angle 4.93344 / 3.59 ( 1345) metal coordination : bond 0.00887 / 0.61 ( 44) metal coordination : angle 6.09245 / 4.50 ( 102) *********************** 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 184 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.397 Fit side-chains REVERT: A 432 ASP cc_start: 0.6674 (m-30) cc_final: 0.6319 (m-30) REVERT: A 506 LYS cc_start: 0.7983 (ttpp) cc_final: 0.7743 (ttpp) REVERT: B 48 PHE cc_start: 0.6818 (OUTLIER) cc_final: 0.5866 (t80) REVERT: C 105 ASN cc_start: 0.7602 (m-40) cc_final: 0.7301 (m-40) REVERT: C 111 MET cc_start: 0.6375 (tpp) cc_final: 0.6117 (tpp) outliers start: 14 outliers final: 6 residues processed: 176 average time/residue: 0.5786 time to fit residues: 108.7305 Evaluate side-chains 170 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 163 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 297 THR Chi-restraints excluded: chain B residue 386 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 ASN B 99 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 = 0.3800 r_free = 0.3800 target = 0.168016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.139944 restraints weight = 17039.936| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.23 r_work: 0.2866 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10532 Z= 0.181 Angle : 0.863 22.082 14303 Z= 0.317 Chirality : 0.046 0.184 1601 Planarity : 0.005 0.057 1810 Dihedral : 6.492 170.790 1455 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.12 % Allowed : 11.79 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.23), residues: 1318 helix: 1.33 (0.21), residues: 584 sheet: -0.90 (0.42), residues: 136 loop : -0.54 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 149 TYR 0.014 0.002 TYR A 459 PHE 0.015 0.002 PHE B 301 TRP 0.007 0.002 TRP B 344 HIS 0.005 0.002 HIS B 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (10488) covalent geometry : angle 0.61693 / 0.31 (14201) hydrogen bonds : bond 0.04763 / 3.08 ( 481) hydrogen bonds : angle 5.12437 / 3.74 ( 1345) metal coordination : bond 0.01478 / 1.03 ( 44) metal coordination : angle 7.16776 / 5.08 ( 102) *********************** 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 186 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.301 Fit side-chains REVERT: A 432 ASP cc_start: 0.7191 (m-30) cc_final: 0.6823 (m-30) REVERT: A 480 MET cc_start: 0.8716 (mmm) cc_final: 0.8402 (mmt) REVERT: A 506 LYS cc_start: 0.8326 (ttpp) cc_final: 0.7953 (ttpp) REVERT: B 48 PHE cc_start: 0.7107 (OUTLIER) cc_final: 0.5778 (t80) REVERT: B 461 VAL cc_start: 0.8453 (t) cc_final: 0.8144 (p) REVERT: B 557 GLU cc_start: 0.6632 (mm-30) cc_final: 0.6128 (mt-10) REVERT: C 105 ASN cc_start: 0.7603 (m-40) cc_final: 0.7036 (m-40) REVERT: C 111 MET cc_start: 0.6761 (tpp) cc_final: 0.6320 (tpp) outliers start: 22 outliers final: 12 residues processed: 174 average time/residue: 0.5704 time to fit residues: 105.9113 Evaluate side-chains 167 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 282 LEU 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 B residue 443 LEU Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 106 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 21 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 119 optimal weight: 0.3980 chunk 7 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3806 r_free = 0.3806 target = 0.168633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.141300 restraints weight = 26325.549| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.80 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3484 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3484 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10532 Z= 0.150 Angle : 0.821 21.935 14303 Z= 0.298 Chirality : 0.044 0.169 1601 Planarity : 0.005 0.051 1810 Dihedral : 6.441 170.749 1455 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.93 % Allowed : 12.80 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.23), residues: 1318 helix: 1.29 (0.21), residues: 585 sheet: -0.92 (0.42), residues: 136 loop : -0.53 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 149 TYR 0.013 0.001 TYR C 73 PHE 0.012 0.002 PHE B 301 TRP 0.005 0.002 TRP B 344 HIS 0.004 0.001 HIS B 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (10488) covalent geometry : angle 0.58477 / 0.29 (14201) hydrogen bonds : bond 0.04369 / 2.83 ( 481) hydrogen bonds : angle 5.05628 / 3.69 ( 1345) metal coordination : bond 0.01294 / 0.90 ( 44) metal coordination : angle 6.84122 / 4.91 ( 102) *********************** 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 176 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.399 Fit side-chains REVERT: A 432 ASP cc_start: 0.6718 (m-30) cc_final: 0.6295 (m-30) REVERT: A 480 MET cc_start: 0.8274 (mmm) cc_final: 0.7915 (mmt) REVERT: A 506 LYS cc_start: 0.8000 (ttpp) cc_final: 0.7752 (ttpp) REVERT: B 48 PHE cc_start: 0.7001 (OUTLIER) cc_final: 0.5907 (t80) REVERT: C 72 LYS cc_start: 0.6473 (OUTLIER) cc_final: 0.6257 (ptmt) outliers start: 20 outliers final: 10 residues processed: 168 average time/residue: 0.5957 time to fit residues: 106.8227 Evaluate side-chains 165 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 215 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 62 optimal weight: 0.0770 chunk 116 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 114 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3804 r_free = 0.3804 target = 0.168522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.139106 restraints weight = 22942.720| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.88 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3471 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3471 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10532 Z= 0.159 Angle : 0.836 21.880 14303 Z= 0.304 Chirality : 0.044 0.173 1601 Planarity : 0.005 0.053 1810 Dihedral : 6.493 170.529 1455 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.03 % Allowed : 13.44 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.23), residues: 1318 helix: 1.22 (0.21), residues: 585 sheet: -0.91 (0.42), residues: 136 loop : -0.53 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 149 TYR 0.014 0.002 TYR C 73 PHE 0.013 0.002 PHE B 301 TRP 0.005 0.002 TRP B 344 HIS 0.004 0.001 HIS B 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (10488) covalent geometry : angle 0.59577 / 0.30 (14201) hydrogen bonds : bond 0.04480 / 2.90 ( 481) hydrogen bonds : angle 5.06726 / 3.70 ( 1345) metal coordination : bond 0.01337 / 0.93 ( 44) metal coordination : angle 6.97027 / 4.97 ( 102) *********************** 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 176 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.287 Fit side-chains REVERT: A 274 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7311 (tp30) REVERT: A 432 ASP cc_start: 0.6738 (m-30) cc_final: 0.6305 (m-30) REVERT: A 480 MET cc_start: 0.8255 (mmm) cc_final: 0.7962 (mmt) REVERT: A 506 LYS cc_start: 0.8007 (ttpp) cc_final: 0.7744 (ttpp) REVERT: B 48 PHE cc_start: 0.7056 (OUTLIER) cc_final: 0.5934 (t80) REVERT: B 207 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.6673 (tttt) REVERT: B 276 MET cc_start: 0.7678 (mmp) cc_final: 0.7455 (mmp) outliers start: 21 outliers final: 11 residues processed: 164 average time/residue: 0.5533 time to fit residues: 96.7903 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 : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET 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 B residue 443 LEU Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 106 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 60 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 6 optimal weight: 0.0170 chunk 1 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3804 r_free = 0.3804 target = 0.168469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.132622 restraints weight = 16076.349| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.78 r_work: 0.2872 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10532 Z= 0.144 Angle : 0.812 22.103 14303 Z= 0.293 Chirality : 0.044 0.167 1601 Planarity : 0.005 0.050 1810 Dihedral : 6.448 170.651 1455 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.03 % Allowed : 14.00 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.23), residues: 1318 helix: 1.27 (0.21), residues: 585 sheet: -0.92 (0.42), residues: 136 loop : -0.51 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 149 TYR 0.014 0.001 TYR C 73 PHE 0.011 0.002 PHE A 467 TRP 0.004 0.002 TRP B 208 HIS 0.004 0.001 HIS B 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (10488) covalent geometry : angle 0.57831 / 0.29 (14201) hydrogen bonds : bond 0.04261 / 2.76 ( 481) hydrogen bonds : angle 5.02049 / 3.67 ( 1345) metal coordination : bond 0.01220 / 0.84 ( 44) metal coordination : angle 6.78057 / 4.87 ( 102) *********************** 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 171 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.415 Fit side-chains REVERT: A 274 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7790 (tp30) REVERT: A 374 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7629 (mt-10) REVERT: A 432 ASP cc_start: 0.7112 (m-30) cc_final: 0.6716 (m-30) REVERT: A 480 MET cc_start: 0.8729 (mmm) cc_final: 0.8468 (mmt) REVERT: A 506 LYS cc_start: 0.8346 (ttpp) cc_final: 0.7984 (ttpp) REVERT: B 48 PHE cc_start: 0.7084 (OUTLIER) cc_final: 0.5847 (t80) REVERT: B 207 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.6528 (tttt) REVERT: B 276 MET cc_start: 0.8196 (mmp) cc_final: 0.7933 (mmp) REVERT: C 134 GLU cc_start: 0.6402 (tp30) cc_final: 0.5658 (mm-30) outliers start: 21 outliers final: 10 residues processed: 162 average time/residue: 0.6095 time to fit residues: 105.3506 Evaluate side-chains 161 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET 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 B residue 443 LEU 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 48 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 87 optimal weight: 0.0870 chunk 53 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 119 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 129 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.169790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.142289 restraints weight = 24395.331| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.72 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (13 function evaluations) r_final: 0.3503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10532 Z= 0.118 Angle : 0.765 22.590 14303 Z= 0.276 Chirality : 0.042 0.154 1601 Planarity : 0.005 0.049 1810 Dihedral : 6.311 170.614 1455 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.75 % Allowed : 14.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.23), residues: 1318 helix: 1.40 (0.22), residues: 585 sheet: -0.71 (0.43), residues: 129 loop : -0.46 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 149 TYR 0.014 0.001 TYR C 73 PHE 0.010 0.001 PHE A 394 TRP 0.005 0.001 TRP B 208 HIS 0.003 0.001 HIS B 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (10488) covalent geometry : angle 0.54527 / 0.27 (14201) hydrogen bonds : bond 0.03856 / 2.49 ( 481) hydrogen bonds : angle 4.88621 / 3.57 ( 1345) metal coordination : bond 0.01011 / 0.69 ( 44) metal coordination : angle 6.37867 / 4.66 ( 102) *********************** 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 168 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.421 Fit side-chains REVERT: A 274 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7311 (tp30) REVERT: A 340 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.6288 (mp0) REVERT: A 432 ASP cc_start: 0.6602 (m-30) cc_final: 0.6157 (m-30) REVERT: A 480 MET cc_start: 0.8161 (mmm) cc_final: 0.7837 (mmt) REVERT: A 506 LYS cc_start: 0.8083 (ttpp) cc_final: 0.7812 (ttpp) REVERT: B 48 PHE cc_start: 0.6949 (OUTLIER) cc_final: 0.5960 (t80) REVERT: B 276 MET cc_start: 0.7632 (mmp) cc_final: 0.7414 (mmp) REVERT: C 18 LYS cc_start: 0.6859 (OUTLIER) cc_final: 0.6606 (ttmm) REVERT: C 134 GLU cc_start: 0.5589 (tp30) cc_final: 0.5194 (mm-30) outliers start: 18 outliers final: 8 residues processed: 159 average time/residue: 0.5880 time to fit residues: 99.8932 Evaluate side-chains 157 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 340 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 18 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 6 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 25 optimal weight: 0.0000 chunk 0 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 114 optimal weight: 0.3980 chunk 28 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 112 optimal weight: 0.1980 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3818 r_free = 0.3818 target = 0.169842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.142111 restraints weight = 20346.400| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.46 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3510 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3510 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10532 Z= 0.118 Angle : 0.766 22.324 14303 Z= 0.275 Chirality : 0.042 0.158 1601 Planarity : 0.005 0.057 1810 Dihedral : 6.296 170.657 1455 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.47 % Allowed : 14.64 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.23), residues: 1318 helix: 1.44 (0.22), residues: 585 sheet: -0.85 (0.42), residues: 136 loop : -0.44 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 149 TYR 0.013 0.001 TYR C 73 PHE 0.010 0.001 PHE A 394 TRP 0.005 0.001 TRP B 208 HIS 0.003 0.001 HIS B 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (10488) covalent geometry : angle 0.54333 / 0.27 (14201) hydrogen bonds : bond 0.03865 / 2.51 ( 481) hydrogen bonds : angle 4.85562 / 3.56 ( 1345) metal coordination : bond 0.01005 / 0.69 ( 44) metal coordination : angle 6.41906 / 4.67 ( 102) *********************** 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: 15 poor density : 150 time to evaluate : 0.260 Fit side-chains REVERT: A 274 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7328 (tp30) REVERT: A 340 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.6296 (mp0) REVERT: A 432 ASP cc_start: 0.6587 (m-30) cc_final: 0.6139 (m-30) REVERT: A 480 MET cc_start: 0.8186 (mmm) cc_final: 0.7877 (mmt) REVERT: A 506 LYS cc_start: 0.8075 (ttpp) cc_final: 0.7812 (ttpp) REVERT: B 48 PHE cc_start: 0.6911 (OUTLIER) cc_final: 0.5962 (t80) REVERT: B 207 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.6669 (tttt) REVERT: B 276 MET cc_start: 0.7637 (mmp) cc_final: 0.7425 (mmp) REVERT: C 18 LYS cc_start: 0.6833 (OUTLIER) cc_final: 0.6571 (ttmm) REVERT: C 134 GLU cc_start: 0.5531 (tp30) cc_final: 0.5179 (mm-30) REVERT: C 149 ARG cc_start: 0.5867 (mtm110) cc_final: 0.5192 (mmm160) outliers start: 15 outliers final: 8 residues processed: 157 average time/residue: 0.5941 time to fit residues: 99.4725 Evaluate side-chains 161 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 340 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 18 LYS 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 51 optimal weight: 0.0670 chunk 96 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 9 optimal weight: 0.0980 chunk 125 optimal weight: 0.4980 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3849 r_free = 0.3849 target = 0.172596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.142206 restraints weight = 16220.855| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.30 r_work: 0.2957 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.2928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10532 Z= 0.092 Angle : 0.707 23.387 14303 Z= 0.253 Chirality : 0.041 0.142 1601 Planarity : 0.004 0.049 1810 Dihedral : 6.053 170.300 1455 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.10 % Allowed : 15.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.24), residues: 1318 helix: 1.65 (0.22), residues: 577 sheet: -0.73 (0.42), residues: 134 loop : -0.39 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 149 TYR 0.010 0.001 TYR A 272 PHE 0.012 0.001 PHE A 394 TRP 0.010 0.001 TRP B 208 HIS 0.002 0.000 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 (10488) covalent geometry : angle 0.50427 / 0.25 (14201) hydrogen bonds : bond 0.03226 / 2.09 ( 481) hydrogen bonds : angle 4.66720 / 3.42 ( 1345) metal coordination : bond 0.00729 / 0.50 ( 44) metal coordination : angle 5.89324 / 4.42 ( 102) ********************** 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 176 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 0.524 Fit side-chains REVERT: A 287 ARG cc_start: 0.7800 (mtp180) cc_final: 0.7435 (mtp180) REVERT: A 290 GLN cc_start: 0.8791 (tt0) cc_final: 0.8554 (tt0) REVERT: A 340 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6773 (mp0) REVERT: A 432 ASP cc_start: 0.6964 (m-30) cc_final: 0.6579 (m-30) REVERT: A 496 ASN cc_start: 0.7908 (t0) cc_final: 0.7449 (t160) REVERT: A 506 LYS cc_start: 0.8322 (ttpp) cc_final: 0.7957 (ttpp) REVERT: A 532 GLU cc_start: 0.6532 (tp30) cc_final: 0.6180 (mt-10) REVERT: B 1 MET cc_start: 0.3512 (pmm) cc_final: 0.2455 (ptp) REVERT: B 48 PHE cc_start: 0.7064 (OUTLIER) cc_final: 0.6114 (t80) REVERT: B 276 MET cc_start: 0.8215 (mmp) cc_final: 0.7943 (mmp) REVERT: B 377 ASN cc_start: 0.5879 (m110) cc_final: 0.5515 (m110) REVERT: C 105 ASN cc_start: 0.7548 (m-40) cc_final: 0.7109 (m-40) REVERT: C 112 PHE cc_start: 0.7139 (m-80) cc_final: 0.6705 (m-10) REVERT: C 134 GLU cc_start: 0.6258 (tp30) cc_final: 0.5556 (mm-30) REVERT: C 149 ARG cc_start: 0.5506 (mtm110) cc_final: 0.4558 (mmm160) outliers start: 11 outliers final: 5 residues processed: 168 average time/residue: 0.6727 time to fit residues: 120.6614 Evaluate side-chains 155 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 148 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 GLU 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 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 41 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 99 optimal weight: 0.4980 chunk 95 optimal weight: 0.0270 chunk 74 optimal weight: 0.0030 chunk 31 optimal weight: 3.9990 overall best weight: 0.3848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3843 r_free = 0.3843 target = 0.172163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.143779 restraints weight = 18248.664| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.34 r_work: 0.2955 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10532 Z= 0.094 Angle : 0.716 22.809 14303 Z= 0.259 Chirality : 0.042 0.173 1601 Planarity : 0.004 0.048 1810 Dihedral : 6.022 170.074 1455 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.74 % Allowed : 16.39 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.24), residues: 1318 helix: 1.69 (0.22), residues: 577 sheet: -0.68 (0.42), residues: 134 loop : -0.36 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 149 TYR 0.011 0.001 TYR A 272 PHE 0.011 0.001 PHE A 394 TRP 0.008 0.001 TRP B 208 HIS 0.002 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.09 (10488) covalent geometry : angle 0.51820 / 0.26 (14201) hydrogen bonds : bond 0.03275 / 2.13 ( 481) hydrogen bonds : angle 4.64872 / 3.41 ( 1345) metal coordination : bond 0.00725 / 0.49 ( 44) metal coordination : angle 5.87620 / 4.39 ( 102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3196.80 seconds wall clock time: 55 minutes 18.38 seconds (3318.38 seconds total)