Starting phenix.real_space_refine on Sat Jul 4 22:20:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fjp_29245/07_2026/8fjp_29245.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fjp_29245/07_2026/8fjp_29245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fjp_29245/07_2026/8fjp_29245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fjp_29245/07_2026/8fjp_29245.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fjp_29245/07_2026/8fjp_29245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fjp_29245/07_2026/8fjp_29245.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8fjp_29245/07_2026/8fjp_29245.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fjp_29245/07_2026/8fjp_29245.cif" } resolution = 3.3 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 71 5.16 5 C 14850 2.51 5 N 3977 2.21 5 O 4492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 23390 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 23348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2932, 23348 Classifications: {'peptide': 2932} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 110, 'TRANS': 2821} Chain breaks: 4 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.64, per 1000 atoms: 0.16 Number of scatterers: 23390 At special positions: 0 Unit cell: (99.28, 125.12, 223.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 71 16.00 O 4492 8.00 N 3977 7.00 C 14850 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 297 " distance=2.02 Simple disulfide: pdb=" SG CYS A1128 " - pdb=" SG CYS A1139 " distance=2.04 Simple disulfide: pdb=" SG CYS A2253 " - pdb=" SG CYS A2285 " distance=2.03 Simple disulfide: pdb=" SG CYS A2407 " - pdb=" SG CYS A2421 " distance=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A4001 " - " ASN A 59 " " NAG B 1 " - " ASN A1149 " Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 919.7 milliseconds 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5454 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 35 sheets defined 15.2% alpha, 35.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 261 through 266 removed outlier: 3.555A pdb=" N ASP A 266 " --> pdb=" O ARG A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.652A pdb=" N SER A 387 " --> pdb=" O TRP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 394 removed outlier: 3.967A pdb=" N LYS A 394 " --> pdb=" O ALA A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 525 Processing helix chain 'A' and resid 899 through 910 Processing helix chain 'A' and resid 920 through 942 removed outlier: 3.728A pdb=" N LYS A 926 " --> pdb=" O ALA A 922 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A 927 " --> pdb=" O GLU A 923 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR A 942 " --> pdb=" O SER A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1060 removed outlier: 3.751A pdb=" N LYS A1050 " --> pdb=" O SER A1046 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLY A1053 " --> pdb=" O GLU A1049 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLN A1054 " --> pdb=" O LYS A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1069 removed outlier: 4.225A pdb=" N TYR A1068 " --> pdb=" O ASP A1064 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET A1069 " --> pdb=" O PHE A1065 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1064 through 1069' Processing helix chain 'A' and resid 1097 through 1102 removed outlier: 3.717A pdb=" N LEU A1101 " --> pdb=" O ASP A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1172 through 1176 removed outlier: 3.530A pdb=" N ARG A1176 " --> pdb=" O ILE A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1214 through 1216 No H-bonds generated for 'chain 'A' and resid 1214 through 1216' Processing helix chain 'A' and resid 1267 through 1272 removed outlier: 4.045A pdb=" N THR A1271 " --> pdb=" O GLY A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1313 removed outlier: 3.947A pdb=" N ARG A1304 " --> pdb=" O GLU A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1585 through 1589 Processing helix chain 'A' and resid 1780 through 1784 removed outlier: 4.207A pdb=" N VAL A1784 " --> pdb=" O ASP A1781 " (cutoff:3.500A) Processing helix chain 'A' and resid 1809 through 1814 Processing helix chain 'A' and resid 1857 through 1864 removed outlier: 3.555A pdb=" N GLN A1861 " --> pdb=" O LEU A1857 " (cutoff:3.500A) Processing helix chain 'A' and resid 1923 through 1931 removed outlier: 3.805A pdb=" N TYR A1927 " --> pdb=" O PRO A1923 " (cutoff:3.500A) Processing helix chain 'A' and resid 2016 through 2030 removed outlier: 4.102A pdb=" N LYS A2028 " --> pdb=" O ARG A2024 " (cutoff:3.500A) Processing helix chain 'A' and resid 2050 through 2054 Processing helix chain 'A' and resid 2077 through 2079 No H-bonds generated for 'chain 'A' and resid 2077 through 2079' Processing helix chain 'A' and resid 2224 through 2227 Processing helix chain 'A' and resid 2229 through 2233 Processing helix chain 'A' and resid 2246 through 2260 removed outlier: 3.524A pdb=" N ALA A2250 " --> pdb=" O ASP A2246 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU A2251 " --> pdb=" O PHE A2247 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A2252 " --> pdb=" O THR A2248 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A2260 " --> pdb=" O ALA A2256 " (cutoff:3.500A) Processing helix chain 'A' and resid 2282 through 2287 Processing helix chain 'A' and resid 2287 through 2301 Processing helix chain 'A' and resid 2327 through 2331 removed outlier: 4.113A pdb=" N LYS A2330 " --> pdb=" O GLY A2327 " (cutoff:3.500A) Processing helix chain 'A' and resid 2341 through 2346 removed outlier: 3.779A pdb=" N GLY A2346 " --> pdb=" O ALA A2343 " (cutoff:3.500A) Processing helix chain 'A' and resid 2348 through 2363 removed outlier: 3.640A pdb=" N ARG A2354 " --> pdb=" O HIS A2350 " (cutoff:3.500A) Processing helix chain 'A' and resid 2364 through 2371 removed outlier: 6.757A pdb=" N THR A2369 " --> pdb=" O VAL A2366 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS A2370 " --> pdb=" O GLU A2367 " (cutoff:3.500A) Processing helix chain 'A' and resid 2388 through 2398 removed outlier: 3.714A pdb=" N LEU A2397 " --> pdb=" O LEU A2393 " (cutoff:3.500A) Processing helix chain 'A' and resid 2406 through 2411 Processing helix chain 'A' and resid 2416 through 2432 removed outlier: 3.750A pdb=" N LYS A2420 " --> pdb=" O THR A2416 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLN A2426 " --> pdb=" O LYS A2422 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLN A2427 " --> pdb=" O ARG A2423 " (cutoff:3.500A) Processing helix chain 'A' and resid 2435 through 2441 Processing helix chain 'A' and resid 2442 through 2447 Processing helix chain 'A' and resid 2448 through 2460 removed outlier: 3.598A pdb=" N ILE A2452 " --> pdb=" O ASN A2448 " (cutoff:3.500A) Processing helix chain 'A' and resid 2549 through 2551 No H-bonds generated for 'chain 'A' and resid 2549 through 2551' Processing helix chain 'A' and resid 2637 through 2639 No H-bonds generated for 'chain 'A' and resid 2637 through 2639' Processing helix chain 'A' and resid 2677 through 2681 removed outlier: 3.553A pdb=" N GLY A2680 " --> pdb=" O ARG A2677 " (cutoff:3.500A) Processing helix chain 'A' and resid 2732 through 2752 Processing helix chain 'A' and resid 2761 through 2765 Processing helix chain 'A' and resid 2811 through 2821 removed outlier: 3.920A pdb=" N ILE A2815 " --> pdb=" O ALA A2811 " (cutoff:3.500A) Processing helix chain 'A' and resid 2822 through 2826 removed outlier: 3.734A pdb=" N ALA A2825 " --> pdb=" O LEU A2822 " (cutoff:3.500A) Processing helix chain 'A' and resid 2832 through 2836 removed outlier: 3.722A pdb=" N TRP A2836 " --> pdb=" O PRO A2833 " (cutoff:3.500A) Processing helix chain 'A' and resid 2840 through 2852 Processing helix chain 'A' and resid 2875 through 2886 removed outlier: 3.753A pdb=" N GLY A2886 " --> pdb=" O SER A2882 " (cutoff:3.500A) Processing helix chain 'A' and resid 2896 through 2900 removed outlier: 4.410A pdb=" N ALA A2899 " --> pdb=" O GLY A2896 " (cutoff:3.500A) Processing helix chain 'A' and resid 2901 through 2908 Processing helix chain 'A' and resid 2913 through 2917 Processing helix chain 'A' and resid 2947 through 2951 removed outlier: 3.590A pdb=" N LEU A2951 " --> pdb=" O PRO A2948 " (cutoff:3.500A) Processing helix chain 'A' and resid 2971 through 2990 Processing helix chain 'A' and resid 3030 through 3041 removed outlier: 3.914A pdb=" N PHE A3041 " --> pdb=" O ASN A3037 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 9 removed outlier: 6.773A pdb=" N THR A 338 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL A 7 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU A 336 " --> pdb=" O VAL A 7 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS A 9 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU A 334 " --> pdb=" O LYS A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 3 through 9 removed outlier: 6.773A pdb=" N THR A 338 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL A 7 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU A 336 " --> pdb=" O VAL A 7 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS A 9 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU A 334 " --> pdb=" O LYS A 9 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 22 through 25 removed outlier: 6.363A pdb=" N LEU A 46 " --> pdb=" O ASN A 59 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASN A 59 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LYS A 48 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP A 50 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER A 55 " --> pdb=" O ASP A 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 74 through 79 Processing sheet with id=AA5, first strand: chain 'A' and resid 123 through 129 Processing sheet with id=AA6, first strand: chain 'A' and resid 170 through 171 removed outlier: 3.603A pdb=" N VAL A 171 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE A 194 " --> pdb=" O ASN A 205 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASN A 205 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N LYS A 196 " --> pdb=" O GLN A 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 170 through 171 removed outlier: 3.603A pdb=" N VAL A 171 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 218 through 221 removed outlier: 3.582A pdb=" N TYR A 249 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N SER A 239 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE A 247 " --> pdb=" O SER A 239 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 269 through 272 Processing sheet with id=AB1, first strand: chain 'A' and resid 360 through 362 removed outlier: 4.471A pdb=" N GLU A 360 " --> pdb=" O VAL A1423 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 362 " --> pdb=" O ALA A1421 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 370 through 372 removed outlier: 6.128A pdb=" N THR A 371 " --> pdb=" O VAL A1598 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 370 through 372 removed outlier: 6.128A pdb=" N THR A 371 " --> pdb=" O VAL A1598 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA A1603 " --> pdb=" O VAL A1706 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL A1706 " --> pdb=" O ALA A1603 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU A1605 " --> pdb=" O GLY A1704 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY A1704 " --> pdb=" O LEU A1605 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY A1607 " --> pdb=" O THR A1702 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N VAL A1698 " --> pdb=" O SER A1611 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 405 through 413 removed outlier: 6.797A pdb=" N LEU A 423 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP A 412 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE A 421 " --> pdb=" O ASP A 412 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 527 through 530 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 527 through 530 current: chain 'A' and resid 463 through 468 removed outlier: 4.378A pdb=" N TYR A 464 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N MET A 492 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ALA A 498 " --> pdb=" O MET A 492 " (cutoff:3.500A) removed outlier: 10.977A pdb=" N ASN A 554 " --> pdb=" O TYR A 572 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N TYR A 572 " --> pdb=" O ASN A 554 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N VAL A 556 " --> pdb=" O TYR A 570 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A 569 " --> pdb=" O THR A 588 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N LEU A 585 " --> pdb=" O PHE A 598 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 596 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LYS A 601 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU A 626 " --> pdb=" O LYS A 601 " (cutoff:3.500A) removed outlier: 11.113A pdb=" N LEU A 625 " --> pdb=" O SER A 644 " (cutoff:3.500A) removed outlier: 9.752A pdb=" N SER A 644 " --> pdb=" O LEU A 625 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N GLU A 627 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N THR A 645 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU A 653 " --> pdb=" O THR A 645 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE A 647 " --> pdb=" O TYR A 651 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N TYR A 651 " --> pdb=" O ILE A 647 " (cutoff:3.500A) removed outlier: 11.094A pdb=" N TYR A 652 " --> pdb=" O TYR A 670 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N TYR A 670 " --> pdb=" O TYR A 652 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N GLU A 654 " --> pdb=" O PHE A 668 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 666 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLY A 667 " --> pdb=" O ILE A 683 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE A 683 " --> pdb=" O GLY A 667 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLU A 669 " --> pdb=" O GLN A 681 " (cutoff:3.500A) removed outlier: 10.940A pdb=" N ARG A 679 " --> pdb=" O TYR A 695 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N TYR A 695 " --> pdb=" O ARG A 679 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N GLN A 681 " --> pdb=" O PHE A 693 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL A 690 " --> pdb=" O LEU A1232 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU A1232 " --> pdb=" O VAL A 690 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASP A 692 " --> pdb=" O GLU A1230 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU A1230 " --> pdb=" O ASP A 692 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LYS A 694 " --> pdb=" O SER A1228 " (cutoff:3.500A) removed outlier: 10.615A pdb=" N ILE A1222 " --> pdb=" O VAL A1249 " (cutoff:3.500A) removed outlier: 10.461A pdb=" N VAL A1249 " --> pdb=" O ILE A1222 " (cutoff:3.500A) removed outlier: 12.449A pdb=" N ALA A1224 " --> pdb=" O ASP A1247 " (cutoff:3.500A) removed outlier: 11.870A pdb=" N ASP A1247 " --> pdb=" O ALA A1224 " (cutoff:3.500A) removed outlier: 9.905A pdb=" N VAL A1226 " --> pdb=" O TYR A1245 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N TYR A1245 " --> pdb=" O VAL A1226 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N SER A1228 " --> pdb=" O TYR A1243 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR A1243 " --> pdb=" O VAL A1262 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A1262 " --> pdb=" O TYR A1243 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TYR A1245 " --> pdb=" O THR A1260 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR A1260 " --> pdb=" O TYR A1245 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASP A1247 " --> pdb=" O LYS A1258 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LYS A1258 " --> pdb=" O ASN A1278 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL A1289 " --> pdb=" O PHE A1297 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 707 through 709 Processing sheet with id=AB7, first strand: chain 'A' and resid 713 through 716 removed outlier: 3.666A pdb=" N SER A 722 " --> pdb=" O LYS A 739 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 762 through 770 removed outlier: 6.255A pdb=" N ILE A 763 " --> pdb=" O ALA A 782 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA A 782 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 765 " --> pdb=" O ARG A 780 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 815 " --> pdb=" O ASN A 790 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 821 through 824 removed outlier: 3.877A pdb=" N VAL A 837 " --> pdb=" O LYS A 854 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS A 854 " --> pdb=" O VAL A 837 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 868 through 869 Processing sheet with id=AC2, first strand: chain 'A' and resid 944 through 947 removed outlier: 7.225A pdb=" N ILE A 964 " --> pdb=" O GLN A 988 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLN A 988 " --> pdb=" O ILE A 964 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL A 966 " --> pdb=" O GLU A 986 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLU A 986 " --> pdb=" O VAL A 966 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL A 968 " --> pdb=" O SER A 984 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N SER A 984 " --> pdb=" O VAL A 968 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU A 970 " --> pdb=" O ARG A 982 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG A 982 " --> pdb=" O LEU A 970 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU A 972 " --> pdb=" O SER A 980 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 996 through 1001 removed outlier: 6.423A pdb=" N LYS A1015 " --> pdb=" O ALA A1034 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA A1034 " --> pdb=" O LYS A1015 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ARG A1017 " --> pdb=" O ILE A1032 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1071 through 1072 Processing sheet with id=AC5, first strand: chain 'A' and resid 1106 through 1109 removed outlier: 3.592A pdb=" N PHE A1106 " --> pdb=" O LYS A1118 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1158 through 1162 Processing sheet with id=AC7, first strand: chain 'A' and resid 1326 through 1327 Processing sheet with id=AC8, first strand: chain 'A' and resid 1350 through 1353 Processing sheet with id=AC9, first strand: chain 'A' and resid 1350 through 1353 removed outlier: 5.227A pdb=" N VAL A1487 " --> pdb=" O ARG A1416 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ARG A1416 " --> pdb=" O VAL A1487 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS A1489 " --> pdb=" O TRP A1414 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE A1409 " --> pdb=" O SER A1457 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A1411 " --> pdb=" O ALA A1455 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN A1445 " --> pdb=" O TYR A1452 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLU A1454 " --> pdb=" O ILE A1443 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE A1443 " --> pdb=" O GLU A1454 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N ASP A1456 " --> pdb=" O GLY A1441 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N GLY A1441 " --> pdb=" O ASP A1456 " (cutoff:3.500A) removed outlier: 9.439A pdb=" N LYS A1437 " --> pdb=" O LEU A1431 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N LEU A1431 " --> pdb=" O LYS A1437 " (cutoff:3.500A) removed outlier: 10.178A pdb=" N MET A1439 " --> pdb=" O MET A1429 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N MET A1429 " --> pdb=" O MET A1439 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY A1441 " --> pdb=" O THR A1427 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N MET A1429 " --> pdb=" O LYS A1478 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL A1471 " --> pdb=" O ASN A1402 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASN A1402 " --> pdb=" O VAL A1471 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1501 through 1504 removed outlier: 3.501A pdb=" N GLY A1501 " --> pdb=" O ILE A1515 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A1513 " --> pdb=" O VAL A1503 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N THR A1512 " --> pdb=" O ARG A1524 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE A1533 " --> pdb=" O LEU A1545 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A1545 " --> pdb=" O ILE A1533 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU A1535 " --> pdb=" O LYS A1543 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE A1719 " --> pdb=" O LEU A1735 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LEU A1735 " --> pdb=" O ILE A1719 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL A1721 " --> pdb=" O GLU A1733 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLU A1733 " --> pdb=" O VAL A1721 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR A1723 " --> pdb=" O LEU A1731 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LEU A1731 " --> pdb=" O MET A1747 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN A1741 " --> pdb=" O LEU A1737 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 1501 through 1504 removed outlier: 3.501A pdb=" N GLY A1501 " --> pdb=" O ILE A1515 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A1513 " --> pdb=" O VAL A1503 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N THR A1512 " --> pdb=" O ARG A1524 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE A1533 " --> pdb=" O LEU A1545 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A1545 " --> pdb=" O ILE A1533 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU A1535 " --> pdb=" O LYS A1543 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE A1719 " --> pdb=" O LEU A1735 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LEU A1735 " --> pdb=" O ILE A1719 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL A1721 " --> pdb=" O GLU A1733 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLU A1733 " --> pdb=" O VAL A1721 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR A1723 " --> pdb=" O LEU A1731 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LEU A1731 " --> pdb=" O MET A1747 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN A1741 " --> pdb=" O LEU A1737 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA A1757 " --> pdb=" O MET A1748 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N VAL A1756 " --> pdb=" O THR A1821 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 1575 through 1578 removed outlier: 6.237A pdb=" N VAL A1678 " --> pdb=" O LEU A1682 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU A1682 " --> pdb=" O VAL A1678 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 1871 through 1877 removed outlier: 3.708A pdb=" N LYS A1881 " --> pdb=" O SER A1877 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A1895 " --> pdb=" O VAL A1886 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N VAL A1894 " --> pdb=" O TYR A1910 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N VAL A1900 " --> pdb=" O ASN A1904 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASN A1904 " --> pdb=" O VAL A1900 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ILE A1919 " --> pdb=" O SER A1951 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER A1962 " --> pdb=" O LYS A1952 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N THR A1961 " --> pdb=" O PHE A1973 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG A1970 " --> pdb=" O TYR A1987 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ARG A1982 " --> pdb=" O TYR A1998 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TYR A1998 " --> pdb=" O ARG A1982 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLN A1984 " --> pdb=" O ILE A1996 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE A1996 " --> pdb=" O GLN A1984 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N HIS A1986 " --> pdb=" O ASP A1994 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N CYS A2008 " --> pdb=" O PHE A2042 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN A2012 " --> pdb=" O GLN A2038 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N GLN A2038 " --> pdb=" O GLN A2012 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A2063 " --> pdb=" O ALA A2039 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG A2083 " --> pdb=" O PHE A2074 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ILE A2082 " --> pdb=" O TYR A2099 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A2095 " --> pdb=" O TYR A2086 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N SER A2096 " --> pdb=" O PRO A2112 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU A2102 " --> pdb=" O VAL A2106 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N VAL A2106 " --> pdb=" O GLU A2102 " (cutoff:3.500A) removed outlier: 11.192A pdb=" N LYS A2105 " --> pdb=" O HIS A2126 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N HIS A2126 " --> pdb=" O LYS A2105 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N SER A2107 " --> pdb=" O TYR A2124 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU A2120 " --> pdb=" O TYR A2111 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N PHE A2113 " --> pdb=" O LYS A2118 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LYS A2118 " --> pdb=" O PHE A2113 " (cutoff:3.500A) removed outlier: 10.346A pdb=" N GLN A2119 " --> pdb=" O GLU A2139 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU A2139 " --> pdb=" O GLN A2119 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE A2121 " --> pdb=" O ARG A2137 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ARG A2137 " --> pdb=" O ILE A2121 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LYS A2123 " --> pdb=" O VAL A2135 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL A2135 " --> pdb=" O LYS A2123 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LYS A2125 " --> pdb=" O VAL A2133 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N VAL A2133 " --> pdb=" O GLY A2153 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLY A2153 " --> pdb=" O VAL A2133 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A2135 " --> pdb=" O ILE A2151 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N THR A2163 " --> pdb=" O TYR A2178 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR A2177 " --> pdb=" O ILE A2189 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE A2189 " --> pdb=" O THR A2177 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LYS A2179 " --> pdb=" O VAL A2187 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL A2187 " --> pdb=" O LEU A2198 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR A2307 " --> pdb=" O PHE A2220 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A2468 " --> pdb=" O ALA A2322 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE A2503 " --> pdb=" O LYS A2512 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 2373 through 2374 removed outlier: 4.483A pdb=" N LYS A2433 " --> pdb=" O GLU A2374 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 2514 through 2516 Processing sheet with id=AD7, first strand: chain 'A' and resid 2530 through 2535 removed outlier: 3.714A pdb=" N LYS A2532 " --> pdb=" O GLU A2546 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N SER A2543 " --> pdb=" O PHE A2556 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR A2553 " --> pdb=" O VAL A2569 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL A2569 " --> pdb=" O THR A2553 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLU A2555 " --> pdb=" O LYS A2567 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS A2567 " --> pdb=" O GLU A2555 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLY A2557 " --> pdb=" O THR A2565 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N THR A2565 " --> pdb=" O TYR A2581 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR A2581 " --> pdb=" O THR A2565 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LYS A2567 " --> pdb=" O VAL A2579 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL A2579 " --> pdb=" O LYS A2567 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL A2569 " --> pdb=" O ILE A2577 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A2592 " --> pdb=" O VAL A2583 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LEU A2591 " --> pdb=" O TYR A2614 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL A2611 " --> pdb=" O ARG A2626 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ARG A2626 " --> pdb=" O VAL A2611 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ALA A2613 " --> pdb=" O PHE A2624 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE A2624 " --> pdb=" O ALA A2613 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE A2615 " --> pdb=" O LEU A2622 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LEU A2622 " --> pdb=" O VAL A2633 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ARG A2642 " --> pdb=" O ALA A2653 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA A2653 " --> pdb=" O ARG A2642 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL A2644 " --> pdb=" O VAL A2651 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 2683 through 2684 removed outlier: 3.572A pdb=" N LEU A2689 " --> pdb=" O ASP A2684 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A2703 " --> pdb=" O ASP A2698 " (cutoff:3.500A) 842 hydrogen bonds defined for protein. 2250 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: 9.58 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6970 1.34 - 1.46: 4170 1.46 - 1.58: 12629 1.58 - 1.70: 0 1.70 - 1.81: 127 Bond restraints: 23896 Sorted by residual: bond pdb=" CA PRO A 100 " pdb=" C PRO A 100 " ideal model delta sigma weight residual 1.517 1.540 -0.023 9.30e-03 1.16e+04 6.04e+00 bond pdb=" N GLU A 97 " pdb=" CA GLU A 97 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.13e-02 7.83e+03 5.61e+00 bond pdb=" N ASP A 99 " pdb=" CA ASP A 99 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.41e-02 5.03e+03 5.25e+00 bond pdb=" C PRO A 100 " pdb=" O PRO A 100 " ideal model delta sigma weight residual 1.240 1.216 0.024 1.12e-02 7.97e+03 4.61e+00 bond pdb=" C PHE A2857 " pdb=" N PRO A2858 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.50e+00 ... (remaining 23891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 31087 2.10 - 4.20: 1058 4.20 - 6.30: 125 6.30 - 8.39: 43 8.39 - 10.49: 6 Bond angle restraints: 32319 Sorted by residual: angle pdb=" CA TYR A2483 " pdb=" CB TYR A2483 " pdb=" CG TYR A2483 " ideal model delta sigma weight residual 113.90 122.01 -8.11 1.80e+00 3.09e-01 2.03e+01 angle pdb=" N PRO A 100 " pdb=" CA PRO A 100 " pdb=" C PRO A 100 " ideal model delta sigma weight residual 110.70 116.15 -5.45 1.22e+00 6.72e-01 1.99e+01 angle pdb=" N ASN A 162 " pdb=" CA ASN A 162 " pdb=" C ASN A 162 " ideal model delta sigma weight residual 109.81 118.93 -9.12 2.21e+00 2.05e-01 1.70e+01 angle pdb=" C LYS A2328 " pdb=" N GLU A2329 " pdb=" CA GLU A2329 " ideal model delta sigma weight residual 120.38 126.12 -5.74 1.46e+00 4.69e-01 1.54e+01 angle pdb=" CA ARG A 517 " pdb=" CB ARG A 517 " pdb=" CG ARG A 517 " ideal model delta sigma weight residual 114.10 121.94 -7.84 2.00e+00 2.50e-01 1.53e+01 ... (remaining 32314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 12362 17.91 - 35.81: 1490 35.81 - 53.72: 372 53.72 - 71.63: 83 71.63 - 89.53: 36 Dihedral angle restraints: 14343 sinusoidal: 5805 harmonic: 8538 Sorted by residual: dihedral pdb=" CB CYS A2253 " pdb=" SG CYS A2253 " pdb=" SG CYS A2285 " pdb=" CB CYS A2285 " ideal model delta sinusoidal sigma weight residual 93.00 163.56 -70.56 1 1.00e+01 1.00e-02 6.41e+01 dihedral pdb=" CA SER A 512 " pdb=" C SER A 512 " pdb=" N ASP A 513 " pdb=" CA ASP A 513 " ideal model delta harmonic sigma weight residual 180.00 151.20 28.80 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA LYS A1153 " pdb=" C LYS A1153 " pdb=" N TYR A1154 " pdb=" CA TYR A1154 " ideal model delta harmonic sigma weight residual -180.00 -152.23 -27.77 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 14340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3002 0.078 - 0.156: 490 0.156 - 0.234: 27 0.234 - 0.312: 2 0.312 - 0.390: 2 Chirality restraints: 3523 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.21e+01 chirality pdb=" CB ILE A1261 " pdb=" CA ILE A1261 " pdb=" CG1 ILE A1261 " pdb=" CG2 ILE A1261 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CB ILE A 288 " pdb=" CA ILE A 288 " pdb=" CG1 ILE A 288 " pdb=" CG2 ILE A 288 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.86e+00 ... (remaining 3520 not shown) Planarity restraints: 4166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " -0.304 2.00e-02 2.50e+03 2.59e-01 8.37e+02 pdb=" C7 NAG B 2 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " -0.181 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " 0.449 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.154 2.00e-02 2.50e+03 1.27e-01 2.03e+02 pdb=" C7 NAG B 1 " -0.042 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.114 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.205 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A4001 " -0.084 2.00e-02 2.50e+03 7.01e-02 6.15e+01 pdb=" C7 NAG A4001 " 0.021 2.00e-02 2.50e+03 pdb=" C8 NAG A4001 " -0.063 2.00e-02 2.50e+03 pdb=" N2 NAG A4001 " 0.114 2.00e-02 2.50e+03 pdb=" O7 NAG A4001 " 0.014 2.00e-02 2.50e+03 ... (remaining 4163 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2940 2.76 - 3.29: 21193 3.29 - 3.83: 37258 3.83 - 4.36: 44284 4.36 - 4.90: 78987 Nonbonded interactions: 184662 Sorted by model distance: nonbonded pdb=" OG1 THR A 65 " pdb=" OE1 GLU A2251 " model vdw 2.224 3.040 nonbonded pdb=" OH TYR A1723 " pdb=" O PHE A1777 " model vdw 2.275 3.040 nonbonded pdb=" OH TYR A2099 " pdb=" OD2 ASP A2585 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR A1403 " pdb=" O VAL A1471 " model vdw 2.290 3.040 nonbonded pdb=" OH TYR A1998 " pdb=" OE2 GLU A2009 " model vdw 2.299 3.040 ... (remaining 184657 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 24.230 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 23903 Z= 0.200 Angle : 0.886 10.662 32336 Z= 0.480 Chirality : 0.056 0.390 3523 Planarity : 0.009 0.259 4164 Dihedral : 17.152 89.534 8877 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.67 % Allowed : 22.47 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.14), residues: 2922 helix: -1.19 (0.26), residues: 304 sheet: -0.46 (0.16), residues: 967 loop : -1.71 (0.13), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG A1017 TYR 0.041 0.003 TYR A2581 PHE 0.031 0.002 PHE A1400 TRP 0.028 0.002 TRP A1414 HIS 0.012 0.002 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 (23896) covalent geometry : angle 0.88166 / 0.48 (32319) SS BOND : bond 0.00421 / 0.21 ( 4) SS BOND : angle 2.05634 / 0.92 ( 8) hydrogen bonds : bond 0.14514 / 9.34 ( 791) hydrogen bonds : angle 8.03502 / 5.41 ( 2250) link_BETA1-4 : bond 0.00153 / 0.08 ( 1) link_BETA1-4 : angle 0.73957 / 0.38 ( 3) link_NAG-ASN : bond 0.00475 / 0.23 ( 2) link_NAG-ASN : angle 5.98978 / 2.91 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 328 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7631 (ttp80) cc_final: 0.7425 (ttp80) REVERT: A 67 LEU cc_start: 0.9070 (mp) cc_final: 0.8675 (mp) REVERT: A 86 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7175 (pt) REVERT: A 262 ARG cc_start: 0.7512 (tmm160) cc_final: 0.7305 (tpt-90) REVERT: A 751 GLN cc_start: 0.7482 (tp40) cc_final: 0.7205 (mt0) REVERT: A 840 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7039 (mt-10) REVERT: A 1142 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7572 (tp) REVERT: A 1458 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7058 (tpt90) REVERT: A 1788 ASN cc_start: 0.6610 (p0) cc_final: 0.6396 (p0) REVERT: A 1959 PHE cc_start: 0.4369 (t80) cc_final: 0.3736 (t80) REVERT: A 2044 TYR cc_start: 0.7491 (m-80) cc_final: 0.7145 (m-10) REVERT: A 2129 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7772 (ttt180) REVERT: A 2500 ILE cc_start: 0.9025 (mt) cc_final: 0.8814 (mt) REVERT: A 2549 ASP cc_start: 0.7014 (p0) cc_final: 0.6796 (p0) REVERT: A 2861 PHE cc_start: 0.6401 (p90) cc_final: 0.5806 (p90) REVERT: A 2893 TYR cc_start: 0.6912 (OUTLIER) cc_final: 0.5389 (m-80) REVERT: A 3029 MET cc_start: 0.6726 (ppp) cc_final: 0.6216 (tmm) outliers start: 17 outliers final: 5 residues processed: 339 average time/residue: 0.1878 time to fit residues: 96.5338 Evaluate side-chains 259 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 249 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 747 PHE Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1453 VAL Chi-restraints excluded: chain A residue 1458 ARG Chi-restraints excluded: chain A residue 1919 ILE Chi-restraints excluded: chain A residue 2129 ARG Chi-restraints excluded: chain A residue 2291 TRP Chi-restraints excluded: chain A residue 2893 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 197 optimal weight: 0.2980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 GLN A 638 GLN A 838 HIS A1083 GLN A1489 HIS A2727 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.152399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.128901 restraints weight = 37908.429| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.97 r_work: 0.3569 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23903 Z= 0.124 Angle : 0.603 8.361 32336 Z= 0.321 Chirality : 0.045 0.170 3523 Planarity : 0.004 0.073 4164 Dihedral : 5.728 57.619 3230 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.08 % Allowed : 24.04 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.15), residues: 2922 helix: -0.04 (0.28), residues: 314 sheet: -0.35 (0.17), residues: 953 loop : -1.51 (0.14), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1057 TYR 0.017 0.001 TYR A2483 PHE 0.016 0.001 PHE A 908 TRP 0.017 0.001 TRP A1677 HIS 0.009 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (23896) covalent geometry : angle 0.59848 / 0.32 (32319) SS BOND : bond 0.01186 / 0.57 ( 4) SS BOND : angle 1.92920 / 0.87 ( 8) hydrogen bonds : bond 0.04201 / 2.78 ( 791) hydrogen bonds : angle 6.31124 / 4.28 ( 2250) link_BETA1-4 : bond 0.01622 / 0.85 ( 1) link_BETA1-4 : angle 2.30513 / 1.28 ( 3) link_NAG-ASN : bond 0.01427 / 0.68 ( 2) link_NAG-ASN : angle 5.07941 / 2.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 271 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8973 (mp) cc_final: 0.8681 (mt) REVERT: A 69 HIS cc_start: 0.7267 (m90) cc_final: 0.7043 (m90) REVERT: A 751 GLN cc_start: 0.7653 (tp40) cc_final: 0.7266 (mt0) REVERT: A 1031 TYR cc_start: 0.7245 (t80) cc_final: 0.6773 (t80) REVERT: A 1040 LYS cc_start: 0.8500 (mttt) cc_final: 0.8189 (tptt) REVERT: A 1080 ASN cc_start: 0.8553 (t0) cc_final: 0.8214 (t0) REVERT: A 1312 GLU cc_start: 0.6003 (tp30) cc_final: 0.5792 (mm-30) REVERT: A 1788 ASN cc_start: 0.6799 (p0) cc_final: 0.6570 (p0) REVERT: A 2044 TYR cc_start: 0.7554 (m-80) cc_final: 0.7226 (m-10) REVERT: A 2100 LEU cc_start: 0.8066 (tt) cc_final: 0.7818 (tt) REVERT: A 2460 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7410 (pp-130) REVERT: A 2549 ASP cc_start: 0.7154 (p0) cc_final: 0.6854 (p0) REVERT: A 2638 GLU cc_start: 0.7743 (tt0) cc_final: 0.7512 (tt0) REVERT: A 2757 ASN cc_start: 0.8555 (OUTLIER) cc_final: 0.8320 (t0) REVERT: A 2857 PHE cc_start: 0.5889 (p90) cc_final: 0.5503 (p90) REVERT: A 2861 PHE cc_start: 0.6725 (p90) cc_final: 0.6185 (p90) REVERT: A 2893 TYR cc_start: 0.6829 (OUTLIER) cc_final: 0.5227 (m-80) REVERT: A 2912 LYS cc_start: 0.6924 (mtpt) cc_final: 0.6172 (mttm) outliers start: 53 outliers final: 27 residues processed: 307 average time/residue: 0.1700 time to fit residues: 81.5740 Evaluate side-chains 274 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 244 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain A residue 1342 TYR Chi-restraints excluded: chain A residue 1349 VAL Chi-restraints excluded: chain A residue 1361 THR Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1453 VAL Chi-restraints excluded: chain A residue 1684 ILE Chi-restraints excluded: chain A residue 2162 VAL Chi-restraints excluded: chain A residue 2171 ASP Chi-restraints excluded: chain A residue 2173 LYS Chi-restraints excluded: chain A residue 2253 CYS Chi-restraints excluded: chain A residue 2291 TRP Chi-restraints excluded: chain A residue 2408 THR Chi-restraints excluded: chain A residue 2460 MET Chi-restraints excluded: chain A residue 2481 VAL Chi-restraints excluded: chain A residue 2542 VAL Chi-restraints excluded: chain A residue 2662 MET Chi-restraints excluded: chain A residue 2757 ASN Chi-restraints excluded: chain A residue 2893 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 239 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 245 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 220 optimal weight: 2.9990 chunk 272 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 262 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 833 HIS A1334 HIS A1741 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.146598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.122954 restraints weight = 38417.148| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.96 r_work: 0.3490 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 23903 Z= 0.267 Angle : 0.679 7.649 32336 Z= 0.360 Chirality : 0.049 0.192 3523 Planarity : 0.005 0.069 4164 Dihedral : 5.623 56.991 3216 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.61 % Favored : 94.35 % Rotamer: Outliers : 5.11 % Allowed : 23.21 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.15), residues: 2922 helix: 0.09 (0.29), residues: 328 sheet: -0.38 (0.16), residues: 972 loop : -1.56 (0.14), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A2137 TYR 0.018 0.002 TYR A2631 PHE 0.020 0.002 PHE A1400 TRP 0.027 0.002 TRP A1577 HIS 0.007 0.001 HIS A2479 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.27 (23896) covalent geometry : angle 0.67396 / 0.36 (32319) SS BOND : bond 0.00723 / 0.37 ( 4) SS BOND : angle 3.22021 / 1.39 ( 8) hydrogen bonds : bond 0.04531 / 3.01 ( 791) hydrogen bonds : angle 6.23853 / 4.22 ( 2250) link_BETA1-4 : bond 0.00978 / 0.51 ( 1) link_BETA1-4 : angle 1.32939 / 0.72 ( 3) link_NAG-ASN : bond 0.01203 / 0.58 ( 2) link_NAG-ASN : angle 5.01710 / 2.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 254 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6853 (pt) REVERT: A 333 GLU cc_start: 0.7898 (tt0) cc_final: 0.7571 (mm-30) REVERT: A 523 ASN cc_start: 0.7938 (t0) cc_final: 0.7546 (m-40) REVERT: A 751 GLN cc_start: 0.7808 (tp40) cc_final: 0.7020 (mt0) REVERT: A 963 ARG cc_start: 0.7871 (ptm160) cc_final: 0.7624 (ptm160) REVERT: A 1031 TYR cc_start: 0.7236 (t80) cc_final: 0.6895 (t80) REVERT: A 1040 LYS cc_start: 0.8509 (mttt) cc_final: 0.8206 (tptt) REVERT: A 1080 ASN cc_start: 0.8688 (t0) cc_final: 0.8352 (t0) REVERT: A 1183 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8110 (m-30) REVERT: A 1282 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.7011 (t0) REVERT: A 1333 TYR cc_start: 0.7447 (OUTLIER) cc_final: 0.5489 (t80) REVERT: A 1355 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7061 (tt0) REVERT: A 1379 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7220 (mt-10) REVERT: A 1718 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8576 (mt-10) REVERT: A 1788 ASN cc_start: 0.6816 (p0) cc_final: 0.6608 (p0) REVERT: A 1831 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.7139 (ptp-170) REVERT: A 1959 PHE cc_start: 0.5601 (t80) cc_final: 0.4297 (t80) REVERT: A 2044 TYR cc_start: 0.7746 (m-80) cc_final: 0.7474 (m-10) REVERT: A 2122 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9149 (mt) REVERT: A 2318 GLU cc_start: 0.8765 (pm20) cc_final: 0.8498 (pm20) REVERT: A 2460 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7417 (pp-130) REVERT: A 2549 ASP cc_start: 0.7136 (p0) cc_final: 0.6755 (p0) REVERT: A 2638 GLU cc_start: 0.8149 (tt0) cc_final: 0.7916 (tt0) REVERT: A 2692 TYR cc_start: 0.8476 (t80) cc_final: 0.8209 (t80) REVERT: A 2822 LEU cc_start: 0.6443 (OUTLIER) cc_final: 0.5649 (mp) REVERT: A 2857 PHE cc_start: 0.5721 (p90) cc_final: 0.5322 (p90) REVERT: A 2861 PHE cc_start: 0.7162 (OUTLIER) cc_final: 0.6630 (p90) REVERT: A 2893 TYR cc_start: 0.7174 (OUTLIER) cc_final: 0.5445 (m-80) REVERT: A 2912 LYS cc_start: 0.7059 (mtpt) cc_final: 0.6283 (mmtm) outliers start: 130 outliers final: 90 residues processed: 350 average time/residue: 0.1556 time to fit residues: 85.7458 Evaluate side-chains 345 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 242 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 747 PHE Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1131 THR Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1183 ASP Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain A residue 1249 VAL Chi-restraints excluded: chain A residue 1260 THR Chi-restraints excluded: chain A residue 1263 VAL Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1329 ASP Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1342 TYR Chi-restraints excluded: chain A residue 1349 VAL Chi-restraints excluded: chain A residue 1355 GLU Chi-restraints excluded: chain A residue 1361 THR Chi-restraints excluded: chain A residue 1379 GLU Chi-restraints excluded: chain A residue 1386 ASN Chi-restraints excluded: chain A residue 1408 ASN Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1426 THR Chi-restraints excluded: chain A residue 1442 THR Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1453 VAL Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1525 LEU Chi-restraints excluded: chain A residue 1569 ILE Chi-restraints excluded: chain A residue 1610 ILE Chi-restraints excluded: chain A residue 1629 SER Chi-restraints excluded: chain A residue 1637 THR Chi-restraints excluded: chain A residue 1645 VAL Chi-restraints excluded: chain A residue 1650 VAL Chi-restraints excluded: chain A residue 1656 THR Chi-restraints excluded: chain A residue 1682 LEU Chi-restraints excluded: chain A residue 1684 ILE Chi-restraints excluded: chain A residue 1718 GLU Chi-restraints excluded: chain A residue 1798 THR Chi-restraints excluded: chain A residue 1805 VAL Chi-restraints excluded: chain A residue 1811 THR Chi-restraints excluded: chain A residue 1831 ARG Chi-restraints excluded: chain A residue 1834 VAL Chi-restraints excluded: chain A residue 1919 ILE Chi-restraints excluded: chain A residue 2000 LEU Chi-restraints excluded: chain A residue 2107 SER Chi-restraints excluded: chain A residue 2122 LEU Chi-restraints excluded: chain A residue 2151 ILE Chi-restraints excluded: chain A residue 2171 ASP Chi-restraints excluded: chain A residue 2173 LYS Chi-restraints excluded: chain A residue 2181 VAL Chi-restraints excluded: chain A residue 2194 LEU Chi-restraints excluded: chain A residue 2195 THR Chi-restraints excluded: chain A residue 2241 VAL Chi-restraints excluded: chain A residue 2253 CYS Chi-restraints excluded: chain A residue 2291 TRP Chi-restraints excluded: chain A residue 2326 VAL Chi-restraints excluded: chain A residue 2384 VAL Chi-restraints excluded: chain A residue 2408 THR Chi-restraints excluded: chain A residue 2460 MET Chi-restraints excluded: chain A residue 2515 VAL Chi-restraints excluded: chain A residue 2542 VAL Chi-restraints excluded: chain A residue 2610 THR Chi-restraints excluded: chain A residue 2640 SER Chi-restraints excluded: chain A residue 2707 MET Chi-restraints excluded: chain A residue 2711 GLU Chi-restraints excluded: chain A residue 2726 SER Chi-restraints excluded: chain A residue 2822 LEU Chi-restraints excluded: chain A residue 2861 PHE Chi-restraints excluded: chain A residue 2862 VAL Chi-restraints excluded: chain A residue 2884 MET Chi-restraints excluded: chain A residue 2885 VAL Chi-restraints excluded: chain A residue 2893 TYR Chi-restraints excluded: chain A residue 2906 ILE Chi-restraints excluded: chain A residue 2985 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 21 optimal weight: 1.9990 chunk 280 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 8 optimal weight: 8.9990 chunk 177 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 274 optimal weight: 1.9990 chunk 290 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 236 ASN A2757 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.149200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.126221 restraints weight = 37554.892| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.92 r_work: 0.3546 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 23903 Z= 0.125 Angle : 0.585 10.109 32336 Z= 0.307 Chirality : 0.045 0.180 3523 Planarity : 0.004 0.058 4164 Dihedral : 5.295 54.118 3216 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.36 % Allowed : 24.78 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.15), residues: 2922 helix: 0.37 (0.30), residues: 321 sheet: -0.39 (0.16), residues: 986 loop : -1.42 (0.14), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2354 TYR 0.016 0.001 TYR A1452 PHE 0.019 0.001 PHE A2004 TRP 0.017 0.001 TRP A1677 HIS 0.003 0.001 HIS A1489 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (23896) covalent geometry : angle 0.57838 / 0.31 (32319) SS BOND : bond 0.00639 / 0.31 ( 4) SS BOND : angle 3.01510 / 1.27 ( 8) hydrogen bonds : bond 0.03551 / 2.36 ( 791) hydrogen bonds : angle 5.84282 / 3.96 ( 2250) link_BETA1-4 : bond 0.00622 / 0.33 ( 1) link_BETA1-4 : angle 1.54545 / 0.84 ( 3) link_NAG-ASN : bond 0.01755 / 0.84 ( 2) link_NAG-ASN : angle 5.49552 / 2.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 260 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 33 PHE cc_start: 0.5431 (OUTLIER) cc_final: 0.5153 (t80) REVERT: A 471 MET cc_start: 0.8383 (ptp) cc_final: 0.8169 (ptp) REVERT: A 523 ASN cc_start: 0.7853 (t0) cc_final: 0.7513 (m-40) REVERT: A 723 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8014 (pp) REVERT: A 751 GLN cc_start: 0.7788 (tp40) cc_final: 0.6980 (mt0) REVERT: A 1040 LYS cc_start: 0.8393 (mttt) cc_final: 0.8140 (tptp) REVERT: A 1080 ASN cc_start: 0.8763 (t0) cc_final: 0.8424 (t0) REVERT: A 1282 ASP cc_start: 0.7173 (OUTLIER) cc_final: 0.6922 (t0) REVERT: A 1312 GLU cc_start: 0.5734 (tp30) cc_final: 0.5328 (tp30) REVERT: A 1333 TYR cc_start: 0.7334 (OUTLIER) cc_final: 0.5313 (t80) REVERT: A 1355 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.7134 (tt0) REVERT: A 1379 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7146 (mt-10) REVERT: A 1718 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8543 (mt-10) REVERT: A 1959 PHE cc_start: 0.5142 (OUTLIER) cc_final: 0.3759 (t80) REVERT: A 2044 TYR cc_start: 0.7692 (m-80) cc_final: 0.7318 (m-10) REVERT: A 2319 LEU cc_start: 0.9007 (tt) cc_final: 0.8797 (tt) REVERT: A 2460 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7292 (pp-130) REVERT: A 2549 ASP cc_start: 0.7151 (p0) cc_final: 0.6764 (p0) REVERT: A 2822 LEU cc_start: 0.6359 (OUTLIER) cc_final: 0.5688 (mp) REVERT: A 2857 PHE cc_start: 0.5818 (p90) cc_final: 0.5422 (p90) REVERT: A 2861 PHE cc_start: 0.7160 (OUTLIER) cc_final: 0.6657 (p90) REVERT: A 2893 TYR cc_start: 0.7041 (OUTLIER) cc_final: 0.5351 (m-80) REVERT: A 2912 LYS cc_start: 0.6929 (mtpt) cc_final: 0.6209 (mmtm) outliers start: 111 outliers final: 68 residues processed: 340 average time/residue: 0.1507 time to fit residues: 79.9927 Evaluate side-chains 328 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 248 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 747 PHE Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1131 THR Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1329 ASP Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1342 TYR Chi-restraints excluded: chain A residue 1349 VAL Chi-restraints excluded: chain A residue 1355 GLU Chi-restraints excluded: chain A residue 1361 THR Chi-restraints excluded: chain A residue 1379 GLU Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1453 VAL Chi-restraints excluded: chain A residue 1492 LEU Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1554 ASN Chi-restraints excluded: chain A residue 1610 ILE Chi-restraints excluded: chain A residue 1621 CYS Chi-restraints excluded: chain A residue 1637 THR Chi-restraints excluded: chain A residue 1650 VAL Chi-restraints excluded: chain A residue 1682 LEU Chi-restraints excluded: chain A residue 1684 ILE Chi-restraints excluded: chain A residue 1718 GLU Chi-restraints excluded: chain A residue 1737 LEU Chi-restraints excluded: chain A residue 1752 ILE Chi-restraints excluded: chain A residue 1834 VAL Chi-restraints excluded: chain A residue 1959 PHE Chi-restraints excluded: chain A residue 2151 ILE Chi-restraints excluded: chain A residue 2171 ASP Chi-restraints excluded: chain A residue 2173 LYS Chi-restraints excluded: chain A residue 2181 VAL Chi-restraints excluded: chain A residue 2194 LEU Chi-restraints excluded: chain A residue 2241 VAL Chi-restraints excluded: chain A residue 2253 CYS Chi-restraints excluded: chain A residue 2287 THR Chi-restraints excluded: chain A residue 2291 TRP Chi-restraints excluded: chain A residue 2326 VAL Chi-restraints excluded: chain A residue 2408 THR Chi-restraints excluded: chain A residue 2460 MET Chi-restraints excluded: chain A residue 2481 VAL Chi-restraints excluded: chain A residue 2514 ILE Chi-restraints excluded: chain A residue 2542 VAL Chi-restraints excluded: chain A residue 2610 THR Chi-restraints excluded: chain A residue 2640 SER Chi-restraints excluded: chain A residue 2662 MET Chi-restraints excluded: chain A residue 2822 LEU Chi-restraints excluded: chain A residue 2861 PHE Chi-restraints excluded: chain A residue 2862 VAL Chi-restraints excluded: chain A residue 2885 VAL Chi-restraints excluded: chain A residue 2893 TYR Chi-restraints excluded: chain A residue 2906 ILE Chi-restraints excluded: chain A residue 2985 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 137 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 175 optimal weight: 0.2980 chunk 243 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 288 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 193 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1374 ASN A2727 GLN A2733 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.150608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.127656 restraints weight = 37598.945| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.90 r_work: 0.3561 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 23903 Z= 0.114 Angle : 0.567 9.907 32336 Z= 0.297 Chirality : 0.045 0.211 3523 Planarity : 0.004 0.054 4164 Dihedral : 5.094 50.289 3216 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.60 % Allowed : 24.71 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.15), residues: 2922 helix: 0.53 (0.30), residues: 321 sheet: -0.34 (0.16), residues: 978 loop : -1.35 (0.14), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2354 TYR 0.024 0.001 TYR A1031 PHE 0.022 0.001 PHE A 908 TRP 0.016 0.001 TRP A1677 HIS 0.003 0.001 HIS A2516 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (23896) covalent geometry : angle 0.55977 / 0.30 (32319) SS BOND : bond 0.00977 / 0.47 ( 4) SS BOND : angle 3.33678 / 1.43 ( 8) hydrogen bonds : bond 0.03365 / 2.23 ( 791) hydrogen bonds : angle 5.58382 / 3.78 ( 2250) link_BETA1-4 : bond 0.00366 / 0.19 ( 1) link_BETA1-4 : angle 1.37606 / 0.75 ( 3) link_NAG-ASN : bond 0.01266 / 0.60 ( 2) link_NAG-ASN : angle 5.45638 / 2.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 270 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 33 PHE cc_start: 0.5483 (OUTLIER) cc_final: 0.5199 (t80) REVERT: A 67 LEU cc_start: 0.8896 (mp) cc_final: 0.8673 (mt) REVERT: A 77 THR cc_start: 0.8374 (m) cc_final: 0.8082 (m) REVERT: A 523 ASN cc_start: 0.7827 (t0) cc_final: 0.7500 (m-40) REVERT: A 723 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.7930 (pp) REVERT: A 729 VAL cc_start: 0.8297 (OUTLIER) cc_final: 0.8094 (m) REVERT: A 751 GLN cc_start: 0.7826 (tp40) cc_final: 0.7001 (mt0) REVERT: A 901 ILE cc_start: 0.7011 (tt) cc_final: 0.6693 (mm) REVERT: A 1040 LYS cc_start: 0.8386 (mttt) cc_final: 0.8142 (tptt) REVERT: A 1080 ASN cc_start: 0.8683 (t0) cc_final: 0.8372 (t0) REVERT: A 1119 ASP cc_start: 0.7267 (OUTLIER) cc_final: 0.7054 (t0) REVERT: A 1282 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6836 (t0) REVERT: A 1312 GLU cc_start: 0.6101 (tp30) cc_final: 0.4384 (mp0) REVERT: A 1379 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7144 (mt-10) REVERT: A 1718 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8556 (mt-10) REVERT: A 1724 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8471 (mt) REVERT: A 1959 PHE cc_start: 0.5021 (OUTLIER) cc_final: 0.3736 (t80) REVERT: A 2044 TYR cc_start: 0.7704 (m-80) cc_final: 0.7367 (m-10) REVERT: A 2122 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9140 (mt) REVERT: A 2319 LEU cc_start: 0.9000 (tt) cc_final: 0.8772 (tt) REVERT: A 2361 ARG cc_start: 0.5965 (ppt170) cc_final: 0.5118 (mmp80) REVERT: A 2549 ASP cc_start: 0.7469 (p0) cc_final: 0.7021 (p0) REVERT: A 2638 GLU cc_start: 0.8051 (tt0) cc_final: 0.7729 (tt0) REVERT: A 2707 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8260 (mtm) REVERT: A 2822 LEU cc_start: 0.6088 (OUTLIER) cc_final: 0.5396 (mp) REVERT: A 2835 LYS cc_start: 0.5490 (pttm) cc_final: 0.5025 (ptpt) REVERT: A 2845 ASN cc_start: 0.8889 (m-40) cc_final: 0.8643 (m-40) REVERT: A 2857 PHE cc_start: 0.5767 (p90) cc_final: 0.5407 (p90) REVERT: A 2861 PHE cc_start: 0.7164 (OUTLIER) cc_final: 0.6711 (p90) REVERT: A 2875 LEU cc_start: 0.7645 (tp) cc_final: 0.7387 (tp) REVERT: A 2889 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7061 (mt) REVERT: A 2893 TYR cc_start: 0.7053 (OUTLIER) cc_final: 0.5569 (m-80) REVERT: A 2912 LYS cc_start: 0.6863 (mtpt) cc_final: 0.6235 (mmtm) outliers start: 117 outliers final: 78 residues processed: 358 average time/residue: 0.1605 time to fit residues: 91.0921 Evaluate side-chains 332 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 239 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 747 PHE Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1119 ASP Chi-restraints excluded: chain A residue 1131 THR Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1329 ASP Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1342 TYR Chi-restraints excluded: chain A residue 1349 VAL Chi-restraints excluded: chain A residue 1361 THR Chi-restraints excluded: chain A residue 1379 GLU Chi-restraints excluded: chain A residue 1408 ASN Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1414 TRP Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1453 VAL Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1554 ASN Chi-restraints excluded: chain A residue 1610 ILE Chi-restraints excluded: chain A residue 1621 CYS Chi-restraints excluded: chain A residue 1637 THR Chi-restraints excluded: chain A residue 1650 VAL Chi-restraints excluded: chain A residue 1682 LEU Chi-restraints excluded: chain A residue 1684 ILE Chi-restraints excluded: chain A residue 1718 GLU Chi-restraints excluded: chain A residue 1724 LEU Chi-restraints excluded: chain A residue 1752 ILE Chi-restraints excluded: chain A residue 1798 THR Chi-restraints excluded: chain A residue 1805 VAL Chi-restraints excluded: chain A residue 1834 VAL Chi-restraints excluded: chain A residue 1959 PHE Chi-restraints excluded: chain A residue 2088 SER Chi-restraints excluded: chain A residue 2122 LEU Chi-restraints excluded: chain A residue 2151 ILE Chi-restraints excluded: chain A residue 2171 ASP Chi-restraints excluded: chain A residue 2173 LYS Chi-restraints excluded: chain A residue 2181 VAL Chi-restraints excluded: chain A residue 2194 LEU Chi-restraints excluded: chain A residue 2241 VAL Chi-restraints excluded: chain A residue 2253 CYS Chi-restraints excluded: chain A residue 2291 TRP Chi-restraints excluded: chain A residue 2331 ASP Chi-restraints excluded: chain A residue 2408 THR Chi-restraints excluded: chain A residue 2481 VAL Chi-restraints excluded: chain A residue 2514 ILE Chi-restraints excluded: chain A residue 2542 VAL Chi-restraints excluded: chain A residue 2610 THR Chi-restraints excluded: chain A residue 2640 SER Chi-restraints excluded: chain A residue 2662 MET Chi-restraints excluded: chain A residue 2707 MET Chi-restraints excluded: chain A residue 2822 LEU Chi-restraints excluded: chain A residue 2861 PHE Chi-restraints excluded: chain A residue 2862 VAL Chi-restraints excluded: chain A residue 2885 VAL Chi-restraints excluded: chain A residue 2889 LEU Chi-restraints excluded: chain A residue 2893 TYR Chi-restraints excluded: chain A residue 2906 ILE Chi-restraints excluded: chain A residue 2985 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 196 optimal weight: 9.9990 chunk 213 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 280 optimal weight: 0.6980 chunk 269 optimal weight: 2.9990 chunk 288 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 290 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 745 ASN A1374 ASN A1872 GLN A1937 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.148173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.124843 restraints weight = 38292.514| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.95 r_work: 0.3521 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 23903 Z= 0.185 Angle : 0.618 9.185 32336 Z= 0.325 Chirality : 0.046 0.248 3523 Planarity : 0.004 0.059 4164 Dihedral : 5.279 52.920 3216 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 5.62 % Allowed : 24.19 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.15), residues: 2922 helix: 0.52 (0.30), residues: 316 sheet: -0.37 (0.16), residues: 963 loop : -1.36 (0.14), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A2137 TYR 0.031 0.002 TYR A1031 PHE 0.032 0.002 PHE A2355 TRP 0.022 0.002 TRP A1577 HIS 0.006 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (23896) covalent geometry : angle 0.61152 / 0.32 (32319) SS BOND : bond 0.00826 / 0.40 ( 4) SS BOND : angle 3.33787 / 1.43 ( 8) hydrogen bonds : bond 0.03769 / 2.49 ( 791) hydrogen bonds : angle 5.68889 / 3.86 ( 2250) link_BETA1-4 : bond 0.00310 / 0.16 ( 1) link_BETA1-4 : angle 1.33481 / 0.73 ( 3) link_NAG-ASN : bond 0.01225 / 0.58 ( 2) link_NAG-ASN : angle 5.38101 / 2.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 243 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: A 33 PHE cc_start: 0.5575 (OUTLIER) cc_final: 0.5198 (t80) REVERT: A 523 ASN cc_start: 0.7878 (t0) cc_final: 0.7560 (m-40) REVERT: A 723 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.7921 (pp) REVERT: A 751 GLN cc_start: 0.7820 (tp40) cc_final: 0.7358 (tp40) REVERT: A 901 ILE cc_start: 0.6902 (tt) cc_final: 0.6647 (mm) REVERT: A 1040 LYS cc_start: 0.8408 (mttt) cc_final: 0.8158 (tptt) REVERT: A 1282 ASP cc_start: 0.7149 (OUTLIER) cc_final: 0.6857 (t0) REVERT: A 1312 GLU cc_start: 0.5814 (tp30) cc_final: 0.5401 (tp30) REVERT: A 1333 TYR cc_start: 0.7324 (OUTLIER) cc_final: 0.5454 (t80) REVERT: A 1379 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7237 (mt-10) REVERT: A 1718 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8637 (mt-10) REVERT: A 1872 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8191 (pt0) REVERT: A 2044 TYR cc_start: 0.7730 (m-80) cc_final: 0.7489 (m-10) REVERT: A 2122 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9140 (mt) REVERT: A 2318 GLU cc_start: 0.8930 (pm20) cc_final: 0.8717 (pm20) REVERT: A 2361 ARG cc_start: 0.6007 (ppt170) cc_final: 0.5633 (ptt180) REVERT: A 2549 ASP cc_start: 0.7409 (p0) cc_final: 0.6934 (p0) REVERT: A 2638 GLU cc_start: 0.8204 (tt0) cc_final: 0.7832 (tt0) REVERT: A 2822 LEU cc_start: 0.6349 (OUTLIER) cc_final: 0.5580 (mp) REVERT: A 2857 PHE cc_start: 0.5935 (p90) cc_final: 0.5578 (p90) REVERT: A 2861 PHE cc_start: 0.7313 (OUTLIER) cc_final: 0.6788 (p90) REVERT: A 2875 LEU cc_start: 0.7609 (tp) cc_final: 0.7357 (tp) REVERT: A 2893 TYR cc_start: 0.7179 (OUTLIER) cc_final: 0.5509 (m-80) REVERT: A 2912 LYS cc_start: 0.6615 (mtpt) cc_final: 0.5935 (mmtm) REVERT: A 2975 ILE cc_start: 0.7530 (mt) cc_final: 0.7267 (mt) outliers start: 143 outliers final: 102 residues processed: 356 average time/residue: 0.1510 time to fit residues: 85.7164 Evaluate side-chains 346 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 233 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 747 PHE Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1131 THR Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1249 VAL Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1263 VAL Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1329 ASP Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1342 TYR Chi-restraints excluded: chain A residue 1349 VAL Chi-restraints excluded: chain A residue 1355 GLU Chi-restraints excluded: chain A residue 1361 THR Chi-restraints excluded: chain A residue 1366 ASN Chi-restraints excluded: chain A residue 1379 GLU Chi-restraints excluded: chain A residue 1408 ASN Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1414 TRP Chi-restraints excluded: chain A residue 1442 THR Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1453 VAL Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1492 LEU Chi-restraints excluded: chain A residue 1495 VAL Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1554 ASN Chi-restraints excluded: chain A residue 1569 ILE Chi-restraints excluded: chain A residue 1610 ILE Chi-restraints excluded: chain A residue 1637 THR Chi-restraints excluded: chain A residue 1645 VAL Chi-restraints excluded: chain A residue 1650 VAL Chi-restraints excluded: chain A residue 1682 LEU Chi-restraints excluded: chain A residue 1684 ILE Chi-restraints excluded: chain A residue 1718 GLU Chi-restraints excluded: chain A residue 1735 LEU Chi-restraints excluded: chain A residue 1752 ILE Chi-restraints excluded: chain A residue 1798 THR Chi-restraints excluded: chain A residue 1805 VAL Chi-restraints excluded: chain A residue 1834 VAL Chi-restraints excluded: chain A residue 1872 GLN Chi-restraints excluded: chain A residue 1911 ILE Chi-restraints excluded: chain A residue 1950 THR Chi-restraints excluded: chain A residue 2088 SER Chi-restraints excluded: chain A residue 2107 SER Chi-restraints excluded: chain A residue 2122 LEU Chi-restraints excluded: chain A residue 2151 ILE Chi-restraints excluded: chain A residue 2171 ASP Chi-restraints excluded: chain A residue 2173 LYS Chi-restraints excluded: chain A residue 2181 VAL Chi-restraints excluded: chain A residue 2194 LEU Chi-restraints excluded: chain A residue 2195 THR Chi-restraints excluded: chain A residue 2233 ILE Chi-restraints excluded: chain A residue 2241 VAL Chi-restraints excluded: chain A residue 2253 CYS Chi-restraints excluded: chain A residue 2272 THR Chi-restraints excluded: chain A residue 2287 THR Chi-restraints excluded: chain A residue 2291 TRP Chi-restraints excluded: chain A residue 2408 THR Chi-restraints excluded: chain A residue 2514 ILE Chi-restraints excluded: chain A residue 2542 VAL Chi-restraints excluded: chain A residue 2578 SER Chi-restraints excluded: chain A residue 2610 THR Chi-restraints excluded: chain A residue 2640 SER Chi-restraints excluded: chain A residue 2707 MET Chi-restraints excluded: chain A residue 2711 GLU Chi-restraints excluded: chain A residue 2822 LEU Chi-restraints excluded: chain A residue 2861 PHE Chi-restraints excluded: chain A residue 2862 VAL Chi-restraints excluded: chain A residue 2885 VAL Chi-restraints excluded: chain A residue 2893 TYR Chi-restraints excluded: chain A residue 2906 ILE Chi-restraints excluded: chain A residue 2985 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 86 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 106 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 248 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1937 GLN A2757 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.149631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.126676 restraints weight = 37893.774| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.90 r_work: 0.3552 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 23903 Z= 0.127 Angle : 0.580 12.297 32336 Z= 0.305 Chirality : 0.045 0.259 3523 Planarity : 0.004 0.057 4164 Dihedral : 5.119 51.269 3216 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.79 % Allowed : 25.10 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.15), residues: 2922 helix: 0.65 (0.30), residues: 314 sheet: -0.31 (0.16), residues: 962 loop : -1.34 (0.14), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2354 TYR 0.029 0.001 TYR A1031 PHE 0.020 0.001 PHE A2004 TRP 0.017 0.001 TRP A1677 HIS 0.003 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (23896) covalent geometry : angle 0.57171 / 0.30 (32319) SS BOND : bond 0.00997 / 0.48 ( 4) SS BOND : angle 3.51341 / 1.50 ( 8) hydrogen bonds : bond 0.03385 / 2.23 ( 791) hydrogen bonds : angle 5.55356 / 3.77 ( 2250) link_BETA1-4 : bond 0.00448 / 0.24 ( 1) link_BETA1-4 : angle 1.61187 / 0.87 ( 3) link_NAG-ASN : bond 0.01580 / 0.75 ( 2) link_NAG-ASN : angle 5.96665 / 2.45 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 254 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7365 (tt) REVERT: A 33 PHE cc_start: 0.5765 (OUTLIER) cc_final: 0.5412 (t80) REVERT: A 523 ASN cc_start: 0.7832 (t0) cc_final: 0.7539 (m-40) REVERT: A 646 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8209 (tptt) REVERT: A 723 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8096 (pt) REVERT: A 751 GLN cc_start: 0.7802 (tp40) cc_final: 0.7383 (tp40) REVERT: A 901 ILE cc_start: 0.6869 (tt) cc_final: 0.6622 (mm) REVERT: A 1040 LYS cc_start: 0.8415 (mttt) cc_final: 0.8157 (tptt) REVERT: A 1049 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6786 (tp30) REVERT: A 1282 ASP cc_start: 0.7081 (OUTLIER) cc_final: 0.6779 (t0) REVERT: A 1312 GLU cc_start: 0.5782 (tp30) cc_final: 0.5357 (tp30) REVERT: A 1379 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7163 (mt-10) REVERT: A 1458 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.6828 (tmm160) REVERT: A 1718 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8608 (mt-10) REVERT: A 1724 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8531 (mt) REVERT: A 1788 ASN cc_start: 0.7043 (p0) cc_final: 0.6799 (p0) REVERT: A 2044 TYR cc_start: 0.7705 (m-80) cc_final: 0.7383 (m-10) REVERT: A 2122 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9135 (mt) REVERT: A 2318 GLU cc_start: 0.8930 (pm20) cc_final: 0.8725 (pm20) REVERT: A 2361 ARG cc_start: 0.6045 (ppt170) cc_final: 0.5655 (ptt180) REVERT: A 2549 ASP cc_start: 0.7485 (p0) cc_final: 0.7024 (p0) REVERT: A 2638 GLU cc_start: 0.8095 (tt0) cc_final: 0.7774 (tt0) REVERT: A 2707 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8280 (mtm) REVERT: A 2711 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7252 (mp0) REVERT: A 2822 LEU cc_start: 0.6359 (OUTLIER) cc_final: 0.5636 (mp) REVERT: A 2857 PHE cc_start: 0.5802 (p90) cc_final: 0.5559 (p90) REVERT: A 2861 PHE cc_start: 0.7230 (OUTLIER) cc_final: 0.6753 (p90) REVERT: A 2875 LEU cc_start: 0.7576 (tp) cc_final: 0.7329 (tp) REVERT: A 2889 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7322 (mt) REVERT: A 2893 TYR cc_start: 0.6817 (OUTLIER) cc_final: 0.5494 (m-80) REVERT: A 2912 LYS cc_start: 0.6539 (mtpt) cc_final: 0.5920 (mmtm) REVERT: A 2975 ILE cc_start: 0.7459 (mt) cc_final: 0.7177 (mt) outliers start: 122 outliers final: 93 residues processed: 347 average time/residue: 0.1670 time to fit residues: 91.0307 Evaluate side-chains 355 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 245 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 747 PHE Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 851 TYR Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1049 GLU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1131 THR Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1249 VAL Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1329 ASP Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1342 TYR Chi-restraints excluded: chain A residue 1349 VAL Chi-restraints excluded: chain A residue 1355 GLU Chi-restraints excluded: chain A residue 1361 THR Chi-restraints excluded: chain A residue 1366 ASN Chi-restraints excluded: chain A residue 1379 GLU Chi-restraints excluded: chain A residue 1408 ASN Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1414 TRP Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1453 VAL Chi-restraints excluded: chain A residue 1458 ARG Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1492 LEU Chi-restraints excluded: chain A residue 1554 ASN Chi-restraints excluded: chain A residue 1569 ILE Chi-restraints excluded: chain A residue 1610 ILE Chi-restraints excluded: chain A residue 1637 THR Chi-restraints excluded: chain A residue 1650 VAL Chi-restraints excluded: chain A residue 1682 LEU Chi-restraints excluded: chain A residue 1684 ILE Chi-restraints excluded: chain A residue 1718 GLU Chi-restraints excluded: chain A residue 1724 LEU Chi-restraints excluded: chain A residue 1752 ILE Chi-restraints excluded: chain A residue 1798 THR Chi-restraints excluded: chain A residue 1805 VAL Chi-restraints excluded: chain A residue 1834 VAL Chi-restraints excluded: chain A residue 2033 ILE Chi-restraints excluded: chain A residue 2088 SER Chi-restraints excluded: chain A residue 2107 SER Chi-restraints excluded: chain A residue 2122 LEU Chi-restraints excluded: chain A residue 2151 ILE Chi-restraints excluded: chain A residue 2171 ASP Chi-restraints excluded: chain A residue 2173 LYS Chi-restraints excluded: chain A residue 2181 VAL Chi-restraints excluded: chain A residue 2194 LEU Chi-restraints excluded: chain A residue 2210 THR Chi-restraints excluded: chain A residue 2241 VAL Chi-restraints excluded: chain A residue 2253 CYS Chi-restraints excluded: chain A residue 2287 THR Chi-restraints excluded: chain A residue 2291 TRP Chi-restraints excluded: chain A residue 2408 THR Chi-restraints excluded: chain A residue 2481 VAL Chi-restraints excluded: chain A residue 2514 ILE Chi-restraints excluded: chain A residue 2515 VAL Chi-restraints excluded: chain A residue 2542 VAL Chi-restraints excluded: chain A residue 2547 MET Chi-restraints excluded: chain A residue 2610 THR Chi-restraints excluded: chain A residue 2640 SER Chi-restraints excluded: chain A residue 2707 MET Chi-restraints excluded: chain A residue 2711 GLU Chi-restraints excluded: chain A residue 2822 LEU Chi-restraints excluded: chain A residue 2861 PHE Chi-restraints excluded: chain A residue 2862 VAL Chi-restraints excluded: chain A residue 2885 VAL Chi-restraints excluded: chain A residue 2889 LEU Chi-restraints excluded: chain A residue 2893 TYR Chi-restraints excluded: chain A residue 2906 ILE Chi-restraints excluded: chain A residue 2985 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 196 optimal weight: 7.9990 chunk 231 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 240 optimal weight: 8.9990 chunk 187 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 168 optimal weight: 0.9990 chunk 218 optimal weight: 0.0470 chunk 188 optimal weight: 2.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2442 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.147134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.123799 restraints weight = 37968.460| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.95 r_work: 0.3507 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 23903 Z= 0.212 Angle : 0.651 14.744 32336 Z= 0.342 Chirality : 0.047 0.245 3523 Planarity : 0.005 0.059 4164 Dihedral : 5.406 55.907 3216 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 5.26 % Allowed : 25.26 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.15), residues: 2922 helix: 0.39 (0.30), residues: 322 sheet: -0.31 (0.17), residues: 942 loop : -1.47 (0.14), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A2354 TYR 0.029 0.002 TYR A1031 PHE 0.026 0.002 PHE A 908 TRP 0.025 0.002 TRP A1577 HIS 0.006 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.21 (23896) covalent geometry : angle 0.64380 / 0.34 (32319) SS BOND : bond 0.01209 / 0.59 ( 4) SS BOND : angle 3.25002 / 1.40 ( 8) hydrogen bonds : bond 0.03919 / 2.59 ( 791) hydrogen bonds : angle 5.73563 / 3.89 ( 2250) link_BETA1-4 : bond 0.00512 / 0.27 ( 1) link_BETA1-4 : angle 1.33739 / 0.73 ( 3) link_NAG-ASN : bond 0.01587 / 0.76 ( 2) link_NAG-ASN : angle 6.03502 / 2.51 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 238 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7636 (tt) REVERT: A 33 PHE cc_start: 0.5911 (OUTLIER) cc_final: 0.5525 (t80) REVERT: A 523 ASN cc_start: 0.7894 (t0) cc_final: 0.7573 (m-40) REVERT: A 646 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8293 (tttt) REVERT: A 723 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8001 (pp) REVERT: A 751 GLN cc_start: 0.7827 (tp40) cc_final: 0.7379 (tp40) REVERT: A 1040 LYS cc_start: 0.8346 (mttt) cc_final: 0.8078 (tptt) REVERT: A 1312 GLU cc_start: 0.5823 (tp30) cc_final: 0.5430 (tp30) REVERT: A 1333 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.5557 (t80) REVERT: A 1379 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7263 (mt-10) REVERT: A 1718 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8575 (mt-10) REVERT: A 1724 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8658 (mt) REVERT: A 1788 ASN cc_start: 0.7139 (p0) cc_final: 0.6884 (p0) REVERT: A 2044 TYR cc_start: 0.7796 (m-80) cc_final: 0.7548 (m-10) REVERT: A 2122 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9154 (mt) REVERT: A 2361 ARG cc_start: 0.5992 (ppt170) cc_final: 0.5589 (ptt180) REVERT: A 2549 ASP cc_start: 0.7393 (p0) cc_final: 0.6908 (p0) REVERT: A 2638 GLU cc_start: 0.8200 (tt0) cc_final: 0.7843 (tt0) REVERT: A 2822 LEU cc_start: 0.6556 (OUTLIER) cc_final: 0.5766 (mp) REVERT: A 2845 ASN cc_start: 0.8755 (m-40) cc_final: 0.8336 (m110) REVERT: A 2857 PHE cc_start: 0.6059 (p90) cc_final: 0.5811 (p90) REVERT: A 2861 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.6877 (p90) REVERT: A 2875 LEU cc_start: 0.7646 (tp) cc_final: 0.7401 (tp) REVERT: A 2889 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7191 (mt) REVERT: A 2893 TYR cc_start: 0.7003 (OUTLIER) cc_final: 0.5561 (m-80) REVERT: A 2912 LYS cc_start: 0.6590 (mtpt) cc_final: 0.5940 (mmtm) REVERT: A 2975 ILE cc_start: 0.7616 (mt) cc_final: 0.7294 (mm) outliers start: 134 outliers final: 103 residues processed: 343 average time/residue: 0.1594 time to fit residues: 86.4911 Evaluate side-chains 350 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 234 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 747 PHE Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1131 THR Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1249 VAL Chi-restraints excluded: chain A residue 1260 THR Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1329 ASP Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1342 TYR Chi-restraints excluded: chain A residue 1349 VAL Chi-restraints excluded: chain A residue 1355 GLU Chi-restraints excluded: chain A residue 1361 THR Chi-restraints excluded: chain A residue 1366 ASN Chi-restraints excluded: chain A residue 1379 GLU Chi-restraints excluded: chain A residue 1408 ASN Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1414 TRP Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1453 VAL Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1492 LEU Chi-restraints excluded: chain A residue 1495 VAL Chi-restraints excluded: chain A residue 1569 ILE Chi-restraints excluded: chain A residue 1610 ILE Chi-restraints excluded: chain A residue 1637 THR Chi-restraints excluded: chain A residue 1650 VAL Chi-restraints excluded: chain A residue 1682 LEU Chi-restraints excluded: chain A residue 1684 ILE Chi-restraints excluded: chain A residue 1718 GLU Chi-restraints excluded: chain A residue 1724 LEU Chi-restraints excluded: chain A residue 1735 LEU Chi-restraints excluded: chain A residue 1752 ILE Chi-restraints excluded: chain A residue 1798 THR Chi-restraints excluded: chain A residue 1805 VAL Chi-restraints excluded: chain A residue 1811 THR Chi-restraints excluded: chain A residue 1834 VAL Chi-restraints excluded: chain A residue 1911 ILE Chi-restraints excluded: chain A residue 1950 THR Chi-restraints excluded: chain A residue 2000 LEU Chi-restraints excluded: chain A residue 2008 CYS Chi-restraints excluded: chain A residue 2088 SER Chi-restraints excluded: chain A residue 2107 SER Chi-restraints excluded: chain A residue 2122 LEU Chi-restraints excluded: chain A residue 2151 ILE Chi-restraints excluded: chain A residue 2171 ASP Chi-restraints excluded: chain A residue 2173 LYS Chi-restraints excluded: chain A residue 2181 VAL Chi-restraints excluded: chain A residue 2194 LEU Chi-restraints excluded: chain A residue 2210 THR Chi-restraints excluded: chain A residue 2233 ILE Chi-restraints excluded: chain A residue 2241 VAL Chi-restraints excluded: chain A residue 2253 CYS Chi-restraints excluded: chain A residue 2287 THR Chi-restraints excluded: chain A residue 2291 TRP Chi-restraints excluded: chain A residue 2408 THR Chi-restraints excluded: chain A residue 2514 ILE Chi-restraints excluded: chain A residue 2515 VAL Chi-restraints excluded: chain A residue 2542 VAL Chi-restraints excluded: chain A residue 2547 MET Chi-restraints excluded: chain A residue 2610 THR Chi-restraints excluded: chain A residue 2640 SER Chi-restraints excluded: chain A residue 2707 MET Chi-restraints excluded: chain A residue 2711 GLU Chi-restraints excluded: chain A residue 2822 LEU Chi-restraints excluded: chain A residue 2861 PHE Chi-restraints excluded: chain A residue 2862 VAL Chi-restraints excluded: chain A residue 2885 VAL Chi-restraints excluded: chain A residue 2889 LEU Chi-restraints excluded: chain A residue 2893 TYR Chi-restraints excluded: chain A residue 2906 ILE Chi-restraints excluded: chain A residue 2985 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 204 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 219 optimal weight: 0.9990 chunk 241 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 149 optimal weight: 0.0770 chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 190 optimal weight: 4.9990 chunk 153 optimal weight: 0.6980 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2442 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.148347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.125096 restraints weight = 38027.213| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.94 r_work: 0.3524 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 23903 Z= 0.160 Angle : 0.610 14.216 32336 Z= 0.320 Chirality : 0.046 0.241 3523 Planarity : 0.004 0.060 4164 Dihedral : 5.291 56.231 3216 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.99 % Allowed : 25.57 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.15), residues: 2922 helix: 0.52 (0.30), residues: 319 sheet: -0.40 (0.16), residues: 968 loop : -1.41 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2354 TYR 0.029 0.002 TYR A1031 PHE 0.024 0.002 PHE A2004 TRP 0.019 0.001 TRP A1577 HIS 0.006 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (23896) covalent geometry : angle 0.60254 / 0.32 (32319) SS BOND : bond 0.01070 / 0.52 ( 4) SS BOND : angle 2.92804 / 1.24 ( 8) hydrogen bonds : bond 0.03580 / 2.36 ( 791) hydrogen bonds : angle 5.62588 / 3.82 ( 2250) link_BETA1-4 : bond 0.00475 / 0.25 ( 1) link_BETA1-4 : angle 1.30375 / 0.70 ( 3) link_NAG-ASN : bond 0.01520 / 0.72 ( 2) link_NAG-ASN : angle 6.05833 / 2.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 235 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 33 PHE cc_start: 0.5473 (OUTLIER) cc_final: 0.4998 (t80) REVERT: A 523 ASN cc_start: 0.7862 (t0) cc_final: 0.7562 (m-40) REVERT: A 646 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8383 (tttt) REVERT: A 723 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8027 (pt) REVERT: A 751 GLN cc_start: 0.7825 (tp40) cc_final: 0.7387 (tp40) REVERT: A 818 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7371 (mmtm) REVERT: A 1031 TYR cc_start: 0.7228 (OUTLIER) cc_final: 0.7022 (t80) REVERT: A 1040 LYS cc_start: 0.8357 (mttt) cc_final: 0.8094 (tptt) REVERT: A 1049 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6664 (tp30) REVERT: A 1282 ASP cc_start: 0.7109 (OUTLIER) cc_final: 0.6766 (t0) REVERT: A 1312 GLU cc_start: 0.5838 (tp30) cc_final: 0.5463 (tp30) REVERT: A 1379 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7262 (mt-10) REVERT: A 1458 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.6898 (tmm160) REVERT: A 1718 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8566 (mt-10) REVERT: A 1724 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8589 (mt) REVERT: A 1788 ASN cc_start: 0.6687 (p0) cc_final: 0.6455 (p0) REVERT: A 2044 TYR cc_start: 0.7777 (m-80) cc_final: 0.7551 (m-10) REVERT: A 2122 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9125 (mt) REVERT: A 2361 ARG cc_start: 0.5864 (ppt170) cc_final: 0.5447 (ptt180) REVERT: A 2549 ASP cc_start: 0.7487 (p0) cc_final: 0.7033 (p0) REVERT: A 2638 GLU cc_start: 0.8155 (tt0) cc_final: 0.7932 (tt0) REVERT: A 2845 ASN cc_start: 0.8717 (m-40) cc_final: 0.8322 (m110) REVERT: A 2857 PHE cc_start: 0.5955 (p90) cc_final: 0.5717 (p90) REVERT: A 2861 PHE cc_start: 0.7332 (OUTLIER) cc_final: 0.6831 (p90) REVERT: A 2875 LEU cc_start: 0.7622 (tp) cc_final: 0.7364 (tp) REVERT: A 2889 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7392 (mt) REVERT: A 2893 TYR cc_start: 0.6909 (OUTLIER) cc_final: 0.5629 (m-80) REVERT: A 2912 LYS cc_start: 0.6543 (mtpt) cc_final: 0.5898 (mmtm) REVERT: A 2975 ILE cc_start: 0.7692 (mt) cc_final: 0.7400 (mm) outliers start: 127 outliers final: 104 residues processed: 336 average time/residue: 0.1657 time to fit residues: 88.5885 Evaluate side-chains 355 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 236 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 747 PHE Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 851 TYR Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1049 GLU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1131 THR Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1249 VAL Chi-restraints excluded: chain A residue 1260 THR Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1329 ASP Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1342 TYR Chi-restraints excluded: chain A residue 1349 VAL Chi-restraints excluded: chain A residue 1355 GLU Chi-restraints excluded: chain A residue 1361 THR Chi-restraints excluded: chain A residue 1366 ASN Chi-restraints excluded: chain A residue 1379 GLU Chi-restraints excluded: chain A residue 1408 ASN Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1414 TRP Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1453 VAL Chi-restraints excluded: chain A residue 1458 ARG Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1492 LEU Chi-restraints excluded: chain A residue 1495 VAL Chi-restraints excluded: chain A residue 1554 ASN Chi-restraints excluded: chain A residue 1569 ILE Chi-restraints excluded: chain A residue 1610 ILE Chi-restraints excluded: chain A residue 1637 THR Chi-restraints excluded: chain A residue 1650 VAL Chi-restraints excluded: chain A residue 1674 THR Chi-restraints excluded: chain A residue 1682 LEU Chi-restraints excluded: chain A residue 1684 ILE Chi-restraints excluded: chain A residue 1718 GLU Chi-restraints excluded: chain A residue 1724 LEU Chi-restraints excluded: chain A residue 1735 LEU Chi-restraints excluded: chain A residue 1752 ILE Chi-restraints excluded: chain A residue 1798 THR Chi-restraints excluded: chain A residue 1805 VAL Chi-restraints excluded: chain A residue 1834 VAL Chi-restraints excluded: chain A residue 1911 ILE Chi-restraints excluded: chain A residue 2008 CYS Chi-restraints excluded: chain A residue 2088 SER Chi-restraints excluded: chain A residue 2107 SER Chi-restraints excluded: chain A residue 2122 LEU Chi-restraints excluded: chain A residue 2151 ILE Chi-restraints excluded: chain A residue 2171 ASP Chi-restraints excluded: chain A residue 2173 LYS Chi-restraints excluded: chain A residue 2181 VAL Chi-restraints excluded: chain A residue 2194 LEU Chi-restraints excluded: chain A residue 2195 THR Chi-restraints excluded: chain A residue 2210 THR Chi-restraints excluded: chain A residue 2233 ILE Chi-restraints excluded: chain A residue 2241 VAL Chi-restraints excluded: chain A residue 2253 CYS Chi-restraints excluded: chain A residue 2287 THR Chi-restraints excluded: chain A residue 2291 TRP Chi-restraints excluded: chain A residue 2408 THR Chi-restraints excluded: chain A residue 2481 VAL Chi-restraints excluded: chain A residue 2514 ILE Chi-restraints excluded: chain A residue 2515 VAL Chi-restraints excluded: chain A residue 2542 VAL Chi-restraints excluded: chain A residue 2547 MET Chi-restraints excluded: chain A residue 2578 SER Chi-restraints excluded: chain A residue 2610 THR Chi-restraints excluded: chain A residue 2640 SER Chi-restraints excluded: chain A residue 2711 GLU Chi-restraints excluded: chain A residue 2861 PHE Chi-restraints excluded: chain A residue 2862 VAL Chi-restraints excluded: chain A residue 2885 VAL Chi-restraints excluded: chain A residue 2889 LEU Chi-restraints excluded: chain A residue 2893 TYR Chi-restraints excluded: chain A residue 2906 ILE Chi-restraints excluded: chain A residue 2985 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 134 optimal weight: 0.4980 chunk 209 optimal weight: 0.0980 chunk 180 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 214 optimal weight: 5.9990 chunk 250 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 chunk 274 optimal weight: 0.8980 chunk 232 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 GLN A2442 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.151274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.128353 restraints weight = 37881.031| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.91 r_work: 0.3573 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 23903 Z= 0.111 Angle : 0.571 13.707 32336 Z= 0.300 Chirality : 0.045 0.229 3523 Planarity : 0.004 0.056 4164 Dihedral : 4.990 51.521 3216 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.24 % Allowed : 26.39 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.15), residues: 2922 helix: 0.76 (0.30), residues: 315 sheet: -0.30 (0.16), residues: 970 loop : -1.30 (0.14), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2354 TYR 0.029 0.001 TYR A1031 PHE 0.033 0.001 PHE A2902 TRP 0.016 0.001 TRP A1677 HIS 0.003 0.001 HIS A 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (23896) covalent geometry : angle 0.56330 / 0.30 (32319) SS BOND : bond 0.00919 / 0.44 ( 4) SS BOND : angle 2.62867 / 1.07 ( 8) hydrogen bonds : bond 0.03144 / 2.07 ( 791) hydrogen bonds : angle 5.38458 / 3.66 ( 2250) link_BETA1-4 : bond 0.00343 / 0.18 ( 1) link_BETA1-4 : angle 1.27071 / 0.69 ( 3) link_NAG-ASN : bond 0.01394 / 0.66 ( 2) link_NAG-ASN : angle 6.03139 / 2.46 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 257 time to evaluate : 0.954 Fit side-chains REVERT: A 1 MET cc_start: 0.7614 (mtm) cc_final: 0.7344 (mpp) REVERT: A 33 PHE cc_start: 0.5395 (OUTLIER) cc_final: 0.4954 (t80) REVERT: A 155 LYS cc_start: 0.7488 (ttpt) cc_final: 0.6738 (tptt) REVERT: A 417 MET cc_start: 0.8420 (mmm) cc_final: 0.8035 (tpt) REVERT: A 523 ASN cc_start: 0.7801 (t0) cc_final: 0.7517 (m-40) REVERT: A 723 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.7987 (pt) REVERT: A 751 GLN cc_start: 0.7849 (tp40) cc_final: 0.7443 (tp40) REVERT: A 818 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7268 (mmtm) REVERT: A 901 ILE cc_start: 0.6910 (tt) cc_final: 0.6679 (mm) REVERT: A 1040 LYS cc_start: 0.8371 (mttt) cc_final: 0.8097 (tptt) REVERT: A 1252 MET cc_start: 0.9061 (tpp) cc_final: 0.8820 (mtp) REVERT: A 1309 GLN cc_start: 0.7517 (tp40) cc_final: 0.7114 (tp40) REVERT: A 1312 GLU cc_start: 0.5823 (tp30) cc_final: 0.5446 (tp30) REVERT: A 1379 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7223 (mt-10) REVERT: A 1458 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.6803 (tmm160) REVERT: A 1718 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8547 (mt-10) REVERT: A 1724 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8435 (mt) REVERT: A 1788 ASN cc_start: 0.6664 (p0) cc_final: 0.6445 (p0) REVERT: A 1872 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8387 (pt0) REVERT: A 2036 ARG cc_start: 0.4027 (mtm180) cc_final: 0.3704 (mtm180) REVERT: A 2044 TYR cc_start: 0.7757 (m-80) cc_final: 0.7439 (m-10) REVERT: A 2122 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9106 (mt) REVERT: A 2361 ARG cc_start: 0.5703 (ppt170) cc_final: 0.5212 (ptt180) REVERT: A 2549 ASP cc_start: 0.7458 (p0) cc_final: 0.7006 (p0) REVERT: A 2638 GLU cc_start: 0.8023 (tt0) cc_final: 0.7718 (tt0) REVERT: A 2707 MET cc_start: 0.8562 (mtm) cc_final: 0.8340 (mtp) REVERT: A 2711 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: A 2822 LEU cc_start: 0.6265 (OUTLIER) cc_final: 0.5537 (mp) REVERT: A 2845 ASN cc_start: 0.8693 (m-40) cc_final: 0.8313 (m110) REVERT: A 2861 PHE cc_start: 0.7205 (OUTLIER) cc_final: 0.6806 (p90) REVERT: A 2875 LEU cc_start: 0.7644 (tp) cc_final: 0.7383 (tp) REVERT: A 2893 TYR cc_start: 0.6799 (OUTLIER) cc_final: 0.5563 (m-80) REVERT: A 2912 LYS cc_start: 0.6456 (mtpt) cc_final: 0.5927 (mmtt) REVERT: A 2975 ILE cc_start: 0.7577 (mt) cc_final: 0.7276 (mt) outliers start: 108 outliers final: 89 residues processed: 339 average time/residue: 0.1660 time to fit residues: 89.4270 Evaluate side-chains 347 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 245 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 747 PHE Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 851 TYR Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1131 THR Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1249 VAL Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1329 ASP Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1342 TYR Chi-restraints excluded: chain A residue 1349 VAL Chi-restraints excluded: chain A residue 1355 GLU Chi-restraints excluded: chain A residue 1366 ASN Chi-restraints excluded: chain A residue 1379 GLU Chi-restraints excluded: chain A residue 1414 TRP Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1453 VAL Chi-restraints excluded: chain A residue 1458 ARG Chi-restraints excluded: chain A residue 1492 LEU Chi-restraints excluded: chain A residue 1495 VAL Chi-restraints excluded: chain A residue 1569 ILE Chi-restraints excluded: chain A residue 1610 ILE Chi-restraints excluded: chain A residue 1611 SER Chi-restraints excluded: chain A residue 1637 THR Chi-restraints excluded: chain A residue 1674 THR Chi-restraints excluded: chain A residue 1682 LEU Chi-restraints excluded: chain A residue 1684 ILE Chi-restraints excluded: chain A residue 1718 GLU Chi-restraints excluded: chain A residue 1724 LEU Chi-restraints excluded: chain A residue 1735 LEU Chi-restraints excluded: chain A residue 1752 ILE Chi-restraints excluded: chain A residue 1798 THR Chi-restraints excluded: chain A residue 1805 VAL Chi-restraints excluded: chain A residue 1834 VAL Chi-restraints excluded: chain A residue 1872 GLN Chi-restraints excluded: chain A residue 2008 CYS Chi-restraints excluded: chain A residue 2088 SER Chi-restraints excluded: chain A residue 2107 SER Chi-restraints excluded: chain A residue 2122 LEU Chi-restraints excluded: chain A residue 2151 ILE Chi-restraints excluded: chain A residue 2171 ASP Chi-restraints excluded: chain A residue 2173 LYS Chi-restraints excluded: chain A residue 2194 LEU Chi-restraints excluded: chain A residue 2195 THR Chi-restraints excluded: chain A residue 2210 THR Chi-restraints excluded: chain A residue 2241 VAL Chi-restraints excluded: chain A residue 2253 CYS Chi-restraints excluded: chain A residue 2272 THR Chi-restraints excluded: chain A residue 2287 THR Chi-restraints excluded: chain A residue 2291 TRP Chi-restraints excluded: chain A residue 2408 THR Chi-restraints excluded: chain A residue 2514 ILE Chi-restraints excluded: chain A residue 2515 VAL Chi-restraints excluded: chain A residue 2542 VAL Chi-restraints excluded: chain A residue 2547 MET Chi-restraints excluded: chain A residue 2578 SER Chi-restraints excluded: chain A residue 2640 SER Chi-restraints excluded: chain A residue 2711 GLU Chi-restraints excluded: chain A residue 2822 LEU Chi-restraints excluded: chain A residue 2861 PHE Chi-restraints excluded: chain A residue 2862 VAL Chi-restraints excluded: chain A residue 2885 VAL Chi-restraints excluded: chain A residue 2889 LEU Chi-restraints excluded: chain A residue 2893 TYR Chi-restraints excluded: chain A residue 2906 ILE Chi-restraints excluded: chain A residue 2985 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 235 optimal weight: 3.9990 chunk 266 optimal weight: 3.9990 chunk 259 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 159 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.150560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.127406 restraints weight = 37715.048| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.95 r_work: 0.3557 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23903 Z= 0.125 Angle : 0.578 13.344 32336 Z= 0.303 Chirality : 0.045 0.207 3523 Planarity : 0.004 0.058 4164 Dihedral : 4.994 52.194 3216 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.24 % Allowed : 26.47 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.15), residues: 2922 helix: 0.78 (0.30), residues: 316 sheet: -0.26 (0.17), residues: 961 loop : -1.28 (0.14), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A2544 TYR 0.042 0.001 TYR A1031 PHE 0.025 0.001 PHE A 908 TRP 0.017 0.001 TRP A1677 HIS 0.004 0.001 HIS A2479 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 (23896) covalent geometry : angle 0.57077 / 0.30 (32319) SS BOND : bond 0.00914 / 0.44 ( 4) SS BOND : angle 2.53439 / 1.04 ( 8) hydrogen bonds : bond 0.03250 / 2.14 ( 791) hydrogen bonds : angle 5.35510 / 3.64 ( 2250) link_BETA1-4 : bond 0.00376 / 0.20 ( 1) link_BETA1-4 : angle 1.26732 / 0.69 ( 3) link_NAG-ASN : bond 0.01370 / 0.65 ( 2) link_NAG-ASN : angle 6.01820 / 2.46 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6039.51 seconds wall clock time: 104 minutes 21.15 seconds (6261.15 seconds total)