Starting phenix.real_space_refine on Sun Aug 24 23:59:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fjp_29245/08_2025/8fjp_29245.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fjp_29245/08_2025/8fjp_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_29245/08_2025/8fjp_29245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fjp_29245/08_2025/8fjp_29245.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fjp_29245/08_2025/8fjp_29245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fjp_29245/08_2025/8fjp_29245.map" } 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-2.0-5787/lib/python3.9/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 dihedrals: 6 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.00, per 1000 atoms: 0.21 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: 1.79 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.94 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: 11.62 Time building geometry restraints manager: 2.35 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: 12419 17.91 - 35.81: 1493 35.81 - 53.72: 375 53.72 - 71.63: 83 71.63 - 89.53: 36 Dihedral angle restraints: 14406 sinusoidal: 5868 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 14403 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: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 29.310 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 : 17.120 89.534 8940 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 aren 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 covalent geometry : bond 0.00435 (23896) covalent geometry : angle 0.88166 (32319) SS BOND : bond 0.00421 ( 4) SS BOND : angle 2.05634 ( 8) hydrogen bonds : bond 0.14514 ( 791) hydrogen bonds : angle 8.03502 ( 2250) link_BETA1-4 : bond 0.00153 ( 1) link_BETA1-4 : angle 0.73957 ( 3) link_NAG-ASN : bond 0.00475 ( 2) link_NAG-ASN : angle 5.98978 ( 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 : 0.658 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: 0.7492 (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: 0.6215 (tmm) outliers start: 17 outliers final: 5 residues processed: 339 average time/residue: 0.1684 time to fit residues: 86.1591 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 : 0.601 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.152389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.128897 restraints weight = 37913.703| |-----------------------------------------------------------------------------| 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: 4.33 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1122 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= 0.122 Angle : 0.600 8.435 32336 Z= 0.319 Chirality : 0.045 0.173 3523 Planarity : 0.004 0.073 4164 Dihedral : 5.973 57.651 3293 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.08 % Allowed : 24.00 % Favored : 73.92 % 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 aren not related in a simple way. whole: -1.39 (0.15), residues: 2922 helix: 0.07 (0.29), residues: 308 sheet: -0.36 (0.16), residues: 960 loop : -1.49 (0.14), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 102 TYR 0.018 0.001 TYR A2483 PHE 0.016 0.001 PHE A 908 TRP 0.017 0.001 TRP A1577 HIS 0.007 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00272 (23896) covalent geometry : angle 0.59516 (32319) SS BOND : bond 0.01443 ( 4) SS BOND : angle 1.76091 ( 8) hydrogen bonds : bond 0.04054 ( 791) hydrogen bonds : angle 6.29441 ( 2250) link_BETA1-4 : bond 0.01605 ( 1) link_BETA1-4 : angle 2.17122 ( 3) link_NAG-ASN : bond 0.01126 ( 2) link_NAG-ASN : angle 5.14713 ( 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 : 0.609 Fit side-chains revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8962 (mp) cc_final: 0.8758 (mt) REVERT: A 751 GLN cc_start: 0.7653 (tp40) cc_final: 0.7265 (mt0) REVERT: A 1031 TYR cc_start: 0.7248 (t80) cc_final: 0.6970 (t80) REVERT: A 1040 LYS cc_start: 0.8498 (mttt) cc_final: 0.8186 (tptt) REVERT: A 1080 ASN cc_start: 0.8596 (t0) cc_final: 0.8161 (t0) REVERT: A 1312 GLU cc_start: 0.5997 (tp30) cc_final: 0.5780 (mm-30) REVERT: A 1788 ASN cc_start: 0.6796 (p0) cc_final: 0.6570 (p0) REVERT: A 1959 PHE cc_start: 0.3853 (t80) cc_final: 0.3155 (t80) REVERT: A 2044 TYR cc_start: 0.7552 (m-80) cc_final: 0.7226 (m-10) REVERT: A 2100 LEU cc_start: 0.8063 (tt) cc_final: 0.7814 (tt) REVERT: A 2460 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7427 (pp-130) REVERT: A 2549 ASP cc_start: 0.7153 (p0) cc_final: 0.6846 (p0) REVERT: A 2638 GLU cc_start: 0.7738 (tt0) cc_final: 0.7520 (tt0) REVERT: A 2757 ASN cc_start: 0.8553 (OUTLIER) cc_final: 0.8322 (t0) REVERT: A 2857 PHE cc_start: 0.5881 (p90) cc_final: 0.5490 (p90) REVERT: A 2861 PHE cc_start: 0.6720 (p90) cc_final: 0.6179 (p90) REVERT: A 2893 TYR cc_start: 0.6828 (OUTLIER) cc_final: 0.5224 (m-80) REVERT: A 2912 LYS cc_start: 0.6924 (mtpt) cc_final: 0.6141 (mmtm) outliers start: 53 outliers final: 28 residues processed: 307 average time/residue: 0.1380 time to fit residues: 66.2630 Evaluate side-chains 273 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 242 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 2862 VAL 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: 0.2980 chunk 99 optimal weight: 7.9990 chunk 245 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 220 optimal weight: 1.9990 chunk 272 optimal weight: 0.9980 chunk 160 optimal weight: 0.7980 chunk 148 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 262 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.151437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.127801 restraints weight = 37978.792| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.97 r_work: 0.3548 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23903 Z= 0.133 Angle : 0.575 7.189 32336 Z= 0.305 Chirality : 0.045 0.175 3523 Planarity : 0.004 0.064 4164 Dihedral : 5.432 54.167 3279 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.93 % Allowed : 23.41 % Favored : 72.66 % 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 aren not related in a simple way. whole: -1.27 (0.15), residues: 2922 helix: 0.35 (0.29), residues: 320 sheet: -0.36 (0.17), residues: 969 loop : -1.41 (0.14), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2137 TYR 0.015 0.001 TYR A1452 PHE 0.019 0.001 PHE A 134 TRP 0.018 0.001 TRP A1577 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00305 (23896) covalent geometry : angle 0.56988 (32319) SS BOND : bond 0.00631 ( 4) SS BOND : angle 2.81409 ( 8) hydrogen bonds : bond 0.03750 ( 791) hydrogen bonds : angle 5.89108 ( 2250) link_BETA1-4 : bond 0.00241 ( 1) link_BETA1-4 : angle 1.38213 ( 3) link_NAG-ASN : bond 0.00974 ( 2) link_NAG-ASN : angle 4.87729 ( 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 361 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 261 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: A 325 LYS cc_start: 0.7840 (mmmt) cc_final: 0.7606 (mmmt) REVERT: A 333 GLU cc_start: 0.7709 (tt0) cc_final: 0.7447 (mm-30) REVERT: A 523 ASN cc_start: 0.7884 (t0) cc_final: 0.7534 (m-40) REVERT: A 751 GLN cc_start: 0.7741 (tp40) cc_final: 0.7275 (mt0) REVERT: A 963 ARG cc_start: 0.7945 (ptm160) cc_final: 0.7723 (ptm160) REVERT: A 1040 LYS cc_start: 0.8523 (mttt) cc_final: 0.8214 (tptp) REVERT: A 1067 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8510 (ptmt) REVERT: A 1080 ASN cc_start: 0.8690 (t0) cc_final: 0.8224 (t0) REVERT: A 1308 MET cc_start: 0.7621 (mtt) cc_final: 0.7252 (mtt) REVERT: A 1309 GLN cc_start: 0.7239 (tp40) cc_final: 0.6930 (tp40) REVERT: A 1312 GLU cc_start: 0.6228 (tp30) cc_final: 0.4442 (mp0) REVERT: A 1355 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6818 (tt0) REVERT: A 1379 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7150 (mt-10) REVERT: A 1718 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8515 (mt-10) REVERT: A 1959 PHE cc_start: 0.3860 (t80) cc_final: 0.3162 (t80) REVERT: A 2044 TYR cc_start: 0.7568 (m-80) cc_final: 0.7221 (m-10) REVERT: A 2065 LYS cc_start: 0.7275 (mmtt) cc_final: 0.6973 (mtpt) REVERT: A 2122 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9140 (mt) REVERT: A 2361 ARG cc_start: 0.5912 (ppt170) cc_final: 0.5093 (mmp80) REVERT: A 2549 ASP cc_start: 0.7185 (p0) cc_final: 0.6864 (p0) REVERT: A 2750 TYR cc_start: 0.8191 (m-80) cc_final: 0.7827 (m-80) REVERT: A 2857 PHE cc_start: 0.5907 (p90) cc_final: 0.5503 (p90) REVERT: A 2861 PHE cc_start: 0.6943 (OUTLIER) cc_final: 0.6431 (p90) REVERT: A 2893 TYR cc_start: 0.6916 (OUTLIER) cc_final: 0.5321 (m-80) REVERT: A 2900 ASN cc_start: 0.5159 (OUTLIER) cc_final: 0.4936 (m-40) REVERT: A 2912 LYS cc_start: 0.6951 (mtpt) cc_final: 0.6217 (mmtm) outliers start: 100 outliers final: 66 residues processed: 335 average time/residue: 0.1559 time to fit residues: 81.3910 Evaluate side-chains 321 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 247 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 106 VAL 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 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 437 VAL Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 610 VAL 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 1067 LYS 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 1240 VAL 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 1408 ASN 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 1472 LEU 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 1798 THR Chi-restraints excluded: chain A residue 1834 VAL Chi-restraints excluded: chain A residue 2000 LEU Chi-restraints excluded: chain A residue 2122 LEU Chi-restraints excluded: chain A residue 2151 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 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 2326 VAL Chi-restraints excluded: chain A residue 2408 THR Chi-restraints excluded: chain A residue 2481 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 2662 MET 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 2900 ASN 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: 9.9990 chunk 280 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 196 optimal weight: 10.0000 chunk 181 optimal weight: 0.5980 chunk 26 optimal weight: 0.2980 chunk 8 optimal weight: 7.9990 chunk 177 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 274 optimal weight: 4.9990 chunk 290 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN A2727 GLN A2733 GLN A2757 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.151284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.127754 restraints weight = 37808.208| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.96 r_work: 0.3546 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23903 Z= 0.127 Angle : 0.570 10.102 32336 Z= 0.298 Chirality : 0.045 0.184 3523 Planarity : 0.004 0.059 4164 Dihedral : 5.314 54.084 3277 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.52 % Allowed : 23.49 % Favored : 72.00 % 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 aren not related in a simple way. whole: -1.16 (0.15), residues: 2922 helix: 0.49 (0.30), residues: 320 sheet: -0.30 (0.16), residues: 984 loop : -1.34 (0.14), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2354 TYR 0.021 0.001 TYR A1031 PHE 0.019 0.001 PHE A 908 TRP 0.017 0.001 TRP A1577 HIS 0.003 0.001 HIS A1489 Details of bonding type rmsd covalent geometry : bond 0.00294 (23896) covalent geometry : angle 0.56208 (32319) SS BOND : bond 0.01295 ( 4) SS BOND : angle 3.13364 ( 8) hydrogen bonds : bond 0.03458 ( 791) hydrogen bonds : angle 5.65000 ( 2250) link_BETA1-4 : bond 0.00603 ( 1) link_BETA1-4 : angle 1.65403 ( 3) link_NAG-ASN : bond 0.01465 ( 2) link_NAG-ASN : angle 5.65608 ( 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 381 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 266 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: A 33 PHE cc_start: 0.5288 (OUTLIER) cc_final: 0.5024 (t80) REVERT: A 523 ASN cc_start: 0.7825 (t0) cc_final: 0.7520 (m-40) REVERT: A 723 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.7993 (pp) REVERT: A 751 GLN cc_start: 0.7769 (tp40) cc_final: 0.7271 (mt0) REVERT: A 840 GLU cc_start: 0.7524 (mt-10) cc_final: 0.6927 (mt-10) REVERT: A 901 ILE cc_start: 0.6943 (tt) cc_final: 0.6709 (mm) REVERT: A 1031 TYR cc_start: 0.7126 (t80) cc_final: 0.6701 (t80) REVERT: A 1040 LYS cc_start: 0.8386 (mttt) cc_final: 0.8132 (tptp) REVERT: A 1067 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8500 (ptmt) REVERT: A 1080 ASN cc_start: 0.8742 (t0) cc_final: 0.8351 (t0) REVERT: A 1312 GLU cc_start: 0.6224 (tp30) cc_final: 0.4437 (mp0) REVERT: A 1355 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6797 (tt0) REVERT: A 1379 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7116 (mt-10) REVERT: A 1718 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8579 (mt-10) REVERT: A 1774 PHE cc_start: 0.7020 (t80) cc_final: 0.6528 (t80) REVERT: A 1959 PHE cc_start: 0.3832 (t80) cc_final: 0.3136 (t80) REVERT: A 2044 TYR cc_start: 0.7652 (m-80) cc_final: 0.7281 (m-10) REVERT: A 2096 SER cc_start: 0.8271 (p) cc_final: 0.8061 (p) REVERT: A 2549 ASP cc_start: 0.7164 (p0) cc_final: 0.6767 (p0) REVERT: A 2707 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8323 (mtp) REVERT: A 2711 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7287 (mp0) REVERT: A 2750 TYR cc_start: 0.8192 (m-80) cc_final: 0.7761 (m-80) REVERT: A 2857 PHE cc_start: 0.5842 (p90) cc_final: 0.5453 (p90) REVERT: A 2861 PHE cc_start: 0.7082 (OUTLIER) cc_final: 0.6611 (p90) REVERT: A 2893 TYR cc_start: 0.6915 (OUTLIER) cc_final: 0.5366 (m-80) REVERT: A 2912 LYS cc_start: 0.6909 (mtpt) cc_final: 0.6212 (mmtm) outliers start: 115 outliers final: 70 residues processed: 355 average time/residue: 0.1577 time to fit residues: 88.4029 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 : 0.838 ------------------------------------------------------------------------------- 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 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 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 594 THR Chi-restraints excluded: chain A residue 643 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 1067 LYS 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 1240 VAL Chi-restraints excluded: chain A residue 1249 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 1361 THR Chi-restraints excluded: chain A residue 1379 GLU Chi-restraints excluded: chain A residue 1408 ASN 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 1492 LEU Chi-restraints excluded: chain A residue 1554 ASN 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 1798 THR Chi-restraints excluded: chain A residue 1805 VAL Chi-restraints excluded: chain A residue 1834 VAL Chi-restraints excluded: chain A residue 1891 ASN Chi-restraints excluded: chain A residue 2151 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 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 2408 THR Chi-restraints excluded: chain A residue 2481 VAL 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 2662 MET Chi-restraints excluded: chain A residue 2707 MET 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 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: 5.9990 chunk 20 optimal weight: 8.9990 chunk 175 optimal weight: 3.9990 chunk 243 optimal weight: 0.0370 chunk 63 optimal weight: 4.9990 chunk 30 optimal weight: 0.2980 chunk 155 optimal weight: 0.0980 chunk 154 optimal weight: 1.9990 chunk 288 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 193 optimal weight: 0.6980 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1334 HIS A1937 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.151620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.128493 restraints weight = 37562.402| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.91 r_work: 0.3573 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 23903 Z= 0.109 Angle : 0.552 9.962 32336 Z= 0.290 Chirality : 0.044 0.203 3523 Planarity : 0.004 0.055 4164 Dihedral : 5.181 54.249 3277 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.28 % Allowed : 24.04 % 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 aren not related in a simple way. whole: -1.08 (0.15), residues: 2922 helix: 0.61 (0.30), residues: 320 sheet: -0.28 (0.16), residues: 986 loop : -1.28 (0.14), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2354 TYR 0.018 0.001 TYR A1031 PHE 0.021 0.001 PHE A 908 TRP 0.016 0.001 TRP A1677 HIS 0.004 0.001 HIS A1334 Details of bonding type rmsd covalent geometry : bond 0.00251 (23896) covalent geometry : angle 0.54420 (32319) SS BOND : bond 0.00807 ( 4) SS BOND : angle 3.15265 ( 8) hydrogen bonds : bond 0.03245 ( 791) hydrogen bonds : angle 5.50021 ( 2250) link_BETA1-4 : bond 0.00435 ( 1) link_BETA1-4 : angle 1.27327 ( 3) link_NAG-ASN : bond 0.01246 ( 2) link_NAG-ASN : angle 5.55814 ( 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 373 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 264 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: A 33 PHE cc_start: 0.5359 (OUTLIER) cc_final: 0.4958 (t80) REVERT: A 523 ASN cc_start: 0.7796 (t0) cc_final: 0.7506 (m-40) REVERT: A 723 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7899 (pp) REVERT: A 729 VAL cc_start: 0.8268 (OUTLIER) cc_final: 0.8067 (m) REVERT: A 751 GLN cc_start: 0.7757 (tp40) cc_final: 0.7240 (mt0) REVERT: A 840 GLU cc_start: 0.7537 (mt-10) cc_final: 0.6960 (mt-10) REVERT: A 901 ILE cc_start: 0.6966 (tt) cc_final: 0.6743 (mm) REVERT: A 1040 LYS cc_start: 0.8377 (mttt) cc_final: 0.8128 (tptt) REVERT: A 1067 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8541 (ptmt) REVERT: A 1080 ASN cc_start: 0.8722 (t0) cc_final: 0.8341 (t0) REVERT: A 1119 ASP cc_start: 0.7258 (OUTLIER) cc_final: 0.7001 (t0) REVERT: A 1312 GLU cc_start: 0.6234 (tp30) cc_final: 0.4455 (mp0) REVERT: A 1355 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6556 (tt0) REVERT: A 1718 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8575 (mt-10) REVERT: A 1724 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8441 (mt) REVERT: A 1774 PHE cc_start: 0.6956 (t80) cc_final: 0.6460 (t80) REVERT: A 1959 PHE cc_start: 0.3890 (t80) cc_final: 0.3222 (t80) REVERT: A 2044 TYR cc_start: 0.7629 (m-80) cc_final: 0.7259 (m-10) REVERT: A 2065 LYS cc_start: 0.7489 (mtpp) cc_final: 0.6803 (mmtt) REVERT: A 2122 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9180 (mt) REVERT: A 2549 ASP cc_start: 0.7236 (p0) cc_final: 0.6836 (p0) REVERT: A 2638 GLU cc_start: 0.8012 (tt0) cc_final: 0.7794 (tt0) REVERT: A 2750 TYR cc_start: 0.8166 (m-80) cc_final: 0.7696 (m-80) REVERT: A 2857 PHE cc_start: 0.5872 (p90) cc_final: 0.5518 (p90) REVERT: A 2861 PHE cc_start: 0.7091 (OUTLIER) cc_final: 0.6656 (p90) REVERT: A 2875 LEU cc_start: 0.7659 (tp) cc_final: 0.7426 (tp) REVERT: A 2889 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.6926 (mt) REVERT: A 2893 TYR cc_start: 0.6857 (OUTLIER) cc_final: 0.5338 (m-80) REVERT: A 2912 LYS cc_start: 0.6850 (mtpt) cc_final: 0.6241 (mmtm) REVERT: A 2920 MET cc_start: 0.5248 (mtp) cc_final: 0.4900 (mtm) outliers start: 109 outliers final: 75 residues processed: 346 average time/residue: 0.1349 time to fit residues: 73.9304 Evaluate side-chains 330 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 243 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 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 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 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 643 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 877 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1067 LYS 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 1160 THR Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1262 VAL 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 1442 THR 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 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 1724 LEU Chi-restraints excluded: chain A residue 1752 ILE Chi-restraints excluded: chain A residue 1805 VAL Chi-restraints excluded: chain A residue 1834 VAL Chi-restraints excluded: chain A residue 1891 ASN Chi-restraints excluded: chain A residue 2098 VAL 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 2162 VAL 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 2241 VAL 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 2481 VAL Chi-restraints excluded: chain A residue 2514 ILE 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 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: 2.9990 chunk 213 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 280 optimal weight: 4.9990 chunk 269 optimal weight: 3.9990 chunk 288 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 290 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1741 ASN A1872 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.144663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.121568 restraints weight = 38448.572| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.91 r_work: 0.3474 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 23903 Z= 0.313 Angle : 0.736 9.317 32336 Z= 0.388 Chirality : 0.051 0.231 3523 Planarity : 0.005 0.061 4164 Dihedral : 5.990 59.330 3277 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.88 % Favored : 93.09 % Rotamer: Outliers : 5.46 % Allowed : 24.08 % Favored : 70.46 % 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 aren not related in a simple way. whole: -1.42 (0.15), residues: 2922 helix: 0.02 (0.29), residues: 334 sheet: -0.37 (0.16), residues: 972 loop : -1.54 (0.14), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2361 TYR 0.024 0.003 TYR A 977 PHE 0.025 0.003 PHE A2471 TRP 0.035 0.002 TRP A1577 HIS 0.010 0.002 HIS A1489 Details of bonding type rmsd covalent geometry : bond 0.00748 (23896) covalent geometry : angle 0.72907 (32319) SS BOND : bond 0.01293 ( 4) SS BOND : angle 3.93485 ( 8) hydrogen bonds : bond 0.04600 ( 791) hydrogen bonds : angle 6.06906 ( 2250) link_BETA1-4 : bond 0.00583 ( 1) link_BETA1-4 : angle 1.24452 ( 3) link_NAG-ASN : bond 0.01357 ( 2) link_NAG-ASN : angle 5.97661 ( 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 377 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 238 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: A 33 PHE cc_start: 0.5569 (OUTLIER) cc_final: 0.5287 (t80) REVERT: A 77 THR cc_start: 0.8708 (OUTLIER) cc_final: 0.8354 (m) REVERT: A 523 ASN cc_start: 0.7929 (t0) cc_final: 0.7580 (m-40) REVERT: A 646 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8321 (tttt) REVERT: A 723 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8001 (pp) REVERT: A 751 GLN cc_start: 0.7857 (tp40) cc_final: 0.7293 (tp40) REVERT: A 1031 TYR cc_start: 0.7069 (t80) cc_final: 0.6859 (t80) REVERT: A 1040 LYS cc_start: 0.8387 (mttt) cc_final: 0.8129 (tptt) REVERT: A 1092 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.8053 (tt) REVERT: A 1183 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8137 (m-30) REVERT: A 1252 MET cc_start: 0.9119 (tpp) cc_final: 0.8879 (mtp) REVERT: A 1312 GLU cc_start: 0.5928 (tp30) cc_final: 0.5543 (tp30) REVERT: A 1333 TYR cc_start: 0.7442 (OUTLIER) cc_final: 0.5833 (t80) REVERT: A 1355 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7257 (tt0) REVERT: A 1379 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7131 (mt-10) REVERT: A 1655 HIS cc_start: 0.7474 (OUTLIER) cc_final: 0.6886 (p-80) REVERT: A 1718 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8583 (mt-10) REVERT: A 1872 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8203 (pt0) REVERT: A 1959 PHE cc_start: 0.5210 (t80) cc_final: 0.4374 (t80) REVERT: A 1987 TYR cc_start: 0.8886 (m-80) cc_final: 0.8672 (m-80) REVERT: A 2065 LYS cc_start: 0.7523 (mtpp) cc_final: 0.6802 (mmtt) REVERT: A 2122 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9186 (mt) REVERT: A 2361 ARG cc_start: 0.5475 (ppt170) cc_final: 0.5061 (ptt180) REVERT: A 2549 ASP cc_start: 0.7389 (p0) cc_final: 0.6914 (p0) REVERT: A 2638 GLU cc_start: 0.8225 (tt0) cc_final: 0.7959 (tt0) REVERT: A 2822 LEU cc_start: 0.6557 (OUTLIER) cc_final: 0.5805 (mp) REVERT: A 2857 PHE cc_start: 0.5921 (p90) cc_final: 0.5594 (p90) REVERT: A 2861 PHE cc_start: 0.7474 (OUTLIER) cc_final: 0.6957 (p90) REVERT: A 2875 LEU cc_start: 0.7778 (tp) cc_final: 0.7561 (tp) REVERT: A 2893 TYR cc_start: 0.7097 (OUTLIER) cc_final: 0.5503 (m-80) REVERT: A 2912 LYS cc_start: 0.6993 (mtpt) cc_final: 0.6252 (mmtm) outliers start: 139 outliers final: 97 residues processed: 347 average time/residue: 0.1573 time to fit residues: 85.5225 Evaluate side-chains 339 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 226 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 77 THR Chi-restraints excluded: chain A residue 85 VAL 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 327 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 646 LYS Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 723 LEU 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 1092 ILE 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 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 1263 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 1361 THR Chi-restraints excluded: chain A residue 1366 ASN 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 1415 ILE 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 1492 LEU Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1569 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 1655 HIS 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 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 1872 GLN Chi-restraints excluded: chain A residue 1911 ILE Chi-restraints excluded: chain A residue 2000 LEU 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 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 2384 VAL 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 2610 THR Chi-restraints excluded: chain A residue 2621 LEU 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 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 Chi-restraints excluded: chain A residue 2989 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 86 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 104 optimal weight: 20.0000 chunk 155 optimal weight: 0.9980 chunk 248 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.149235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.125886 restraints weight = 38007.652| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.96 r_work: 0.3535 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 23903 Z= 0.128 Angle : 0.594 12.806 32336 Z= 0.313 Chirality : 0.045 0.263 3523 Planarity : 0.004 0.056 4164 Dihedral : 5.547 58.967 3277 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.24 % Allowed : 25.57 % 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 aren not related in a simple way. whole: -1.27 (0.15), residues: 2922 helix: 0.54 (0.30), residues: 315 sheet: -0.41 (0.16), residues: 971 loop : -1.40 (0.14), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2354 TYR 0.016 0.001 TYR A1452 PHE 0.021 0.002 PHE A2004 TRP 0.017 0.001 TRP A1577 HIS 0.004 0.001 HIS A1082 Details of bonding type rmsd covalent geometry : bond 0.00300 (23896) covalent geometry : angle 0.58650 (32319) SS BOND : bond 0.00865 ( 4) SS BOND : angle 3.46335 ( 8) hydrogen bonds : bond 0.03489 ( 791) hydrogen bonds : angle 5.68301 ( 2250) link_BETA1-4 : bond 0.00311 ( 1) link_BETA1-4 : angle 1.18593 ( 3) link_NAG-ASN : bond 0.01109 ( 2) link_NAG-ASN : angle 5.71100 ( 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 354 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 246 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: A 33 PHE cc_start: 0.5645 (OUTLIER) cc_final: 0.5282 (t80) REVERT: A 523 ASN cc_start: 0.7863 (t0) cc_final: 0.7569 (m-40) REVERT: A 723 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.7967 (pp) REVERT: A 751 GLN cc_start: 0.7837 (tp40) cc_final: 0.7350 (tp40) REVERT: A 840 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7327 (mt-10) REVERT: A 963 ARG cc_start: 0.8212 (ptm160) cc_final: 0.8003 (ptm160) REVERT: A 1040 LYS cc_start: 0.8395 (mttt) cc_final: 0.8127 (tptt) REVERT: A 1252 MET cc_start: 0.9099 (tpp) cc_final: 0.8832 (mtp) REVERT: A 1305 MET cc_start: 0.7784 (mtp) cc_final: 0.7484 (mtp) REVERT: A 1312 GLU cc_start: 0.5782 (tp30) cc_final: 0.5398 (tp30) REVERT: A 1355 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6919 (tt0) REVERT: A 1379 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6889 (mt-10) REVERT: A 1718 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8537 (mt-10) REVERT: A 1724 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8559 (mt) REVERT: A 1872 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.8091 (pt0) REVERT: A 1959 PHE cc_start: 0.4295 (t80) cc_final: 0.3465 (t80) REVERT: A 2044 TYR cc_start: 0.7882 (m-10) cc_final: 0.7525 (m-10) REVERT: A 2065 LYS cc_start: 0.7507 (mtpp) cc_final: 0.6799 (mmtt) REVERT: A 2122 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9144 (mt) REVERT: A 2361 ARG cc_start: 0.6090 (ppt170) cc_final: 0.5297 (mmp80) REVERT: A 2549 ASP cc_start: 0.7407 (p0) cc_final: 0.6940 (p0) REVERT: A 2857 PHE cc_start: 0.5810 (p90) cc_final: 0.5586 (p90) REVERT: A 2861 PHE cc_start: 0.7284 (OUTLIER) cc_final: 0.6830 (p90) REVERT: A 2875 LEU cc_start: 0.7582 (tp) cc_final: 0.7325 (tp) REVERT: A 2889 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7181 (mt) REVERT: A 2893 TYR cc_start: 0.6847 (OUTLIER) cc_final: 0.5518 (m-80) REVERT: A 2900 ASN cc_start: 0.4946 (OUTLIER) cc_final: 0.4623 (m-40) REVERT: A 2912 LYS cc_start: 0.6549 (mtpt) cc_final: 0.5917 (mmtm) REVERT: A 2975 ILE cc_start: 0.7470 (mt) cc_final: 0.7230 (mm) outliers start: 108 outliers final: 84 residues processed: 333 average time/residue: 0.1573 time to fit residues: 83.4983 Evaluate side-chains 335 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 239 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 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 424 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 493 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 851 TYR Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 968 VAL 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 1263 VAL 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 1379 GLU 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 1611 SER 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 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 1811 THR Chi-restraints excluded: chain A residue 1834 VAL Chi-restraints excluded: chain A residue 1872 GLN 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 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 2542 VAL 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 2900 ASN 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: 6.9990 chunk 231 optimal weight: 0.0030 chunk 202 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 240 optimal weight: 6.9990 chunk 187 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 218 optimal weight: 0.0770 chunk 188 optimal weight: 0.9980 overall best weight: 0.9950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1872 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.149422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.126177 restraints weight = 37790.551| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.95 r_work: 0.3539 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 23903 Z= 0.135 Angle : 0.592 14.613 32336 Z= 0.310 Chirality : 0.045 0.252 3523 Planarity : 0.004 0.056 4164 Dihedral : 5.435 55.422 3277 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.32 % Allowed : 25.61 % Favored : 70.07 % 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 aren not related in a simple way. whole: -1.20 (0.15), residues: 2922 helix: 0.53 (0.30), residues: 321 sheet: -0.31 (0.16), residues: 957 loop : -1.38 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2354 TYR 0.026 0.001 TYR A1031 PHE 0.038 0.002 PHE A2355 TRP 0.018 0.001 TRP A1577 HIS 0.003 0.001 HIS A2479 Details of bonding type rmsd covalent geometry : bond 0.00318 (23896) covalent geometry : angle 0.58282 (32319) SS BOND : bond 0.01227 ( 4) SS BOND : angle 3.15676 ( 8) hydrogen bonds : bond 0.03390 ( 791) hydrogen bonds : angle 5.51886 ( 2250) link_BETA1-4 : bond 0.00087 ( 1) link_BETA1-4 : angle 1.45149 ( 3) link_NAG-ASN : bond 0.01589 ( 2) link_NAG-ASN : angle 6.52748 ( 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 348 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 238 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: A 33 PHE cc_start: 0.5685 (OUTLIER) cc_final: 0.5350 (t80) REVERT: A 523 ASN cc_start: 0.7889 (t0) cc_final: 0.7584 (m-40) REVERT: A 723 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8051 (pt) REVERT: A 751 GLN cc_start: 0.7837 (tp40) cc_final: 0.7288 (tp40) REVERT: A 818 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7383 (mmtm) REVERT: A 840 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7138 (mt-10) REVERT: A 901 ILE cc_start: 0.6888 (tt) cc_final: 0.6627 (mm) REVERT: A 1031 TYR cc_start: 0.7200 (t80) cc_final: 0.6948 (t80) REVERT: A 1040 LYS cc_start: 0.8354 (mttt) cc_final: 0.8090 (tptt) REVERT: A 1252 MET cc_start: 0.9099 (tpp) cc_final: 0.8849 (mtp) REVERT: A 1305 MET cc_start: 0.7593 (mtp) cc_final: 0.7362 (mtp) REVERT: A 1312 GLU cc_start: 0.5790 (tp30) cc_final: 0.5411 (tp30) REVERT: A 1355 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6902 (tt0) REVERT: A 1379 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6863 (mt-10) REVERT: A 1458 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.6876 (tmm160) REVERT: A 1718 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8586 (mt-10) REVERT: A 2065 LYS cc_start: 0.7508 (mtpp) cc_final: 0.6800 (mmtt) REVERT: A 2122 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9121 (mt) REVERT: A 2361 ARG cc_start: 0.5743 (ppt170) cc_final: 0.5206 (ptt180) REVERT: A 2549 ASP cc_start: 0.7492 (p0) cc_final: 0.7036 (p0) REVERT: A 2711 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: A 2845 ASN cc_start: 0.8636 (m-40) cc_final: 0.8319 (m110) REVERT: A 2857 PHE cc_start: 0.5824 (p90) cc_final: 0.5615 (p90) REVERT: A 2861 PHE cc_start: 0.7314 (OUTLIER) cc_final: 0.6830 (p90) REVERT: A 2875 LEU cc_start: 0.7570 (tp) cc_final: 0.7307 (tp) REVERT: A 2893 TYR cc_start: 0.6902 (OUTLIER) cc_final: 0.5626 (m-80) REVERT: A 2900 ASN cc_start: 0.5103 (OUTLIER) cc_final: 0.4764 (m-40) REVERT: A 2912 LYS cc_start: 0.6532 (mtpt) cc_final: 0.5895 (mmtm) REVERT: A 2975 ILE cc_start: 0.7501 (mt) cc_final: 0.7227 (mt) outliers start: 110 outliers final: 87 residues processed: 322 average time/residue: 0.1738 time to fit residues: 88.5000 Evaluate side-chains 332 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 233 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 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 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 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 851 TYR Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 968 VAL 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 1263 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 1361 THR Chi-restraints excluded: chain A residue 1379 GLU Chi-restraints excluded: chain A residue 1410 ILE 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 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 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 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 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 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 2893 TYR Chi-restraints excluded: chain A residue 2900 ASN 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: 2.9990 chunk 61 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 219 optimal weight: 1.9990 chunk 241 optimal weight: 0.3980 chunk 191 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 80 optimal weight: 2.9990 chunk 190 optimal weight: 0.6980 chunk 153 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A1788 ASN A2442 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.151224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.128031 restraints weight = 37810.372| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.95 r_work: 0.3558 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 23903 Z= 0.112 Angle : 0.569 13.798 32336 Z= 0.298 Chirality : 0.044 0.229 3523 Planarity : 0.004 0.056 4164 Dihedral : 5.258 55.164 3277 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.24 % Allowed : 25.65 % 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 aren not related in a simple way. whole: -1.07 (0.15), residues: 2922 helix: 0.69 (0.30), residues: 317 sheet: -0.21 (0.17), residues: 953 loop : -1.32 (0.14), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A2544 TYR 0.020 0.001 TYR A1031 PHE 0.025 0.001 PHE A 908 TRP 0.016 0.001 TRP A1677 HIS 0.003 0.001 HIS A 441 Details of bonding type rmsd covalent geometry : bond 0.00259 (23896) covalent geometry : angle 0.56029 (32319) SS BOND : bond 0.00969 ( 4) SS BOND : angle 2.80886 ( 8) hydrogen bonds : bond 0.03163 ( 791) hydrogen bonds : angle 5.35605 ( 2250) link_BETA1-4 : bond 0.00394 ( 1) link_BETA1-4 : angle 1.21716 ( 3) link_NAG-ASN : bond 0.01468 ( 2) link_NAG-ASN : angle 6.44242 ( 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 352 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 244 time to evaluate : 1.058 Fit side-chains REVERT: A 33 PHE cc_start: 0.5560 (OUTLIER) cc_final: 0.5261 (t80) REVERT: A 155 LYS cc_start: 0.7441 (ttpt) cc_final: 0.6678 (tptt) REVERT: A 523 ASN cc_start: 0.7806 (t0) cc_final: 0.7488 (m-40) REVERT: A 723 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8003 (pt) REVERT: A 751 GLN cc_start: 0.7885 (tp40) cc_final: 0.7347 (tp40) REVERT: A 818 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7288 (mmtm) REVERT: A 840 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7161 (mt-10) REVERT: A 901 ILE cc_start: 0.6944 (tt) cc_final: 0.6695 (mm) REVERT: A 1031 TYR cc_start: 0.7352 (t80) cc_final: 0.7109 (t80) REVERT: A 1040 LYS cc_start: 0.8361 (mttt) cc_final: 0.8091 (tptt) REVERT: A 1049 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6731 (tp30) REVERT: A 1252 MET cc_start: 0.9051 (tpp) cc_final: 0.8807 (mtp) REVERT: A 1305 MET cc_start: 0.7531 (mtp) cc_final: 0.7302 (mtp) REVERT: A 1309 GLN cc_start: 0.7516 (tp40) cc_final: 0.7102 (tp40) REVERT: A 1312 GLU cc_start: 0.5650 (tp30) cc_final: 0.5255 (tp30) REVERT: A 1355 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6773 (tt0) REVERT: A 1379 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6959 (mt-10) REVERT: A 1458 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.6830 (tmm160) REVERT: A 1718 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8517 (mt-10) REVERT: A 2044 TYR cc_start: 0.7844 (m-80) cc_final: 0.7478 (m-10) REVERT: A 2065 LYS cc_start: 0.7479 (mtpp) cc_final: 0.6766 (mmtt) REVERT: A 2122 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9150 (mt) REVERT: A 2361 ARG cc_start: 0.5933 (ppt170) cc_final: 0.5361 (ptt180) REVERT: A 2549 ASP cc_start: 0.7480 (p0) cc_final: 0.7033 (p0) REVERT: A 2711 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: A 2845 ASN cc_start: 0.8618 (m-40) cc_final: 0.8273 (m110) REVERT: A 2861 PHE cc_start: 0.7266 (OUTLIER) cc_final: 0.6847 (p90) REVERT: A 2875 LEU cc_start: 0.7594 (tp) cc_final: 0.7320 (tp) REVERT: A 2893 TYR cc_start: 0.6775 (OUTLIER) cc_final: 0.5450 (m-80) REVERT: A 2912 LYS cc_start: 0.6474 (mtpt) cc_final: 0.5921 (mmtt) REVERT: A 2920 MET cc_start: 0.5160 (mtp) cc_final: 0.4763 (mtm) REVERT: A 2975 ILE cc_start: 0.7579 (mt) cc_final: 0.7321 (mt) outliers start: 108 outliers final: 81 residues processed: 327 average time/residue: 0.1492 time to fit residues: 76.8364 Evaluate side-chains 329 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 236 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 106 VAL Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 124 ILE 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 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 1049 GLU 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 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 1454 GLU Chi-restraints excluded: chain A residue 1458 ARG Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1495 VAL Chi-restraints excluded: chain A residue 1554 ASN 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 1682 LEU Chi-restraints excluded: chain A residue 1684 ILE Chi-restraints excluded: chain A residue 1718 GLU 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 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 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 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: 0.9990 chunk 209 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 214 optimal weight: 4.9990 chunk 250 optimal weight: 0.4980 chunk 160 optimal weight: 0.8980 chunk 274 optimal weight: 0.9990 chunk 232 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.150779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.127599 restraints weight = 37884.917| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.95 r_work: 0.3560 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 23903 Z= 0.123 Angle : 0.579 13.582 32336 Z= 0.302 Chirality : 0.045 0.211 3523 Planarity : 0.004 0.055 4164 Dihedral : 5.238 54.859 3277 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.01 % Allowed : 26.04 % Favored : 69.95 % 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 aren not related in a simple way. whole: -1.06 (0.15), residues: 2922 helix: 0.61 (0.30), residues: 323 sheet: -0.19 (0.17), residues: 953 loop : -1.31 (0.14), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2354 TYR 0.023 0.001 TYR A2697 PHE 0.028 0.001 PHE A2902 TRP 0.016 0.001 TRP A1577 HIS 0.003 0.001 HIS A2479 Details of bonding type rmsd covalent geometry : bond 0.00288 (23896) covalent geometry : angle 0.57065 (32319) SS BOND : bond 0.00933 ( 4) SS BOND : angle 2.58456 ( 8) hydrogen bonds : bond 0.03226 ( 791) hydrogen bonds : angle 5.32788 ( 2250) link_BETA1-4 : bond 0.00350 ( 1) link_BETA1-4 : angle 1.25252 ( 3) link_NAG-ASN : bond 0.01431 ( 2) link_NAG-ASN : angle 6.43413 ( 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 340 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 238 time to evaluate : 0.700 Fit side-chains REVERT: A 33 PHE cc_start: 0.5691 (OUTLIER) cc_final: 0.5265 (t80) REVERT: A 155 LYS cc_start: 0.7465 (ttpt) cc_final: 0.6719 (tptt) REVERT: A 523 ASN cc_start: 0.7833 (t0) cc_final: 0.7499 (m-40) REVERT: A 723 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8021 (pt) REVERT: A 751 GLN cc_start: 0.7863 (tp40) cc_final: 0.7426 (tp40) REVERT: A 818 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7323 (mmtm) REVERT: A 840 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7174 (mt-10) REVERT: A 901 ILE cc_start: 0.6929 (tt) cc_final: 0.6699 (mm) REVERT: A 1040 LYS cc_start: 0.8366 (mttt) cc_final: 0.8096 (tptt) REVERT: A 1049 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6722 (tp30) REVERT: A 1252 MET cc_start: 0.9058 (tpp) cc_final: 0.8827 (mtp) REVERT: A 1312 GLU cc_start: 0.5825 (tp30) cc_final: 0.5419 (tp30) REVERT: A 1355 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6733 (tt0) REVERT: A 1379 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6973 (mt-10) REVERT: A 1458 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.6845 (tmm160) REVERT: A 1718 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8561 (mt-10) REVERT: A 2065 LYS cc_start: 0.7480 (mtpp) cc_final: 0.6764 (mmtt) REVERT: A 2122 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9132 (mt) REVERT: A 2361 ARG cc_start: 0.5639 (ppt170) cc_final: 0.5074 (ptt180) REVERT: A 2549 ASP cc_start: 0.7473 (p0) cc_final: 0.7019 (p0) REVERT: A 2711 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7245 (mp0) REVERT: A 2845 ASN cc_start: 0.8640 (m-40) cc_final: 0.8239 (m110) REVERT: A 2857 PHE cc_start: 0.5982 (p90) cc_final: 0.5632 (p90) REVERT: A 2861 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.6813 (p90) REVERT: A 2875 LEU cc_start: 0.7598 (tp) cc_final: 0.7325 (tp) REVERT: A 2893 TYR cc_start: 0.6813 (OUTLIER) cc_final: 0.5467 (m-80) REVERT: A 2912 LYS cc_start: 0.6490 (mtpt) cc_final: 0.5922 (mmtt) REVERT: A 2920 MET cc_start: 0.5153 (mtp) cc_final: 0.4752 (mtm) REVERT: A 2975 ILE cc_start: 0.7657 (mt) cc_final: 0.7389 (mt) outliers start: 102 outliers final: 86 residues processed: 318 average time/residue: 0.1458 time to fit residues: 73.6947 Evaluate side-chains 328 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 230 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 106 VAL Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 124 ILE 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 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 851 TYR Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1049 GLU 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 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 1408 ASN 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 1610 ILE Chi-restraints excluded: chain A residue 1637 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 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 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 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 2514 ILE Chi-restraints excluded: chain A residue 2515 VAL Chi-restraints excluded: chain A residue 2542 VAL 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 235 optimal weight: 0.9990 chunk 266 optimal weight: 0.0970 chunk 259 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 91 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.149659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.126418 restraints weight = 37803.754| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.94 r_work: 0.3542 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 23903 Z= 0.146 Angle : 0.596 13.403 32336 Z= 0.311 Chirality : 0.045 0.209 3523 Planarity : 0.004 0.057 4164 Dihedral : 5.327 54.309 3277 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.12 % Allowed : 25.81 % Favored : 70.07 % 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 aren not related in a simple way. whole: -1.10 (0.15), residues: 2922 helix: 0.59 (0.30), residues: 323 sheet: -0.24 (0.16), residues: 963 loop : -1.33 (0.14), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2544 TYR 0.044 0.002 TYR A1031 PHE 0.026 0.002 PHE A 908 TRP 0.020 0.001 TRP A1577 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00347 (23896) covalent geometry : angle 0.58781 (32319) SS BOND : bond 0.00965 ( 4) SS BOND : angle 2.58761 ( 8) hydrogen bonds : bond 0.03389 ( 791) hydrogen bonds : angle 5.37911 ( 2250) link_BETA1-4 : bond 0.00394 ( 1) link_BETA1-4 : angle 1.23745 ( 3) link_NAG-ASN : bond 0.01455 ( 2) link_NAG-ASN : angle 6.45543 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5463.19 seconds wall clock time: 94 minutes 42.02 seconds (5682.02 seconds total)