Starting phenix.real_space_refine on Tue Oct 27 16:13:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6tg9_10495/10_2026/6tg9_10495.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tg9_10495/10_2026/6tg9_10495.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6tg9_10495/10_2026/6tg9_10495.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tg9_10495/10_2026/6tg9_10495.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6tg9_10495/10_2026/6tg9_10495.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6tg9_10495/10_2026/6tg9_10495.cif" model { file = "/net/cci-nas-00/data/ceres_data/6tg9_10495/10_2026/6tg9_10495.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tg9_10495/10_2026/6tg9_10495.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mo 2 10.26 5 Fe 48 7.16 5 P 14 5.49 5 S 232 5.16 5 C 15818 2.51 5 N 4546 2.21 5 O 4752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 134 residue(s): 0.20s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25412 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7261 Classifications: {'peptide': 949} Link IDs: {'PTRANS': 55, 'TRANS': 893} Chain: "B" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3645 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 30, 'TRANS': 462} Chain: "G" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1076 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "D" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 505 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 8, 'TRANS': 60} Chain: "A" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 131 Ad-hoc single atom residues: {'6MO': 1} Unusual residues: {'FES': 1, 'H2S': 1, 'MGD': 2, 'SF4': 4} Classifications: {'undetermined': 8} Link IDs: {None: 6} Chain breaks: 1 Chain: "B" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: E, F, C, H List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2875 SG CYS A 386 117.182 70.640 77.272 1.00 7.54 S ATOM 368 SG CYS A 57 89.637 94.653 56.321 1.00 3.56 S ATOM 442 SG CYS A 68 85.866 95.047 55.342 1.00 3.19 S ATOM 467 SG CYS A 71 85.021 98.459 59.082 1.00 6.31 S ATOM 568 SG CYS A 85 88.693 99.076 59.391 1.00 7.88 S ATOM 909 SG CYS A 130 84.111 81.763 52.937 1.00 3.17 S ATOM 852 SG CYS A 121 79.595 79.452 48.578 1.00 16.27 S ATOM 873 SG CYS A 124 85.380 76.133 49.472 1.00 4.70 S ATOM 1347 SG CYS A 185 91.443 88.462 53.256 1.00 4.93 S ATOM 1326 SG CYS A 182 93.268 86.268 47.471 1.00 5.76 S ATOM 1698 SG CYS A 234 92.098 82.196 52.783 1.00 16.27 S ATOM 1372 SG CYS A 188 97.400 86.449 52.275 1.00 5.12 S ATOM 1671 SG CYS A 230 99.486 80.178 55.402 1.00 6.94 S ATOM 1637 SG CYS A 224 104.914 78.460 54.122 1.00 7.72 S ATOM 1656 SG CYS A 227 103.209 80.005 60.480 1.00 16.27 S ATOM 1401 SG CYS A 192 104.854 84.620 56.440 1.00 3.35 S ATOM 1879 SG CYS A 258 103.168 70.723 70.038 1.00 5.48 S ATOM 2135 SG CYS A 293 105.565 73.915 65.834 1.00 16.27 S ATOM 1902 SG CYS A 261 108.688 74.919 71.417 1.00 5.21 S ATOM 1923 SG CYS A 265 103.038 77.511 70.955 1.00 5.41 S ATOM 10736 SG CYS B 471 92.222 106.680 46.250 1.00 7.07 S ATOM 10464 SG CYS B 433 90.747 101.868 42.412 1.00 3.44 S ATOM 10444 SG CYS B 430 89.010 101.057 48.203 1.00 3.21 S ATOM 10427 SG CYS B 427 95.285 100.838 46.917 1.00 4.74 S ATOM 11482 SG CYS G 77 99.187 111.666 27.782 1.00 19.46 S ATOM 11518 SG CYS G 82 98.825 114.152 25.823 1.00 19.75 S ATOM 11763 SG CYS G 116 100.317 114.663 31.851 1.00 17.51 S ATOM 11789 SG CYS G 120 98.921 117.866 30.579 1.00 20.46 S ATOM 15362 SG CYS E 386 36.893 85.570 77.274 1.00 7.46 S ATOM 12855 SG CYS E 57 64.443 61.567 56.321 1.00 3.83 S ATOM 12929 SG CYS E 68 68.208 61.173 55.344 1.00 3.38 S ATOM 12954 SG CYS E 71 69.060 57.758 59.086 1.00 6.44 S ATOM 13055 SG CYS E 85 65.383 57.136 59.392 1.00 8.09 S ATOM 13396 SG CYS E 130 69.963 74.450 52.937 1.00 4.11 S ATOM 13339 SG CYS E 121 74.479 76.761 48.578 1.00 6.47 S ATOM 13360 SG CYS E 124 68.694 80.079 49.472 1.00 3.69 S ATOM 13834 SG CYS E 185 62.632 67.750 53.257 1.00 3.95 S ATOM 13813 SG CYS E 182 60.806 69.944 47.472 1.00 5.85 S ATOM 14185 SG CYS E 234 61.977 74.016 52.784 1.00 16.27 S ATOM 13859 SG CYS E 188 56.674 69.763 52.276 1.00 6.15 S ATOM 14158 SG CYS E 230 54.588 76.033 55.404 1.00 6.85 S ATOM 14124 SG CYS E 224 49.160 77.751 54.124 1.00 7.97 S ATOM 14143 SG CYS E 227 50.866 76.206 60.482 1.00 7.86 S ATOM 13888 SG CYS E 192 49.221 71.591 56.442 1.00 4.36 S ATOM 14366 SG CYS E 258 50.906 85.488 70.040 1.00 5.53 S ATOM 14622 SG CYS E 293 48.509 82.296 65.836 1.00 16.27 S ATOM 14389 SG CYS E 261 45.387 81.292 71.419 1.00 5.15 S ATOM 14410 SG CYS E 265 51.037 78.700 70.957 1.00 5.57 S ATOM 23223 SG CYS F 471 61.854 49.532 46.251 1.00 7.06 S ATOM 22951 SG CYS F 433 63.329 54.344 42.413 1.00 3.42 S ATOM 22931 SG CYS F 430 65.066 55.156 48.205 1.00 3.20 S ATOM 22914 SG CYS F 427 58.791 55.373 46.919 1.00 4.74 S ATOM 23969 SG CYS C 77 55.046 44.537 27.849 1.00 19.85 S ATOM 24005 SG CYS C 82 55.411 42.045 25.897 1.00 19.67 S ATOM 24250 SG CYS C 116 53.871 41.553 31.915 1.00 17.79 S ATOM 24276 SG CYS C 120 55.261 38.341 30.660 1.00 20.77 S Time building chain proxies: 9.29, per 1000 atoms: 0.37 Number of scatterers: 25412 At special positions: 0 Unit cell: (155.15, 157.29, 116.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mo 2 41.97 Fe 48 26.01 S 232 16.00 P 14 15.00 O 4752 8.00 N 4546 7.00 C 15818 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A1004 " pdb="FE1 FES A1004 " - pdb=" SG CYS A 68 " pdb="FE2 FES A1004 " - pdb=" SG CYS A 85 " pdb="FE1 FES A1004 " - pdb=" SG CYS A 57 " pdb="FE2 FES A1004 " - pdb=" SG CYS A 71 " pdb=" FES C 201 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 82 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 77 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 120 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 116 " pdb=" FES E1004 " pdb="FE1 FES E1004 " - pdb=" SG CYS E 68 " pdb="FE2 FES E1004 " - pdb=" SG CYS E 85 " pdb="FE1 FES E1004 " - pdb=" SG CYS E 57 " pdb="FE2 FES E1004 " - pdb=" SG CYS E 71 " pdb=" FES G 201 " pdb="FE1 FES G 201 " - pdb=" SG CYS G 82 " pdb="FE1 FES G 201 " - pdb=" SG CYS G 77 " pdb="FE2 FES G 201 " - pdb=" SG CYS G 120 " pdb="FE2 FES G 201 " - pdb=" SG CYS G 116 " pdb=" SF4 A1005 " pdb="FE2 SF4 A1005 " - pdb=" SG CYS A 121 " pdb="FE4 SF4 A1005 " - pdb=" NE2 HIS A 117 " pdb="FE3 SF4 A1005 " - pdb=" SG CYS A 124 " pdb="FE1 SF4 A1005 " - pdb=" SG CYS A 130 " pdb=" SF4 A1006 " pdb="FE2 SF4 A1006 " - pdb=" SG CYS A 182 " pdb="FE3 SF4 A1006 " - pdb=" SG CYS A 234 " pdb="FE1 SF4 A1006 " - pdb=" SG CYS A 185 " pdb="FE4 SF4 A1006 " - pdb=" SG CYS A 188 " pdb=" SF4 A1007 " pdb="FE2 SF4 A1007 " - pdb=" SG CYS A 224 " pdb="FE4 SF4 A1007 " - pdb=" SG CYS A 192 " pdb="FE3 SF4 A1007 " - pdb=" SG CYS A 227 " pdb="FE1 SF4 A1007 " - pdb=" SG CYS A 230 " pdb=" SF4 A1008 " pdb="FE2 SF4 A1008 " - pdb=" SG CYS A 293 " pdb="FE3 SF4 A1008 " - pdb=" SG CYS A 261 " pdb="FE4 SF4 A1008 " - pdb=" SG CYS A 265 " pdb="FE1 SF4 A1008 " - pdb=" SG CYS A 258 " pdb=" SF4 B 602 " pdb="FE3 SF4 B 602 " - pdb=" SG CYS B 430 " pdb="FE4 SF4 B 602 " - pdb=" SG CYS B 427 " pdb="FE1 SF4 B 602 " - pdb=" SG CYS B 471 " pdb="FE2 SF4 B 602 " - pdb=" SG CYS B 433 " pdb=" SF4 E1005 " pdb="FE2 SF4 E1005 " - pdb=" SG CYS E 121 " pdb="FE4 SF4 E1005 " - pdb=" NE2 HIS E 117 " pdb="FE3 SF4 E1005 " - pdb=" SG CYS E 124 " pdb="FE1 SF4 E1005 " - pdb=" SG CYS E 130 " pdb=" SF4 E1006 " pdb="FE2 SF4 E1006 " - pdb=" SG CYS E 182 " pdb="FE3 SF4 E1006 " - pdb=" SG CYS E 234 " pdb="FE1 SF4 E1006 " - pdb=" SG CYS E 185 " pdb="FE4 SF4 E1006 " - pdb=" SG CYS E 188 " pdb=" SF4 E1007 " pdb="FE2 SF4 E1007 " - pdb=" SG CYS E 224 " pdb="FE4 SF4 E1007 " - pdb=" SG CYS E 192 " pdb="FE3 SF4 E1007 " - pdb=" SG CYS E 227 " pdb="FE1 SF4 E1007 " - pdb=" SG CYS E 230 " pdb=" SF4 E1008 " pdb="FE2 SF4 E1008 " - pdb=" SG CYS E 293 " pdb="FE3 SF4 E1008 " - pdb=" SG CYS E 261 " pdb="FE4 SF4 E1008 " - pdb=" SG CYS E 265 " pdb="FE1 SF4 E1008 " - pdb=" SG CYS E 258 " pdb=" SF4 F 602 " pdb="FE3 SF4 F 602 " - pdb=" SG CYS F 430 " pdb="FE4 SF4 F 602 " - pdb=" SG CYS F 427 " pdb="FE1 SF4 F 602 " - pdb=" SG CYS F 471 " pdb="FE2 SF4 F 602 " - pdb=" SG CYS F 433 " Number of angles added : 138 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6008 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 32 sheets defined 43.9% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 41 through 49 Processing helix chain 'A' and resid 99 through 115 Processing helix chain 'A' and resid 132 through 139 removed outlier: 3.616A pdb=" N VAL A 139 " --> pdb=" O MET A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 182 Processing helix chain 'A' and resid 186 through 195 Processing helix chain 'A' and resid 228 through 234 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 293 through 298 Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.528A pdb=" N HIS A 305 " --> pdb=" O TYR A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 345 removed outlier: 3.876A pdb=" N ALA A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 359 through 372 removed outlier: 3.502A pdb=" N THR A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 removed outlier: 3.547A pdb=" N ARG A 384 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 398 removed outlier: 4.200A pdb=" N LYS A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 427 through 439 removed outlier: 3.712A pdb=" N ARG A 433 " --> pdb=" O VAL A 429 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 487 removed outlier: 3.830A pdb=" N MET A 477 " --> pdb=" O ASN A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 499 removed outlier: 3.631A pdb=" N ILE A 495 " --> pdb=" O ASP A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 512 removed outlier: 3.774A pdb=" N ASP A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 516 removed outlier: 3.521A pdb=" N TYR A 516 " --> pdb=" O ASN A 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 513 through 516' Processing helix chain 'A' and resid 517 through 526 removed outlier: 5.450A pdb=" N SER A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 542 removed outlier: 3.859A pdb=" N LEU A 532 " --> pdb=" O PRO A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 555 removed outlier: 3.818A pdb=" N THR A 554 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 550 through 555' Processing helix chain 'A' and resid 559 through 574 Processing helix chain 'A' and resid 591 through 598 Processing helix chain 'A' and resid 613 through 625 removed outlier: 3.632A pdb=" N LEU A 619 " --> pdb=" O ALA A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 646 Processing helix chain 'A' and resid 664 through 674 removed outlier: 3.524A pdb=" N ALA A 674 " --> pdb=" O ALA A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 692 removed outlier: 3.551A pdb=" N ASN A 690 " --> pdb=" O GLU A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 742 Processing helix chain 'A' and resid 749 through 761 removed outlier: 3.995A pdb=" N ILE A 753 " --> pdb=" O HIS A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 776 Processing helix chain 'A' and resid 843 through 847 removed outlier: 3.996A pdb=" N THR A 846 " --> pdb=" O THR A 843 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL A 847 " --> pdb=" O GLU A 844 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 843 through 847' Processing helix chain 'A' and resid 858 through 863 removed outlier: 4.382A pdb=" N THR A 863 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 950 removed outlier: 3.814A pdb=" N ASP A 943 " --> pdb=" O ASP A 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 13 Processing helix chain 'B' and resid 15 through 30 Processing helix chain 'B' and resid 44 through 48 removed outlier: 3.622A pdb=" N LEU B 47 " --> pdb=" O MET B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 73 Processing helix chain 'B' and resid 90 through 95 Processing helix chain 'B' and resid 111 through 118 Processing helix chain 'B' and resid 121 through 128 removed outlier: 3.532A pdb=" N ARG B 125 " --> pdb=" O TRP B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 143 removed outlier: 3.713A pdb=" N SER B 142 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 163 Processing helix chain 'B' and resid 183 through 191 Processing helix chain 'B' and resid 193 through 208 removed outlier: 3.574A pdb=" N VAL B 197 " --> pdb=" O PRO B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 234 Processing helix chain 'B' and resid 234 through 240 removed outlier: 3.628A pdb=" N GLU B 240 " --> pdb=" O PRO B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 258 through 267 Processing helix chain 'B' and resid 284 through 288 Processing helix chain 'B' and resid 294 through 308 removed outlier: 4.003A pdb=" N VAL B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Proline residue: B 302 - end of helix Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.571A pdb=" N TYR B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 352 Processing helix chain 'B' and resid 377 through 383 removed outlier: 4.359A pdb=" N HIS B 382 " --> pdb=" O SER B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 393 Processing helix chain 'B' and resid 410 through 425 removed outlier: 3.689A pdb=" N MET B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 450 removed outlier: 3.945A pdb=" N GLY B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA B 437 " --> pdb=" O CYS B 433 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU B 442 " --> pdb=" O VAL B 438 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP B 445 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 469 Processing helix chain 'B' and resid 477 through 488 removed outlier: 4.134A pdb=" N VAL B 481 " --> pdb=" O THR B 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 14 Processing helix chain 'G' and resid 20 through 33 Processing helix chain 'G' and resid 36 through 39 Processing helix chain 'G' and resid 40 through 48 removed outlier: 3.627A pdb=" N ALA G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 61 Processing helix chain 'G' and resid 79 through 85 Processing helix chain 'G' and resid 86 through 98 removed outlier: 4.072A pdb=" N VAL G 90 " --> pdb=" O GLY G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 147 removed outlier: 3.887A pdb=" N GLY G 143 " --> pdb=" O ALA G 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 19 removed outlier: 4.324A pdb=" N VAL D 19 " --> pdb=" O ALA D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 36 Processing helix chain 'D' and resid 37 through 51 Processing helix chain 'D' and resid 56 through 63 Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'E' and resid 41 through 49 Processing helix chain 'E' and resid 99 through 115 Processing helix chain 'E' and resid 132 through 139 removed outlier: 3.616A pdb=" N VAL E 139 " --> pdb=" O MET E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 182 Processing helix chain 'E' and resid 186 through 195 Processing helix chain 'E' and resid 228 through 234 Processing helix chain 'E' and resid 242 through 247 Processing helix chain 'E' and resid 293 through 298 Processing helix chain 'E' and resid 301 through 305 removed outlier: 3.528A pdb=" N HIS E 305 " --> pdb=" O TYR E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 345 removed outlier: 3.875A pdb=" N ALA E 330 " --> pdb=" O ASN E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 350 Processing helix chain 'E' and resid 359 through 372 removed outlier: 3.502A pdb=" N THR E 363 " --> pdb=" O THR E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 385 removed outlier: 3.547A pdb=" N ARG E 384 " --> pdb=" O THR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 398 removed outlier: 4.199A pdb=" N LYS E 395 " --> pdb=" O GLY E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 413 Processing helix chain 'E' and resid 427 through 439 removed outlier: 3.713A pdb=" N ARG E 433 " --> pdb=" O VAL E 429 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG E 437 " --> pdb=" O ARG E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 487 removed outlier: 3.831A pdb=" N MET E 477 " --> pdb=" O ASN E 473 " (cutoff:3.500A) Processing helix chain 'E' and resid 491 through 499 removed outlier: 3.631A pdb=" N ILE E 495 " --> pdb=" O ASP E 491 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 512 removed outlier: 3.773A pdb=" N ASP E 506 " --> pdb=" O ASP E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 513 through 516 removed outlier: 3.521A pdb=" N TYR E 516 " --> pdb=" O ASN E 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 513 through 516' Processing helix chain 'E' and resid 517 through 526 removed outlier: 5.450A pdb=" N SER E 523 " --> pdb=" O GLU E 519 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU E 524 " --> pdb=" O ALA E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 542 removed outlier: 3.859A pdb=" N LEU E 532 " --> pdb=" O PRO E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 550 through 555 removed outlier: 3.818A pdb=" N THR E 554 " --> pdb=" O GLY E 550 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU E 555 " --> pdb=" O LEU E 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 550 through 555' Processing helix chain 'E' and resid 559 through 574 Processing helix chain 'E' and resid 591 through 598 Processing helix chain 'E' and resid 613 through 625 removed outlier: 3.632A pdb=" N LEU E 619 " --> pdb=" O ALA E 615 " (cutoff:3.500A) Processing helix chain 'E' and resid 635 through 646 Processing helix chain 'E' and resid 664 through 674 removed outlier: 3.524A pdb=" N ALA E 674 " --> pdb=" O ALA E 670 " (cutoff:3.500A) Processing helix chain 'E' and resid 686 through 692 removed outlier: 3.551A pdb=" N ASN E 690 " --> pdb=" O GLU E 687 " (cutoff:3.500A) Processing helix chain 'E' and resid 729 through 742 Processing helix chain 'E' and resid 749 through 761 removed outlier: 3.995A pdb=" N ILE E 753 " --> pdb=" O HIS E 749 " (cutoff:3.500A) Processing helix chain 'E' and resid 768 through 776 Processing helix chain 'E' and resid 843 through 847 removed outlier: 3.995A pdb=" N THR E 846 " --> pdb=" O THR E 843 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL E 847 " --> pdb=" O GLU E 844 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 843 through 847' Processing helix chain 'E' and resid 858 through 863 removed outlier: 4.382A pdb=" N THR E 863 " --> pdb=" O THR E 859 " (cutoff:3.500A) Processing helix chain 'E' and resid 939 through 950 removed outlier: 3.815A pdb=" N ASP E 943 " --> pdb=" O ASP E 939 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 13 Processing helix chain 'F' and resid 15 through 30 Processing helix chain 'F' and resid 44 through 48 removed outlier: 3.622A pdb=" N LEU F 47 " --> pdb=" O MET F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 73 Processing helix chain 'F' and resid 90 through 95 Processing helix chain 'F' and resid 111 through 118 Processing helix chain 'F' and resid 121 through 128 removed outlier: 3.532A pdb=" N ARG F 125 " --> pdb=" O TRP F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 143 removed outlier: 3.712A pdb=" N SER F 142 " --> pdb=" O GLU F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 163 Processing helix chain 'F' and resid 183 through 191 Processing helix chain 'F' and resid 193 through 208 removed outlier: 3.575A pdb=" N VAL F 197 " --> pdb=" O PRO F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 234 Processing helix chain 'F' and resid 234 through 240 removed outlier: 3.627A pdb=" N GLU F 240 " --> pdb=" O PRO F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 257 Processing helix chain 'F' and resid 258 through 267 Processing helix chain 'F' and resid 284 through 288 Processing helix chain 'F' and resid 294 through 308 removed outlier: 4.001A pdb=" N VAL F 301 " --> pdb=" O SER F 297 " (cutoff:3.500A) Proline residue: F 302 - end of helix Processing helix chain 'F' and resid 308 through 313 removed outlier: 3.570A pdb=" N TYR F 312 " --> pdb=" O GLY F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 352 Processing helix chain 'F' and resid 377 through 383 removed outlier: 4.361A pdb=" N HIS F 382 " --> pdb=" O SER F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 393 Processing helix chain 'F' and resid 410 through 425 removed outlier: 3.689A pdb=" N MET F 419 " --> pdb=" O ALA F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 450 removed outlier: 3.945A pdb=" N GLY F 436 " --> pdb=" O PRO F 432 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA F 437 " --> pdb=" O CYS F 433 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL F 438 " --> pdb=" O ARG F 434 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU F 442 " --> pdb=" O VAL F 438 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP F 445 " --> pdb=" O VAL F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 469 Processing helix chain 'F' and resid 477 through 488 removed outlier: 4.134A pdb=" N VAL F 481 " --> pdb=" O THR F 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 14 Processing helix chain 'C' and resid 20 through 33 Processing helix chain 'C' and resid 36 through 39 Processing helix chain 'C' and resid 40 through 48 removed outlier: 3.628A pdb=" N ALA C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 61 Processing helix chain 'C' and resid 79 through 85 Processing helix chain 'C' and resid 86 through 98 removed outlier: 4.072A pdb=" N VAL C 90 " --> pdb=" O GLY C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 147 removed outlier: 3.887A pdb=" N GLY C 143 " --> pdb=" O ALA C 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 19 removed outlier: 4.324A pdb=" N VAL H 19 " --> pdb=" O ALA H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 36 Processing helix chain 'H' and resid 37 through 51 Processing helix chain 'H' and resid 56 through 63 Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 36 removed outlier: 9.358A pdb=" N VAL A 95 " --> pdb=" O HIS A 26 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR A 28 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 175 through 177 Processing sheet with id=AA3, first strand: chain 'A' and resid 202 through 204 Processing sheet with id=AA4, first strand: chain 'A' and resid 252 through 257 removed outlier: 3.622A pdb=" N ARG A 278 " --> pdb=" O HIS A 270 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU A 272 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 353 removed outlier: 5.925A pdb=" N ILE A 353 " --> pdb=" O GLN A 654 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 463 through 465 removed outlier: 6.470A pdb=" N LEU A 444 " --> pdb=" O TRP A 464 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ALA A 545 " --> pdb=" O GLY A 582 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N ASN A 584 " --> pdb=" O ALA A 545 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE A 547 " --> pdb=" O ASN A 584 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 604 through 605 removed outlier: 3.586A pdb=" N ARG A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 706 through 709 removed outlier: 3.753A pdb=" N VAL A 778 " --> pdb=" O ILE A 715 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 827 through 828 Processing sheet with id=AB2, first strand: chain 'A' and resid 853 through 856 Processing sheet with id=AB3, first strand: chain 'B' and resid 35 through 37 removed outlier: 5.450A pdb=" N LYS B 2 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU B 54 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU B 52 " --> pdb=" O TRP B 4 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY B 85 " --> pdb=" O GLY B 61 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 244 through 249 removed outlier: 6.645A pdb=" N GLY B 212 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ARG B 248 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL B 214 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE B 171 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N TYR B 215 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N CYS B 173 " --> pdb=" O TYR B 215 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 323 through 328 Processing sheet with id=AB6, first strand: chain 'B' and resid 375 through 376 removed outlier: 7.005A pdb=" N HIS B 405 " --> pdb=" O LYS B 364 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VAL B 366 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL B 403 " --> pdb=" O VAL B 366 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 111 through 112 removed outlier: 6.191A pdb=" N ILE G 74 " --> pdb=" O GLU G 112 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 36 removed outlier: 9.358A pdb=" N VAL E 95 " --> pdb=" O HIS E 26 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR E 28 " --> pdb=" O VAL E 95 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 175 through 177 Processing sheet with id=AC1, first strand: chain 'E' and resid 202 through 204 Processing sheet with id=AC2, first strand: chain 'E' and resid 252 through 257 removed outlier: 3.623A pdb=" N ARG E 278 " --> pdb=" O HIS E 270 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU E 272 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU E 276 " --> pdb=" O LEU E 272 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 313 through 314 Processing sheet with id=AC4, first strand: chain 'E' and resid 352 through 353 removed outlier: 5.926A pdb=" N ILE E 353 " --> pdb=" O GLN E 654 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 463 through 465 removed outlier: 6.471A pdb=" N LEU E 444 " --> pdb=" O TRP E 464 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ALA E 545 " --> pdb=" O GLY E 582 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ASN E 584 " --> pdb=" O ALA E 545 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE E 547 " --> pdb=" O ASN E 584 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 604 through 605 removed outlier: 3.585A pdb=" N ARG E 609 " --> pdb=" O PHE E 605 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 706 through 709 removed outlier: 3.753A pdb=" N VAL E 778 " --> pdb=" O ILE E 715 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 827 through 828 Processing sheet with id=AC9, first strand: chain 'E' and resid 853 through 856 Processing sheet with id=AD1, first strand: chain 'F' and resid 35 through 37 removed outlier: 5.451A pdb=" N LYS F 2 " --> pdb=" O GLU F 54 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU F 54 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU F 52 " --> pdb=" O TRP F 4 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY F 85 " --> pdb=" O GLY F 61 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 244 through 249 removed outlier: 6.645A pdb=" N GLY F 212 " --> pdb=" O GLU F 246 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ARG F 248 " --> pdb=" O GLY F 212 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL F 214 " --> pdb=" O ARG F 248 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE F 171 " --> pdb=" O TYR F 213 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N TYR F 215 " --> pdb=" O ILE F 171 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N CYS F 173 " --> pdb=" O TYR F 215 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 323 through 328 Processing sheet with id=AD4, first strand: chain 'F' and resid 375 through 376 removed outlier: 7.005A pdb=" N HIS F 405 " --> pdb=" O LYS F 364 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VAL F 366 " --> pdb=" O VAL F 403 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL F 403 " --> pdb=" O VAL F 366 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 111 through 112 removed outlier: 6.191A pdb=" N ILE C 74 " --> pdb=" O GLU C 112 " (cutoff:3.500A) 958 hydrogen bonds defined for protein. 2670 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: 5.09 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 10681 1.42 - 1.64: 14919 1.64 - 1.85: 286 1.85 - 2.07: 2 2.07 - 2.28: 136 Bond restraints: 26024 Sorted by residual: bond pdb=" O5' FMN B 601 " pdb=" P FMN B 601 " ideal model delta sigma weight residual 1.610 1.842 -0.232 2.00e-02 2.50e+03 1.35e+02 bond pdb=" O5' FMN F 601 " pdb=" P FMN F 601 " ideal model delta sigma weight residual 1.610 1.842 -0.232 2.00e-02 2.50e+03 1.34e+02 bond pdb=" O3A MGD E1001 " pdb=" PA MGD E1001 " ideal model delta sigma weight residual 1.649 1.858 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" O3A MGD A1001 " pdb=" PA MGD A1001 " ideal model delta sigma weight residual 1.649 1.857 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" O3A MGD E1002 " pdb=" PA MGD E1002 " ideal model delta sigma weight residual 1.649 1.851 -0.202 2.00e-02 2.50e+03 1.02e+02 ... (remaining 26019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.18: 35146 4.18 - 8.37: 332 8.37 - 12.55: 20 12.55 - 16.74: 14 16.74 - 20.92: 8 Bond angle restraints: 35520 Sorted by residual: angle pdb=" S1 FES G 201 " pdb="FE2 FES G 201 " pdb=" S2 FES G 201 " ideal model delta sigma weight residual 104.33 83.44 20.89 1.14e+00 7.69e-01 3.36e+02 angle pdb=" S1 FES C 201 " pdb="FE2 FES C 201 " pdb=" S2 FES C 201 " ideal model delta sigma weight residual 104.33 83.46 20.87 1.14e+00 7.69e-01 3.35e+02 angle pdb=" S1 FES G 201 " pdb="FE1 FES G 201 " pdb=" S2 FES G 201 " ideal model delta sigma weight residual 104.33 83.41 20.92 1.20e+00 6.94e-01 3.04e+02 angle pdb=" S1 FES E1004 " pdb="FE2 FES E1004 " pdb=" S2 FES E1004 " ideal model delta sigma weight residual 104.33 84.46 19.87 1.14e+00 7.69e-01 3.04e+02 angle pdb=" S1 FES A1004 " pdb="FE2 FES A1004 " pdb=" S2 FES A1004 " ideal model delta sigma weight residual 104.33 84.47 19.86 1.14e+00 7.69e-01 3.03e+02 ... (remaining 35515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.50: 15011 34.50 - 69.00: 305 69.00 - 103.50: 26 103.50 - 137.99: 2 137.99 - 172.49: 2 Dihedral angle restraints: 15346 sinusoidal: 5952 harmonic: 9394 Sorted by residual: dihedral pdb=" C10 FMN B 601 " pdb=" C1' FMN B 601 " pdb=" N10 FMN B 601 " pdb=" C2' FMN B 601 " ideal model delta sinusoidal sigma weight residual 257.59 85.10 172.49 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C10 FMN F 601 " pdb=" C1' FMN F 601 " pdb=" N10 FMN F 601 " pdb=" C2' FMN F 601 " ideal model delta sinusoidal sigma weight residual 257.59 85.12 172.47 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C5' FMN B 601 " pdb=" O5' FMN B 601 " pdb=" P FMN B 601 " pdb=" O1P FMN B 601 " ideal model delta sinusoidal sigma weight residual 75.26 -59.96 135.22 1 2.00e+01 2.50e-03 4.10e+01 ... (remaining 15343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3499 0.087 - 0.173: 407 0.173 - 0.260: 47 0.260 - 0.347: 11 0.347 - 0.433: 4 Chirality restraints: 3968 Sorted by residual: chirality pdb=" C14 MGD A1002 " pdb=" C13 MGD A1002 " pdb=" C23 MGD A1002 " pdb=" N15 MGD A1002 " both_signs ideal model delta sigma weight residual False -2.55 -2.99 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" C14 MGD E1002 " pdb=" C13 MGD E1002 " pdb=" C23 MGD E1002 " pdb=" N15 MGD E1002 " both_signs ideal model delta sigma weight residual False -2.55 -2.99 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" C23 MGD E1002 " pdb=" C14 MGD E1002 " pdb=" N22 MGD E1002 " pdb=" O11 MGD E1002 " both_signs ideal model delta sigma weight residual False 2.33 2.75 -0.42 2.00e-01 2.50e+01 4.49e+00 ... (remaining 3965 not shown) Planarity restraints: 4610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 477 " -0.033 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO B 478 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 478 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 478 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 477 " 0.033 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO F 478 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO F 478 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 478 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 280 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO A 281 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 281 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 281 " -0.024 5.00e-02 4.00e+02 ... (remaining 4607 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 186 2.46 - 3.07: 18468 3.07 - 3.68: 38601 3.68 - 4.29: 58339 4.29 - 4.90: 101374 Nonbonded interactions: 216968 Sorted by model distance: nonbonded pdb=" OG1 THR E 882 " pdb=" O PRO E 937 " model vdw 1.847 3.040 nonbonded pdb=" OG1 THR A 882 " pdb=" O PRO A 937 " model vdw 1.848 3.040 nonbonded pdb=" OG1 THR F 357 " pdb=" O ARG F 361 " model vdw 2.015 3.040 nonbonded pdb=" OG1 THR B 357 " pdb=" O ARG B 361 " model vdw 2.016 3.040 nonbonded pdb=" O LYS E 395 " pdb=" NH2 ARG E 800 " model vdw 2.019 3.120 ... (remaining 216963 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 30.390 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 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 : 0.017 0.409 26080 Z= 0.843 Angle : 1.508 38.872 35658 Z= 0.891 Chirality : 0.062 0.433 3968 Planarity : 0.004 0.049 4610 Dihedral : 14.649 172.492 9338 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.78 % Favored : 91.97 % Rotamer: Outliers : 0.62 % Allowed : 5.39 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.02 (0.12), residues: 3302 helix: -2.11 (0.12), residues: 1246 sheet: -3.07 (0.23), residues: 344 loop : -3.06 (0.12), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 713 TYR 0.020 0.002 TYR A 260 PHE 0.014 0.002 PHE A 407 TRP 0.013 0.001 TRP A 11 HIS 0.010 0.002 HIS E 603 Details of bonding type rmsd/Z covalent geometry : bond 0.01571 / 0.83 (26024) covalent geometry : angle 1.32732 / 0.89 (35520) hydrogen bonds : bond 0.15734 / 10.92 ( 958) hydrogen bonds : angle 7.35676 / 5.15 ( 2670) metal coordination : bond 0.12231 / 7.93 ( 56) metal coordination : angle 11.57455 / 7.96 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 575 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 PHE cc_start: 0.8469 (m-10) cc_final: 0.8219 (m-80) REVERT: A 209 ASP cc_start: 0.7466 (t0) cc_final: 0.7006 (t0) REVERT: A 328 THR cc_start: 0.7645 (m) cc_final: 0.7267 (m) REVERT: A 501 TRP cc_start: 0.7047 (t-100) cc_final: 0.6383 (t-100) REVERT: A 728 PHE cc_start: 0.7192 (m-80) cc_final: 0.6837 (m-10) REVERT: B 170 TYR cc_start: 0.7894 (m-80) cc_final: 0.7672 (m-80) REVERT: B 349 LEU cc_start: 0.8126 (tp) cc_final: 0.7875 (tp) REVERT: G 136 LEU cc_start: 0.7194 (mp) cc_final: 0.6994 (mt) REVERT: E 199 PHE cc_start: 0.8464 (m-10) cc_final: 0.8239 (m-10) REVERT: E 209 ASP cc_start: 0.7471 (t0) cc_final: 0.7020 (t0) REVERT: E 328 THR cc_start: 0.7658 (m) cc_final: 0.7278 (m) REVERT: E 501 TRP cc_start: 0.6979 (t-100) cc_final: 0.6349 (t-100) REVERT: E 728 PHE cc_start: 0.7221 (m-80) cc_final: 0.6840 (m-10) REVERT: F 349 LEU cc_start: 0.8116 (tp) cc_final: 0.7873 (tp) REVERT: C 115 TYR cc_start: 0.7783 (m-80) cc_final: 0.7506 (m-80) outliers start: 16 outliers final: 2 residues processed: 589 average time/residue: 0.2023 time to fit residues: 176.6651 Evaluate side-chains 364 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 362 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain E residue 12 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.0170 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 3.9990 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 275 GLN A 405 GLN ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 GLN A 558 GLN ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN D 31 HIS E 275 GLN ** E 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 GLN ** E 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 534 GLN E 558 GLN ** E 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.166270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.135553 restraints weight = 32335.626| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.76 r_work: 0.3267 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 26080 Z= 0.158 Angle : 0.851 27.171 35658 Z= 0.334 Chirality : 0.044 0.207 3968 Planarity : 0.005 0.050 4610 Dihedral : 8.335 176.365 3696 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.18 % Favored : 95.58 % Rotamer: Outliers : 1.45 % Allowed : 11.88 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.14), residues: 3302 helix: -0.48 (0.14), residues: 1254 sheet: -2.52 (0.24), residues: 362 loop : -2.29 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 101 TYR 0.018 0.001 TYR A 260 PHE 0.014 0.001 PHE E 333 TRP 0.020 0.001 TRP A 780 HIS 0.010 0.001 HIS A 901 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (26024) covalent geometry : angle 0.66098 / 0.33 (35520) hydrogen bonds : bond 0.03946 / 2.71 ( 958) hydrogen bonds : angle 5.18444 / 3.62 ( 2670) metal coordination : bond 0.01755 / 1.08 ( 56) metal coordination : angle 8.63191 / 5.80 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 424 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.8027 (mmt180) cc_final: 0.7765 (mmt-90) REVERT: A 209 ASP cc_start: 0.7997 (t0) cc_final: 0.7558 (t0) REVERT: A 501 TRP cc_start: 0.7130 (t-100) cc_final: 0.6123 (t-100) REVERT: A 728 PHE cc_start: 0.7361 (m-80) cc_final: 0.7030 (m-10) REVERT: B 185 ASP cc_start: 0.7690 (m-30) cc_final: 0.7391 (m-30) REVERT: B 198 GLU cc_start: 0.7265 (tt0) cc_final: 0.6900 (pt0) REVERT: B 233 MET cc_start: 0.7638 (mtp) cc_final: 0.7275 (mtp) REVERT: B 349 LEU cc_start: 0.8451 (tp) cc_final: 0.8133 (tp) REVERT: B 381 TYR cc_start: 0.7222 (m-10) cc_final: 0.7018 (m-10) REVERT: G 3 ASP cc_start: 0.6408 (m-30) cc_final: 0.5657 (t0) REVERT: D 45 LEU cc_start: 0.7696 (mt) cc_final: 0.7469 (mt) REVERT: E 20 ARG cc_start: 0.7997 (mmt180) cc_final: 0.7734 (mmt-90) REVERT: E 209 ASP cc_start: 0.7954 (t0) cc_final: 0.7531 (t0) REVERT: E 501 TRP cc_start: 0.7124 (t-100) cc_final: 0.6122 (t-100) REVERT: E 728 PHE cc_start: 0.7320 (m-80) cc_final: 0.7000 (m-10) REVERT: F 185 ASP cc_start: 0.7691 (m-30) cc_final: 0.7429 (m-30) REVERT: F 198 GLU cc_start: 0.7285 (tt0) cc_final: 0.6902 (pt0) REVERT: F 233 MET cc_start: 0.7637 (mtp) cc_final: 0.7278 (mtp) REVERT: F 264 ASN cc_start: 0.8845 (t0) cc_final: 0.8638 (t0) REVERT: F 349 LEU cc_start: 0.8460 (tp) cc_final: 0.8156 (tp) REVERT: F 381 TYR cc_start: 0.7113 (m-10) cc_final: 0.6912 (m-10) REVERT: C 115 TYR cc_start: 0.8195 (m-80) cc_final: 0.7483 (m-80) outliers start: 37 outliers final: 15 residues processed: 447 average time/residue: 0.1883 time to fit residues: 128.7293 Evaluate side-chains 357 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 342 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 253 LYS Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 813 THR Chi-restraints excluded: chain E residue 827 THR Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain C residue 94 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: [166, 170, 105, 135, 17, 161, 308, 276, 269, 184, 158] chunk 166 optimal weight: 1.9990 chunk 170 optimal weight: 0.0010 chunk 105 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 chunk 308 optimal weight: 0.7980 chunk 276 optimal weight: 10.0000 chunk 269 optimal weight: 10.0000 chunk 184 optimal weight: 0.5980 chunk 158 optimal weight: 1.9990 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 275 GLN ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 HIS ** A 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 GLN ** E 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS ** E 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.164748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.135095 restraints weight = 32151.545| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.78 r_work: 0.3244 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26080 Z= 0.129 Angle : 0.775 29.041 35658 Z= 0.297 Chirality : 0.043 0.159 3968 Planarity : 0.005 0.051 4610 Dihedral : 7.813 175.080 3694 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.94 % Favored : 94.94 % Rotamer: Outliers : 1.99 % Allowed : 13.48 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.14), residues: 3302 helix: 0.07 (0.15), residues: 1282 sheet: -1.96 (0.25), residues: 370 loop : -1.84 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 101 TYR 0.018 0.001 TYR E 260 PHE 0.014 0.001 PHE A 333 TRP 0.019 0.001 TRP E 780 HIS 0.006 0.001 HIS E 901 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (26024) covalent geometry : angle 0.59131 / 0.29 (35520) hydrogen bonds : bond 0.03321 / 2.27 ( 958) hydrogen bonds : angle 4.73096 / 3.30 ( 2670) metal coordination : bond 0.01484 / 0.88 ( 56) metal coordination : angle 8.07314 / 5.47 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 358 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7933 (mmt180) cc_final: 0.7598 (mmt-90) REVERT: A 209 ASP cc_start: 0.8055 (t0) cc_final: 0.7607 (t0) REVERT: A 501 TRP cc_start: 0.7039 (t-100) cc_final: 0.5999 (t-100) REVERT: A 728 PHE cc_start: 0.7122 (m-80) cc_final: 0.6832 (m-80) REVERT: B 47 LEU cc_start: 0.6676 (OUTLIER) cc_final: 0.6251 (pp) REVERT: B 185 ASP cc_start: 0.7542 (m-30) cc_final: 0.7243 (m-30) REVERT: B 198 GLU cc_start: 0.7238 (tt0) cc_final: 0.6880 (pt0) REVERT: B 233 MET cc_start: 0.7526 (mtp) cc_final: 0.7108 (mtp) REVERT: D 34 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6741 (mp0) REVERT: E 60 ASP cc_start: 0.8158 (m-30) cc_final: 0.7909 (m-30) REVERT: E 209 ASP cc_start: 0.8040 (t0) cc_final: 0.7604 (t0) REVERT: E 501 TRP cc_start: 0.7085 (t-100) cc_final: 0.6047 (t-100) REVERT: E 728 PHE cc_start: 0.7158 (m-80) cc_final: 0.6837 (m-80) REVERT: E 793 MET cc_start: 0.7171 (mtm) cc_final: 0.6968 (mtm) REVERT: F 47 LEU cc_start: 0.6625 (OUTLIER) cc_final: 0.6256 (pp) REVERT: F 185 ASP cc_start: 0.7496 (m-30) cc_final: 0.7197 (m-30) REVERT: F 198 GLU cc_start: 0.7273 (tt0) cc_final: 0.6876 (pt0) REVERT: F 233 MET cc_start: 0.7516 (mtp) cc_final: 0.7117 (mtp) REVERT: C 115 TYR cc_start: 0.8092 (m-80) cc_final: 0.7416 (m-80) REVERT: H 45 LEU cc_start: 0.7490 (mt) cc_final: 0.7251 (mt) outliers start: 51 outliers final: 27 residues processed: 399 average time/residue: 0.1730 time to fit residues: 107.6910 Evaluate side-chains 358 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 329 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 253 LYS Chi-restraints excluded: chain E residue 659 LEU Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 813 THR Chi-restraints excluded: chain E residue 827 THR Chi-restraints excluded: chain E residue 898 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain H residue 7 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: [94, 82, 4, 159, 195, 248, 70, 91, 29, 271, 175] chunk 94 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 195 optimal weight: 10.0000 chunk 248 optimal weight: 0.0980 chunk 70 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 271 optimal weight: 20.0000 chunk 175 optimal weight: 0.9980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 GLN A 794 HIS A 941 GLN ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN ** E 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 941 GLN ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.159522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.127992 restraints weight = 32109.671| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.85 r_work: 0.3135 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26080 Z= 0.181 Angle : 0.856 33.664 35658 Z= 0.316 Chirality : 0.045 0.185 3968 Planarity : 0.005 0.054 4610 Dihedral : 7.811 173.042 3694 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.15 % Favored : 94.73 % Rotamer: Outliers : 2.38 % Allowed : 14.45 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.14), residues: 3302 helix: 0.12 (0.15), residues: 1292 sheet: -1.79 (0.26), residues: 386 loop : -1.66 (0.14), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 101 TYR 0.018 0.002 TYR A 260 PHE 0.015 0.001 PHE E 333 TRP 0.017 0.001 TRP E 780 HIS 0.006 0.001 HIS E 794 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (26024) covalent geometry : angle 0.62832 / 0.31 (35520) hydrogen bonds : bond 0.03416 / 2.35 ( 958) hydrogen bonds : angle 4.66599 / 3.25 ( 2670) metal coordination : bond 0.01936 / 1.19 ( 56) metal coordination : angle 9.36853 / 6.44 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 354 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.8185 (t0) cc_final: 0.7688 (t0) REVERT: A 736 MET cc_start: 0.8002 (mtt) cc_final: 0.7633 (mtt) REVERT: A 874 LEU cc_start: 0.8056 (mp) cc_final: 0.7761 (mt) REVERT: B 47 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6391 (pp) REVERT: B 125 ARG cc_start: 0.7264 (ptp90) cc_final: 0.6799 (mmt90) REVERT: B 185 ASP cc_start: 0.7738 (m-30) cc_final: 0.7389 (m-30) REVERT: B 198 GLU cc_start: 0.7301 (tt0) cc_final: 0.6961 (pt0) REVERT: B 233 MET cc_start: 0.7605 (mtp) cc_final: 0.7318 (mtp) REVERT: B 361 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7709 (mtt-85) REVERT: G 46 ASP cc_start: 0.8372 (t0) cc_final: 0.8098 (t0) REVERT: D 34 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7206 (mp0) REVERT: E 209 ASP cc_start: 0.8188 (t0) cc_final: 0.7689 (t0) REVERT: E 736 MET cc_start: 0.7936 (mtt) cc_final: 0.7583 (mtt) REVERT: E 874 LEU cc_start: 0.8052 (mp) cc_final: 0.7765 (mt) REVERT: F 47 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6389 (pp) REVERT: F 125 ARG cc_start: 0.7239 (ptp90) cc_final: 0.6793 (mmt90) REVERT: F 185 ASP cc_start: 0.7698 (m-30) cc_final: 0.7359 (m-30) REVERT: F 198 GLU cc_start: 0.7290 (tt0) cc_final: 0.6951 (pt0) REVERT: F 361 ARG cc_start: 0.8055 (mtt-85) cc_final: 0.7675 (mtt180) REVERT: C 115 TYR cc_start: 0.8466 (m-80) cc_final: 0.7974 (m-80) outliers start: 61 outliers final: 41 residues processed: 396 average time/residue: 0.1811 time to fit residues: 110.2232 Evaluate side-chains 363 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 319 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 361 ARG Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 199 PHE Chi-restraints excluded: chain E residue 408 ASP Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 659 LEU Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 813 THR Chi-restraints excluded: chain E residue 827 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: [90, 112, 279, 237, 2, 109, 225, 45, 13, 268, 131] chunk 90 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 279 optimal weight: 0.9990 chunk 237 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 268 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 GLN ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 HIS ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 GLN ** E 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.155650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.124852 restraints weight = 32504.416| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.90 r_work: 0.3056 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 26080 Z= 0.268 Angle : 0.944 34.651 35658 Z= 0.356 Chirality : 0.049 0.227 3968 Planarity : 0.005 0.061 4610 Dihedral : 7.878 170.837 3694 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.57 % Favored : 94.28 % Rotamer: Outliers : 3.40 % Allowed : 15.00 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.14), residues: 3302 helix: 0.10 (0.15), residues: 1276 sheet: -1.71 (0.26), residues: 402 loop : -1.56 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 101 TYR 0.020 0.002 TYR E 260 PHE 0.015 0.002 PHE E 333 TRP 0.017 0.002 TRP E 780 HIS 0.005 0.001 HIS F 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00651 / 0.27 (26024) covalent geometry : angle 0.70597 / 0.35 (35520) hydrogen bonds : bond 0.03815 / 2.62 ( 958) hydrogen bonds : angle 4.82653 / 3.37 ( 2670) metal coordination : bond 0.02548 / 1.56 ( 56) metal coordination : angle 10.10507 / 6.97 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 347 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.8344 (t0) cc_final: 0.7777 (t0) REVERT: A 453 ASP cc_start: 0.7822 (t70) cc_final: 0.7598 (t0) REVERT: A 501 TRP cc_start: 0.7392 (t-100) cc_final: 0.7116 (t-100) REVERT: A 510 PHE cc_start: 0.7245 (t80) cc_final: 0.7041 (t80) REVERT: A 736 MET cc_start: 0.8004 (mtt) cc_final: 0.7783 (mtp) REVERT: B 47 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6429 (pp) REVERT: B 125 ARG cc_start: 0.7399 (ptp90) cc_final: 0.6901 (mmt90) REVERT: B 198 GLU cc_start: 0.7538 (tt0) cc_final: 0.7320 (pt0) REVERT: G 46 ASP cc_start: 0.8676 (t0) cc_final: 0.8384 (t0) REVERT: D 34 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7338 (mp0) REVERT: E 209 ASP cc_start: 0.8347 (t0) cc_final: 0.7794 (t0) REVERT: E 453 ASP cc_start: 0.7865 (t70) cc_final: 0.7632 (t0) REVERT: E 501 TRP cc_start: 0.7398 (t-100) cc_final: 0.7134 (t-100) REVERT: E 736 MET cc_start: 0.7998 (mtt) cc_final: 0.7778 (mtp) REVERT: F 47 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6460 (pp) REVERT: F 125 ARG cc_start: 0.7379 (ptp90) cc_final: 0.6878 (mmt90) REVERT: F 198 GLU cc_start: 0.7542 (tt0) cc_final: 0.7317 (pt0) REVERT: F 233 MET cc_start: 0.8009 (mtm) cc_final: 0.7623 (mtp) REVERT: F 331 ASN cc_start: 0.8618 (t0) cc_final: 0.8327 (t0) REVERT: F 361 ARG cc_start: 0.8086 (mtt-85) cc_final: 0.7865 (mtt180) REVERT: C 115 TYR cc_start: 0.8731 (m-80) cc_final: 0.8519 (m-80) outliers start: 87 outliers final: 63 residues processed: 412 average time/residue: 0.1843 time to fit residues: 116.5787 Evaluate side-chains 386 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 321 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 888 THR Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 935 ASN Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 199 PHE Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 592 VAL Chi-restraints excluded: chain E residue 601 PHE Chi-restraints excluded: chain E residue 611 VAL Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 793 MET Chi-restraints excluded: chain E residue 813 THR Chi-restraints excluded: chain E residue 827 THR Chi-restraints excluded: chain E residue 888 THR Chi-restraints excluded: chain E residue 898 THR Chi-restraints excluded: chain E residue 905 THR Chi-restraints excluded: chain E residue 935 ASN Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: [290, 106, 113, 273, 300, 278, 255, 133, 178, 41, 126] chunk 290 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 273 optimal weight: 0.8980 chunk 300 optimal weight: 0.2980 chunk 278 optimal weight: 6.9990 chunk 255 optimal weight: 5.9990 chunk 133 optimal weight: 20.0000 chunk 178 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 405 GLN ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN A 794 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 GLN ** E 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 584 ASN ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.155724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.126018 restraints weight = 32612.615| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.97 r_work: 0.3085 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 26080 Z= 0.231 Angle : 0.900 34.971 35658 Z= 0.336 Chirality : 0.047 0.206 3968 Planarity : 0.005 0.057 4610 Dihedral : 7.753 170.431 3694 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.69 % Favored : 94.19 % Rotamer: Outliers : 3.32 % Allowed : 16.21 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.14), residues: 3302 helix: 0.18 (0.15), residues: 1284 sheet: -1.68 (0.26), residues: 402 loop : -1.45 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 622 TYR 0.021 0.002 TYR A 260 PHE 0.015 0.002 PHE E 333 TRP 0.018 0.002 TRP E 780 HIS 0.005 0.001 HIS B 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.23 (26024) covalent geometry : angle 0.66770 / 0.33 (35520) hydrogen bonds : bond 0.03604 / 2.47 ( 958) hydrogen bonds : angle 4.81071 / 3.35 ( 2670) metal coordination : bond 0.02262 / 1.37 ( 56) metal coordination : angle 9.71189 / 6.65 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 331 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.8327 (t0) cc_final: 0.7821 (t0) REVERT: B 47 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6474 (pp) REVERT: B 125 ARG cc_start: 0.7384 (ptp90) cc_final: 0.6926 (mmt90) REVERT: B 198 GLU cc_start: 0.7393 (tt0) cc_final: 0.7162 (pt0) REVERT: B 233 MET cc_start: 0.7967 (mtm) cc_final: 0.7667 (mtp) REVERT: G 46 ASP cc_start: 0.8535 (t0) cc_final: 0.8251 (t0) REVERT: D 34 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7263 (mp0) REVERT: E 209 ASP cc_start: 0.8308 (t0) cc_final: 0.7776 (t0) REVERT: F 47 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6370 (pp) REVERT: F 125 ARG cc_start: 0.7349 (ptp90) cc_final: 0.6973 (mmt90) REVERT: F 198 GLU cc_start: 0.7436 (tt0) cc_final: 0.7202 (pt0) REVERT: F 233 MET cc_start: 0.7881 (mtm) cc_final: 0.7537 (mtp) REVERT: F 331 ASN cc_start: 0.8644 (t0) cc_final: 0.8376 (t0) REVERT: C 95 GLU cc_start: 0.7389 (pt0) cc_final: 0.7169 (mp0) REVERT: H 34 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6795 (mp0) outliers start: 85 outliers final: 62 residues processed: 400 average time/residue: 0.1801 time to fit residues: 111.7371 Evaluate side-chains 381 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 316 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 935 ASN Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 457 THR Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 592 VAL Chi-restraints excluded: chain E residue 601 PHE Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 813 THR Chi-restraints excluded: chain E residue 827 THR Chi-restraints excluded: chain E residue 832 SER Chi-restraints excluded: chain E residue 888 THR Chi-restraints excluded: chain E residue 898 THR Chi-restraints excluded: chain E residue 905 THR Chi-restraints excluded: chain E residue 935 ASN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 34 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: [172, 265, 154, 284, 126, 258, 113, 206, 179, 116, 203] chunk 172 optimal weight: 6.9990 chunk 265 optimal weight: 1.9990 chunk 154 optimal weight: 0.0060 chunk 284 optimal weight: 0.0980 chunk 126 optimal weight: 9.9990 chunk 258 optimal weight: 0.6980 chunk 113 optimal weight: 9.9990 chunk 206 optimal weight: 0.7980 chunk 179 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 GLN G 29 GLN ** E 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 660 GLN E 794 HIS ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.162291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.131786 restraints weight = 32238.980| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.77 r_work: 0.3199 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26080 Z= 0.107 Angle : 0.786 32.268 35658 Z= 0.285 Chirality : 0.042 0.151 3968 Planarity : 0.004 0.055 4610 Dihedral : 7.201 171.058 3694 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.72 % Favored : 95.22 % Rotamer: Outliers : 2.27 % Allowed : 17.38 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.15), residues: 3302 helix: 0.55 (0.15), residues: 1288 sheet: -1.46 (0.26), residues: 414 loop : -1.20 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 622 TYR 0.021 0.001 TYR B 215 PHE 0.014 0.001 PHE E 333 TRP 0.022 0.001 TRP E 780 HIS 0.004 0.001 HIS E 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (26024) covalent geometry : angle 0.56865 / 0.28 (35520) hydrogen bonds : bond 0.02892 / 1.99 ( 958) hydrogen bonds : angle 4.49007 / 3.13 ( 2670) metal coordination : bond 0.01262 / 0.73 ( 56) metal coordination : angle 8.74664 / 5.93 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 349 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.8217 (t0) cc_final: 0.7716 (t0) REVERT: B 47 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6385 (pp) REVERT: B 125 ARG cc_start: 0.7317 (ptp90) cc_final: 0.6901 (mmt90) REVERT: B 198 GLU cc_start: 0.7323 (tt0) cc_final: 0.6992 (pt0) REVERT: B 233 MET cc_start: 0.7803 (mtm) cc_final: 0.7431 (mtp) REVERT: G 46 ASP cc_start: 0.8416 (t0) cc_final: 0.8162 (t0) REVERT: E 135 MET cc_start: 0.8585 (mmt) cc_final: 0.8353 (mmp) REVERT: E 209 ASP cc_start: 0.8159 (t0) cc_final: 0.7670 (t0) REVERT: F 47 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6365 (pp) REVERT: F 125 ARG cc_start: 0.7304 (ptp90) cc_final: 0.6892 (mmt90) REVERT: F 198 GLU cc_start: 0.7347 (tt0) cc_final: 0.7009 (pt0) REVERT: F 233 MET cc_start: 0.7738 (mtm) cc_final: 0.7415 (mtp) REVERT: C 115 TYR cc_start: 0.8189 (m-80) cc_final: 0.7851 (m-80) REVERT: H 45 LEU cc_start: 0.7542 (mt) cc_final: 0.7323 (mt) outliers start: 58 outliers final: 41 residues processed: 393 average time/residue: 0.1795 time to fit residues: 109.9984 Evaluate side-chains 362 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 319 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 601 PHE Chi-restraints excluded: chain E residue 659 LEU Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 898 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: [32, 224, 236, 9, 245, 161, 75, 319, 31, 43, 312] chunk 32 optimal weight: 10.0000 chunk 224 optimal weight: 9.9990 chunk 236 optimal weight: 0.5980 chunk 9 optimal weight: 6.9990 chunk 245 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 319 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 312 optimal weight: 0.0030 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 HIS B 168 GLN ** E 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS E 835 ASN ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.160716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.129791 restraints weight = 32417.480| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.87 r_work: 0.3155 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26080 Z= 0.123 Angle : 0.791 32.733 35658 Z= 0.289 Chirality : 0.042 0.153 3968 Planarity : 0.004 0.057 4610 Dihedral : 7.056 170.367 3694 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.03 % Favored : 94.91 % Rotamer: Outliers : 2.30 % Allowed : 17.62 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.15), residues: 3302 helix: 0.67 (0.15), residues: 1278 sheet: -1.35 (0.27), residues: 398 loop : -1.14 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 101 TYR 0.019 0.001 TYR B 215 PHE 0.023 0.001 PHE E 510 TRP 0.019 0.001 TRP E 780 HIS 0.004 0.001 HIS D 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (26024) covalent geometry : angle 0.57837 / 0.28 (35520) hydrogen bonds : bond 0.02933 / 2.02 ( 958) hydrogen bonds : angle 4.42982 / 3.09 ( 2670) metal coordination : bond 0.01335 / 0.77 ( 56) metal coordination : angle 8.69219 / 5.94 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 333 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.8283 (t0) cc_final: 0.7783 (t0) REVERT: B 47 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6445 (pp) REVERT: B 125 ARG cc_start: 0.7284 (ptp90) cc_final: 0.6849 (mmt90) REVERT: B 198 GLU cc_start: 0.7380 (tt0) cc_final: 0.7048 (pt0) REVERT: B 233 MET cc_start: 0.7822 (mtm) cc_final: 0.7442 (mtp) REVERT: B 303 TRP cc_start: 0.7552 (t60) cc_final: 0.7339 (t60) REVERT: G 46 ASP cc_start: 0.8493 (t0) cc_final: 0.8249 (t0) REVERT: E 135 MET cc_start: 0.8610 (mmt) cc_final: 0.8361 (mmp) REVERT: E 209 ASP cc_start: 0.8229 (t0) cc_final: 0.7742 (t0) REVERT: E 728 PHE cc_start: 0.8078 (m-10) cc_final: 0.7873 (m-10) REVERT: F 47 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6317 (pp) REVERT: F 125 ARG cc_start: 0.7318 (ptp90) cc_final: 0.6874 (mmt90) REVERT: F 198 GLU cc_start: 0.7387 (tt0) cc_final: 0.7058 (pt0) REVERT: F 233 MET cc_start: 0.7754 (mtm) cc_final: 0.7438 (mtp) REVERT: F 303 TRP cc_start: 0.7551 (t60) cc_final: 0.7337 (t60) REVERT: F 331 ASN cc_start: 0.8562 (t0) cc_final: 0.8241 (t0) REVERT: C 115 TYR cc_start: 0.8343 (m-80) cc_final: 0.8090 (m-80) outliers start: 59 outliers final: 52 residues processed: 370 average time/residue: 0.1698 time to fit residues: 99.3549 Evaluate side-chains 368 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 314 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 592 VAL Chi-restraints excluded: chain E residue 601 PHE Chi-restraints excluded: chain E residue 659 LEU Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 751 SER Chi-restraints excluded: chain E residue 817 THR Chi-restraints excluded: chain E residue 882 THR Chi-restraints excluded: chain E residue 898 THR Chi-restraints excluded: chain E residue 905 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: [163, 167, 198, 49, 120, 31, 243, 100, 252, 285, 114] chunk 163 optimal weight: 10.0000 chunk 167 optimal weight: 0.7980 chunk 198 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 243 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 chunk 252 optimal weight: 0.9990 chunk 285 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 HIS B 114 GLN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS E 835 ASN E 935 ASN ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.158619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.127644 restraints weight = 32492.844| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.87 r_work: 0.3133 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26080 Z= 0.161 Angle : 0.833 34.137 35658 Z= 0.307 Chirality : 0.044 0.165 3968 Planarity : 0.005 0.057 4610 Dihedral : 7.102 170.350 3694 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.27 % Favored : 94.61 % Rotamer: Outliers : 2.34 % Allowed : 17.97 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.15), residues: 3302 helix: 0.59 (0.15), residues: 1292 sheet: -1.42 (0.27), residues: 406 loop : -1.13 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 101 TYR 0.019 0.002 TYR B 215 PHE 0.025 0.001 PHE A 510 TRP 0.016 0.001 TRP E 780 HIS 0.004 0.001 HIS E 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (26024) covalent geometry : angle 0.61534 / 0.30 (35520) hydrogen bonds : bond 0.03151 / 2.18 ( 958) hydrogen bonds : angle 4.49703 / 3.13 ( 2670) metal coordination : bond 0.01649 / 0.99 ( 56) metal coordination : angle 9.05361 / 6.18 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 323 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.8338 (t0) cc_final: 0.7829 (t0) REVERT: B 47 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6456 (pp) REVERT: B 125 ARG cc_start: 0.7271 (ptp90) cc_final: 0.6876 (mmt90) REVERT: B 198 GLU cc_start: 0.7384 (tt0) cc_final: 0.7063 (pt0) REVERT: B 233 MET cc_start: 0.7885 (mtm) cc_final: 0.7499 (mtp) REVERT: G 46 ASP cc_start: 0.8492 (t0) cc_final: 0.8254 (t0) REVERT: E 135 MET cc_start: 0.8676 (mmt) cc_final: 0.8414 (mmp) REVERT: E 209 ASP cc_start: 0.8230 (t0) cc_final: 0.7728 (t0) REVERT: E 728 PHE cc_start: 0.8052 (m-10) cc_final: 0.7845 (m-10) REVERT: F 47 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6320 (pp) REVERT: F 125 ARG cc_start: 0.7367 (ptp90) cc_final: 0.6908 (mmt90) REVERT: F 126 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8093 (tptp) REVERT: F 198 GLU cc_start: 0.7361 (tt0) cc_final: 0.7044 (pt0) REVERT: F 233 MET cc_start: 0.7736 (mtm) cc_final: 0.7456 (mtp) REVERT: F 331 ASN cc_start: 0.8597 (t0) cc_final: 0.8303 (t0) REVERT: F 361 ARG cc_start: 0.7994 (mtt-85) cc_final: 0.7754 (mtt180) outliers start: 60 outliers final: 54 residues processed: 367 average time/residue: 0.1668 time to fit residues: 97.0832 Evaluate side-chains 372 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 315 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 592 VAL Chi-restraints excluded: chain E residue 601 PHE Chi-restraints excluded: chain E residue 659 LEU Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 751 SER Chi-restraints excluded: chain E residue 827 THR Chi-restraints excluded: chain E residue 832 SER Chi-restraints excluded: chain E residue 882 THR Chi-restraints excluded: chain E residue 898 THR Chi-restraints excluded: chain E residue 905 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: [41, 90, 13, 45, 263, 176, 233, 238, 136, 27, 227] chunk 41 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 263 optimal weight: 10.0000 chunk 176 optimal weight: 4.9990 chunk 233 optimal weight: 7.9990 chunk 238 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 HIS A 935 ASN B 293 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.156394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.121515 restraints weight = 32569.624| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.94 r_work: 0.3079 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 26080 Z= 0.209 Angle : 0.891 34.721 35658 Z= 0.333 Chirality : 0.046 0.191 3968 Planarity : 0.005 0.058 4610 Dihedral : 7.301 170.256 3694 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.72 % Favored : 94.16 % Rotamer: Outliers : 2.54 % Allowed : 18.01 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.15), residues: 3302 helix: 0.46 (0.15), residues: 1304 sheet: -1.46 (0.26), residues: 406 loop : -1.17 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 101 TYR 0.020 0.002 TYR B 215 PHE 0.027 0.001 PHE E 510 TRP 0.015 0.001 TRP A 780 HIS 0.005 0.001 HIS E 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.21 (26024) covalent geometry : angle 0.66359 / 0.33 (35520) hydrogen bonds : bond 0.03473 / 2.39 ( 958) hydrogen bonds : angle 4.66081 / 3.25 ( 2670) metal coordination : bond 0.02086 / 1.26 ( 56) metal coordination : angle 9.59085 / 6.54 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 322 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.8466 (t0) cc_final: 0.7950 (t0) REVERT: A 603 HIS cc_start: 0.8312 (p90) cc_final: 0.8023 (p-80) REVERT: B 47 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6422 (pp) REVERT: B 125 ARG cc_start: 0.7403 (ptp90) cc_final: 0.6886 (mmt90) REVERT: B 198 GLU cc_start: 0.7451 (tt0) cc_final: 0.7226 (pt0) REVERT: B 233 MET cc_start: 0.7970 (mtm) cc_final: 0.7532 (mtp) REVERT: G 46 ASP cc_start: 0.8571 (t0) cc_final: 0.8322 (t0) REVERT: E 209 ASP cc_start: 0.8398 (t0) cc_final: 0.7893 (t0) REVERT: E 728 PHE cc_start: 0.8214 (m-10) cc_final: 0.8009 (m-10) REVERT: F 47 LEU cc_start: 0.6803 (OUTLIER) cc_final: 0.6223 (pp) REVERT: F 125 ARG cc_start: 0.7404 (ptp90) cc_final: 0.6905 (mmt90) REVERT: F 126 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8039 (tptp) REVERT: F 134 GLU cc_start: 0.7378 (tt0) cc_final: 0.7086 (tt0) REVERT: F 198 GLU cc_start: 0.7423 (tt0) cc_final: 0.7197 (pt0) REVERT: F 233 MET cc_start: 0.7870 (mtm) cc_final: 0.7586 (mtp) REVERT: F 331 ASN cc_start: 0.8635 (t0) cc_final: 0.8358 (t0) REVERT: F 361 ARG cc_start: 0.8015 (mtt-85) cc_final: 0.7766 (mtt180) outliers start: 65 outliers final: 54 residues processed: 369 average time/residue: 0.1727 time to fit residues: 100.3120 Evaluate side-chains 373 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 316 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 457 THR Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 592 VAL Chi-restraints excluded: chain E residue 601 PHE Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 751 SER Chi-restraints excluded: chain E residue 827 THR Chi-restraints excluded: chain E residue 832 SER Chi-restraints excluded: chain E residue 882 THR Chi-restraints excluded: chain E residue 898 THR Chi-restraints excluded: chain E residue 905 THR Chi-restraints excluded: chain E residue 939 ASP Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 34 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: [9, 17, 50, 124, 291, 216, 22, 237, 123, 132, 230] chunk 9 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 291 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 237 optimal weight: 10.0000 chunk 123 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 230 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.159237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.128140 restraints weight = 32370.393| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.84 r_work: 0.3135 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26080 Z= 0.135 Angle : 0.815 33.369 35658 Z= 0.299 Chirality : 0.043 0.158 3968 Planarity : 0.004 0.057 4610 Dihedral : 7.025 170.586 3694 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.27 % Favored : 94.64 % Rotamer: Outliers : 2.27 % Allowed : 18.44 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.15), residues: 3302 helix: 0.57 (0.15), residues: 1314 sheet: -1.35 (0.27), residues: 398 loop : -1.10 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 101 TYR 0.019 0.001 TYR B 215 PHE 0.028 0.001 PHE A 510 TRP 0.020 0.001 TRP F 303 HIS 0.005 0.001 HIS E 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.13 (26024) covalent geometry : angle 0.59921 / 0.29 (35520) hydrogen bonds : bond 0.03074 / 2.12 ( 958) hydrogen bonds : angle 4.49936 / 3.14 ( 2670) metal coordination : bond 0.01527 / 0.90 ( 56) metal coordination : angle 8.90111 / 6.05 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5243.33 seconds wall clock time: 90 minutes 51.33 seconds (5451.33 seconds total)