Starting phenix.real_space_refine on Sun Sep 13 18:39:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6tga_10496/09_2026/6tga_10496.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tga_10496/09_2026/6tga_10496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6tga_10496/09_2026/6tga_10496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tga_10496/09_2026/6tga_10496.map" model { file = "/net/cci-nas-00/data/ceres_data/6tga_10496/09_2026/6tga_10496.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tga_10496/09_2026/6tga_10496.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6tga_10496/09_2026/6tga_10496.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6tga_10496/09_2026/6tga_10496.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mo 2 10.26 5 Fe 48 7.16 5 P 10 5.49 5 S 232 5.16 5 C 15776 2.51 5 N 4532 2.21 5 O 4724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 140 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25324 Number of models: 1 Model: "" Number of chains: 14 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: "E" 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: "F" 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: "C" 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: "H" 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "E" 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: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2875 SG CYS A 386 116.556 69.425 78.410 1.00 6.09 S ATOM 368 SG CYS A 57 89.219 94.275 56.606 1.00 8.15 S ATOM 442 SG CYS A 68 85.474 94.995 55.951 1.00 3.98 S ATOM 467 SG CYS A 71 84.557 97.849 59.408 1.00 5.50 S ATOM 568 SG CYS A 85 88.262 98.592 59.851 1.00 7.04 S ATOM 909 SG CYS A 130 83.391 81.453 53.387 1.00 4.61 S ATOM 852 SG CYS A 121 79.099 79.273 49.052 1.00 2.95 S ATOM 873 SG CYS A 124 84.958 75.817 49.774 1.00 3.21 S ATOM 1347 SG CYS A 185 90.941 88.646 53.416 1.00 9.80 S ATOM 1326 SG CYS A 182 92.850 86.054 47.794 1.00 4.41 S ATOM 1698 SG CYS A 234 91.780 81.968 53.123 1.00 7.16 S ATOM 1372 SG CYS A 188 97.011 86.071 52.504 1.00 3.22 S ATOM 1671 SG CYS A 230 98.808 80.330 55.534 1.00 9.80 S ATOM 1637 SG CYS A 224 104.503 78.220 54.814 1.00 3.75 S ATOM 1656 SG CYS A 227 102.601 80.080 60.920 1.00 4.59 S ATOM 1401 SG CYS A 192 103.977 84.451 56.575 1.00 9.80 S ATOM 1879 SG CYS A 258 102.858 70.500 70.464 1.00 4.29 S ATOM 2135 SG CYS A 293 105.400 74.121 66.122 1.00 1.82 S ATOM 1902 SG CYS A 261 108.358 74.594 72.028 1.00 5.49 S ATOM 1923 SG CYS A 265 102.440 76.972 71.241 1.00 4.42 S ATOM 10736 SG CYS B 471 92.016 106.310 46.912 1.00 2.23 S ATOM 10464 SG CYS B 433 90.388 101.454 42.898 1.00 1.99 S ATOM 10444 SG CYS B 430 88.688 100.837 48.933 1.00 9.80 S ATOM 10427 SG CYS B 427 95.203 100.641 47.206 1.00 4.11 S ATOM 11482 SG CYS G 77 98.517 111.382 28.371 1.00 10.11 S ATOM 11518 SG CYS G 82 98.221 114.214 26.470 1.00 10.17 S ATOM 11763 SG CYS G 116 100.079 114.499 32.379 1.00 9.16 S ATOM 11789 SG CYS G 120 98.851 117.830 30.897 1.00 11.13 S ATOM 15362 SG CYS E 386 36.669 86.314 78.414 1.00 6.01 S ATOM 12855 SG CYS E 57 64.006 61.470 56.611 1.00 8.30 S ATOM 12929 SG CYS E 68 67.755 60.750 55.954 1.00 4.20 S ATOM 12954 SG CYS E 71 68.673 57.896 59.411 1.00 5.45 S ATOM 13055 SG CYS E 85 64.968 57.153 59.854 1.00 7.48 S ATOM 13396 SG CYS E 130 69.836 74.292 53.391 1.00 3.86 S ATOM 13339 SG CYS E 121 74.128 76.474 49.056 1.00 3.03 S ATOM 13360 SG CYS E 124 68.268 79.929 49.779 1.00 2.73 S ATOM 13834 SG CYS E 185 62.288 67.098 53.420 1.00 9.80 S ATOM 13813 SG CYS E 182 60.378 69.691 47.798 1.00 3.21 S ATOM 14185 SG CYS E 234 61.447 73.776 53.127 1.00 5.48 S ATOM 13859 SG CYS E 188 56.217 69.673 52.507 1.00 3.69 S ATOM 14158 SG CYS E 230 54.419 75.413 55.538 1.00 9.80 S ATOM 14124 SG CYS E 224 48.729 77.522 54.813 1.00 4.21 S ATOM 14143 SG CYS E 227 50.642 75.663 60.926 1.00 2.20 S ATOM 13888 SG CYS E 192 49.251 71.292 56.578 1.00 9.80 S ATOM 14366 SG CYS E 258 50.367 85.241 70.468 1.00 4.42 S ATOM 14622 SG CYS E 293 47.826 81.620 66.126 1.00 9.80 S ATOM 14389 SG CYS E 261 44.868 81.147 72.032 1.00 5.25 S ATOM 14410 SG CYS E 265 50.786 78.770 71.245 1.00 4.13 S ATOM 23223 SG CYS F 471 61.219 49.436 46.915 1.00 1.95 S ATOM 22951 SG CYS F 433 62.847 54.292 42.901 1.00 1.49 S ATOM 22931 SG CYS F 430 64.546 54.909 48.936 1.00 3.24 S ATOM 22914 SG CYS F 427 58.031 55.105 47.209 1.00 4.24 S ATOM 23969 SG CYS C 77 54.720 44.363 28.374 1.00 10.14 S ATOM 24005 SG CYS C 82 55.016 41.531 26.473 1.00 9.72 S ATOM 24250 SG CYS C 116 53.157 41.246 32.382 1.00 9.28 S ATOM 24276 SG CYS C 120 54.386 37.915 30.900 1.00 10.98 S Time building chain proxies: 5.72, per 1000 atoms: 0.23 Number of scatterers: 25324 At special positions: 0 Unit cell: (153.86, 155.744, 116.18, 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 10 15.00 O 4724 8.00 N 4532 7.00 C 15776 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 1.3 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 71 " pdb="FE2 FES A1004 " - pdb=" SG CYS A 85 " pdb="FE1 FES A1004 " - pdb=" SG CYS A 57 " 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 116 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 120 " pdb=" FES E1004 " pdb="FE1 FES E1004 " - pdb=" SG CYS E 68 " pdb="FE2 FES E1004 " - pdb=" SG CYS E 71 " pdb="FE2 FES E1004 " - pdb=" SG CYS E 85 " pdb="FE1 FES E1004 " - pdb=" SG CYS E 57 " 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 116 " pdb="FE2 FES G 201 " - pdb=" SG CYS G 120 " 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="FE4 SF4 A1006 " - pdb=" SG CYS A 188 " pdb="FE1 SF4 A1006 " - pdb=" SG CYS A 185 " pdb=" SF4 A1007 " pdb="FE3 SF4 A1007 " - pdb=" SG CYS A 227 " pdb="FE2 SF4 A1007 " - pdb=" SG CYS A 224 " pdb="FE4 SF4 A1007 " - pdb=" SG CYS A 192 " pdb="FE1 SF4 A1007 " - pdb=" SG CYS A 230 " pdb=" SF4 A1008 " pdb="FE2 SF4 A1008 " - pdb=" SG CYS A 293 " pdb="FE4 SF4 A1008 " - pdb=" SG CYS A 265 " pdb="FE1 SF4 A1008 " - pdb=" SG CYS A 258 " pdb="FE3 SF4 A1008 " - pdb=" SG CYS A 261 " pdb=" SF4 B 602 " pdb="FE2 SF4 B 602 " - pdb=" SG CYS B 433 " 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=" 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="FE4 SF4 E1006 " - pdb=" SG CYS E 188 " pdb="FE1 SF4 E1006 " - pdb=" SG CYS E 185 " pdb=" SF4 E1007 " pdb="FE3 SF4 E1007 " - pdb=" SG CYS E 227 " pdb="FE2 SF4 E1007 " - pdb=" SG CYS E 224 " pdb="FE4 SF4 E1007 " - pdb=" SG CYS E 192 " pdb="FE1 SF4 E1007 " - pdb=" SG CYS E 230 " pdb=" SF4 E1008 " pdb="FE2 SF4 E1008 " - pdb=" SG CYS E 293 " pdb="FE4 SF4 E1008 " - pdb=" SG CYS E 265 " pdb="FE1 SF4 E1008 " - pdb=" SG CYS E 258 " pdb="FE3 SF4 E1008 " - pdb=" SG CYS E 261 " pdb=" SF4 F 602 " pdb="FE2 SF4 F 602 " - pdb=" SG CYS F 433 " 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 " 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: 142 helices and 32 sheets defined 43.2% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 8 through 13 removed outlier: 4.526A pdb=" N THR A 12 " --> pdb=" O PRO A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 50 Processing helix chain 'A' and resid 99 through 115 Processing helix chain 'A' and resid 130 through 139 removed outlier: 3.639A pdb=" N ASP A 134 " --> pdb=" O CYS A 130 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET A 135 " --> pdb=" O GLU A 131 " (cutoff:3.500A) removed outlier: 3.869A 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 206 through 210 removed outlier: 4.277A pdb=" N ASP A 209 " --> pdb=" O ARG A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 229 through 234 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 326 through 346 removed outlier: 3.757A pdb=" N ALA A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 350 Processing helix chain 'A' and resid 359 through 372 Processing helix chain 'A' and resid 389 through 397 removed outlier: 4.040A pdb=" N LYS A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 412 Processing helix chain 'A' and resid 427 through 439 removed outlier: 3.653A pdb=" N ARG A 433 " --> pdb=" O VAL A 429 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 487 removed outlier: 3.655A pdb=" N MET A 477 " --> pdb=" O ASN A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 499 Processing helix chain 'A' and resid 501 through 512 removed outlier: 3.750A pdb=" N ASP A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 526 removed outlier: 3.716A pdb=" N GLU A 522 " --> pdb=" O PRO A 518 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N SER A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LEU A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 542 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: 3.900A 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 Processing helix chain 'A' and resid 687 through 691 Processing helix chain 'A' and resid 729 through 742 Processing helix chain 'A' and resid 749 through 761 removed outlier: 3.982A pdb=" N ILE A 753 " --> pdb=" O HIS A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 775 Processing helix chain 'A' and resid 858 through 863 removed outlier: 4.193A pdb=" N THR A 863 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 952 removed outlier: 3.806A 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: 3.653A pdb=" N LEU B 47 " --> pdb=" O MET B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 73 Proline residue: B 71 - end of helix Processing helix chain 'B' and resid 90 through 95 removed outlier: 3.638A pdb=" N ARG B 95 " --> pdb=" O PRO B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 118 Processing helix chain 'B' and resid 121 through 128 Processing helix chain 'B' and resid 131 through 142 removed outlier: 3.693A pdb=" N VAL B 136 " --> pdb=" O PRO B 132 " (cutoff:3.500A) removed outlier: 3.552A 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 Processing helix chain 'B' and resid 220 through 234 removed outlier: 3.789A pdb=" N ALA B 225 " --> pdb=" O PRO B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 240 removed outlier: 3.696A 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 300 through 307 Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.549A 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: 4.363A 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: 3.693A pdb=" N MET B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 450 removed outlier: 3.822A pdb=" N GLY B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA B 437 " --> pdb=" O CYS B 433 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU B 442 " --> pdb=" O VAL B 438 " (cutoff:3.500A) removed outlier: 3.684A 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: 3.971A 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 32 Processing helix chain 'G' and resid 36 through 39 Processing helix chain 'G' and resid 40 through 48 Processing helix chain 'G' and resid 50 through 61 removed outlier: 3.535A pdb=" N VAL G 58 " --> pdb=" O VAL G 54 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR G 61 " --> pdb=" O VAL G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 85 Processing helix chain 'G' and resid 86 through 99 removed outlier: 3.827A pdb=" N VAL G 90 " --> pdb=" O GLY G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 147 removed outlier: 3.898A pdb=" N GLY G 143 " --> pdb=" O ALA G 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 19 removed outlier: 4.385A pdb=" N VAL D 19 " --> pdb=" O ALA D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 36 removed outlier: 3.813A pdb=" N VAL D 28 " --> pdb=" O ARG D 24 " (cutoff:3.500A) 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 8 through 13 removed outlier: 4.527A pdb=" N THR E 12 " --> pdb=" O PRO E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 50 Processing helix chain 'E' and resid 99 through 115 Processing helix chain 'E' and resid 130 through 139 removed outlier: 3.639A pdb=" N ASP E 134 " --> pdb=" O CYS E 130 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET E 135 " --> pdb=" O GLU E 131 " (cutoff:3.500A) removed outlier: 3.870A 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 206 through 210 removed outlier: 4.277A pdb=" N ASP E 209 " --> pdb=" O ARG E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 222 Processing helix chain 'E' and resid 229 through 234 Processing helix chain 'E' and resid 242 through 247 Processing helix chain 'E' and resid 293 through 299 Processing helix chain 'E' and resid 326 through 346 removed outlier: 3.757A pdb=" N ALA E 330 " --> pdb=" O ASN E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 350 Processing helix chain 'E' and resid 359 through 372 Processing helix chain 'E' and resid 389 through 397 removed outlier: 4.039A pdb=" N LYS E 395 " --> pdb=" O GLY E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 412 Processing helix chain 'E' and resid 427 through 439 removed outlier: 3.653A pdb=" N ARG E 433 " --> pdb=" O VAL E 429 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG E 437 " --> pdb=" O ARG E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 487 removed outlier: 3.655A pdb=" N MET E 477 " --> pdb=" O ASN E 473 " (cutoff:3.500A) Processing helix chain 'E' and resid 491 through 499 Processing helix chain 'E' and resid 501 through 512 removed outlier: 3.750A pdb=" N ASP E 506 " --> pdb=" O ASP E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 526 removed outlier: 3.716A pdb=" N GLU E 522 " --> pdb=" O PRO E 518 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N SER E 523 " --> pdb=" O GLU E 519 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU E 524 " --> pdb=" O ALA E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 542 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: 3.900A 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 Processing helix chain 'E' and resid 687 through 691 Processing helix chain 'E' and resid 729 through 742 Processing helix chain 'E' and resid 749 through 761 removed outlier: 3.982A pdb=" N ILE E 753 " --> pdb=" O HIS E 749 " (cutoff:3.500A) Processing helix chain 'E' and resid 768 through 775 Processing helix chain 'E' and resid 858 through 863 removed outlier: 4.192A pdb=" N THR E 863 " --> pdb=" O THR E 859 " (cutoff:3.500A) Processing helix chain 'E' and resid 939 through 952 removed outlier: 3.806A 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: 3.653A pdb=" N LEU F 47 " --> pdb=" O MET F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 73 Proline residue: F 71 - end of helix Processing helix chain 'F' and resid 90 through 95 removed outlier: 3.637A pdb=" N ARG F 95 " --> pdb=" O PRO F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 118 Processing helix chain 'F' and resid 121 through 128 Processing helix chain 'F' and resid 131 through 143 removed outlier: 3.694A pdb=" N VAL F 136 " --> pdb=" O PRO F 132 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER F 142 " --> pdb=" O GLU F 138 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY F 143 " --> pdb=" O VAL F 139 " (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 Processing helix chain 'F' and resid 220 through 234 removed outlier: 3.790A pdb=" N ALA F 225 " --> pdb=" O PRO F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 240 removed outlier: 3.696A 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 300 through 307 Processing helix chain 'F' and resid 308 through 313 removed outlier: 3.548A 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: 4.363A 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: 3.693A pdb=" N MET F 419 " --> pdb=" O ALA F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 450 removed outlier: 3.823A pdb=" N GLY F 436 " --> pdb=" O PRO F 432 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA F 437 " --> pdb=" O CYS F 433 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL F 438 " --> pdb=" O ARG F 434 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU F 442 " --> pdb=" O VAL F 438 " (cutoff:3.500A) removed outlier: 3.684A 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: 3.971A 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 32 Processing helix chain 'C' and resid 36 through 39 Processing helix chain 'C' and resid 40 through 48 Processing helix chain 'C' and resid 50 through 61 removed outlier: 3.535A pdb=" N VAL C 58 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR C 61 " --> pdb=" O VAL C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 85 Processing helix chain 'C' and resid 86 through 99 removed outlier: 3.828A pdb=" N VAL C 90 " --> pdb=" O GLY C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 147 removed outlier: 3.898A pdb=" N GLY C 143 " --> pdb=" O ALA C 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 19 removed outlier: 4.384A pdb=" N VAL H 19 " --> pdb=" O ALA H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 36 removed outlier: 3.814A pdb=" N VAL H 28 " --> pdb=" O ARG H 24 " (cutoff:3.500A) 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 37 removed outlier: 9.305A pdb=" N VAL A 95 " --> pdb=" O HIS A 26 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR A 28 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 157 Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 177 Processing sheet with id=AA4, first strand: chain 'A' and resid 202 through 204 Processing sheet with id=AA5, first strand: chain 'A' and resid 252 through 257 removed outlier: 3.516A pdb=" N ARG A 278 " --> pdb=" O HIS A 270 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU A 272 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA7, first strand: chain 'A' and resid 352 through 353 removed outlier: 5.854A pdb=" N ILE A 353 " --> pdb=" O GLN A 654 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 463 through 465 removed outlier: 6.501A pdb=" N LEU A 444 " --> pdb=" O TRP A 464 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ALA A 545 " --> pdb=" O GLY A 582 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ASN A 584 " --> pdb=" O ALA A 545 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE A 547 " --> pdb=" O ASN A 584 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 604 through 605 removed outlier: 3.578A pdb=" N ARG A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 706 through 709 removed outlier: 3.559A pdb=" N VAL A 778 " --> pdb=" O ILE A 715 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 827 through 828 Processing sheet with id=AB3, first strand: chain 'A' and resid 853 through 856 Processing sheet with id=AB4, first strand: chain 'B' and resid 35 through 37 removed outlier: 6.510A pdb=" N ILE B 3 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LYS B 2 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU B 54 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU B 52 " --> pdb=" O TRP B 4 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY B 85 " --> pdb=" O GLY B 61 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 244 through 249 removed outlier: 6.799A pdb=" N GLY B 212 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ARG B 248 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N VAL B 214 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE B 171 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N TYR B 215 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N CYS B 173 " --> pdb=" O TYR B 215 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N TYR B 170 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ASN B 293 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL B 172 " --> pdb=" O ASN B 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 336 through 341 removed outlier: 7.822A pdb=" N LEU B 402 " --> pdb=" O PRO B 325 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N GLN B 327 " --> pdb=" O LEU B 402 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL B 404 " --> pdb=" O GLN B 327 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLY B 401 " --> pdb=" O VAL B 368 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL B 368 " --> pdb=" O GLY B 401 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL B 403 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL B 366 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N HIS B 405 " --> pdb=" O LYS B 364 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 111 through 112 removed outlier: 6.343A 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 37 removed outlier: 9.304A pdb=" N VAL E 95 " --> pdb=" O HIS E 26 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR E 28 " --> pdb=" O VAL E 95 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 156 through 157 Processing sheet with id=AC1, first strand: chain 'E' and resid 175 through 177 Processing sheet with id=AC2, first strand: chain 'E' and resid 202 through 204 Processing sheet with id=AC3, first strand: chain 'E' and resid 252 through 257 removed outlier: 3.514A pdb=" N ARG E 278 " --> pdb=" O HIS E 270 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU E 272 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LEU E 276 " --> pdb=" O LEU E 272 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 313 through 314 Processing sheet with id=AC5, first strand: chain 'E' and resid 352 through 353 removed outlier: 5.854A pdb=" N ILE E 353 " --> pdb=" O GLN E 654 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 463 through 465 removed outlier: 6.501A pdb=" N LEU E 444 " --> pdb=" O TRP E 464 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ALA E 545 " --> pdb=" O GLY E 582 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ASN E 584 " --> pdb=" O ALA E 545 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE E 547 " --> pdb=" O ASN E 584 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 604 through 605 removed outlier: 3.577A pdb=" N ARG E 609 " --> pdb=" O PHE E 605 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 706 through 709 removed outlier: 3.559A pdb=" N VAL E 778 " --> pdb=" O ILE E 715 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 827 through 828 Processing sheet with id=AD1, first strand: chain 'E' and resid 853 through 856 Processing sheet with id=AD2, first strand: chain 'F' and resid 35 through 37 removed outlier: 6.510A pdb=" N ILE F 3 " --> pdb=" O ALA F 37 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LYS F 2 " --> pdb=" O GLU F 54 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU F 54 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU F 52 " --> pdb=" O TRP F 4 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY F 85 " --> pdb=" O GLY F 61 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 244 through 249 removed outlier: 6.798A pdb=" N GLY F 212 " --> pdb=" O GLU F 246 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ARG F 248 " --> pdb=" O GLY F 212 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N VAL F 214 " --> pdb=" O ARG F 248 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE F 171 " --> pdb=" O TYR F 213 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N TYR F 215 " --> pdb=" O ILE F 171 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N CYS F 173 " --> pdb=" O TYR F 215 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N TYR F 170 " --> pdb=" O VAL F 291 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ASN F 293 " --> pdb=" O TYR F 170 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL F 172 " --> pdb=" O ASN F 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'F' and resid 336 through 341 removed outlier: 7.822A pdb=" N LEU F 402 " --> pdb=" O PRO F 325 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N GLN F 327 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL F 404 " --> pdb=" O GLN F 327 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY F 401 " --> pdb=" O VAL F 368 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL F 368 " --> pdb=" O GLY F 401 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL F 403 " --> pdb=" O VAL F 366 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL F 366 " --> pdb=" O VAL F 403 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N HIS F 405 " --> pdb=" O LYS F 364 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 111 through 112 removed outlier: 6.343A pdb=" N ILE C 74 " --> pdb=" O GLU C 112 " (cutoff:3.500A) 950 hydrogen bonds defined for protein. 2664 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: 5.43 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 10625 1.42 - 1.64: 14883 1.64 - 1.85: 276 1.85 - 2.07: 8 2.07 - 2.28: 136 Bond restraints: 25928 Sorted by residual: bond pdb=" O5' FMN B 601 " pdb=" P FMN B 601 " ideal model delta sigma weight residual 1.610 1.852 -0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" O5' FMN F 601 " pdb=" P FMN F 601 " ideal model delta sigma weight residual 1.610 1.852 -0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" O3A MGD E1001 " pdb=" PA MGD E1001 " 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 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=" O5' MGD A1001 " pdb=" PB MGD A1001 " ideal model delta sigma weight residual 1.646 1.850 -0.204 2.00e-02 2.50e+03 1.04e+02 ... (remaining 25923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.10: 35053 4.10 - 8.21: 277 8.21 - 12.31: 22 12.31 - 16.41: 14 16.41 - 20.51: 8 Bond angle restraints: 35374 Sorted by residual: angle pdb=" S1 FES C 201 " pdb="FE2 FES C 201 " pdb=" S2 FES C 201 " ideal model delta sigma weight residual 104.33 83.82 20.51 1.14e+00 7.69e-01 3.24e+02 angle pdb=" S1 FES G 201 " pdb="FE2 FES G 201 " pdb=" S2 FES G 201 " ideal model delta sigma weight residual 104.33 83.83 20.50 1.14e+00 7.69e-01 3.23e+02 angle pdb=" S1 FES E1004 " pdb="FE2 FES E1004 " pdb=" S2 FES E1004 " ideal model delta sigma weight residual 104.33 83.85 20.48 1.14e+00 7.69e-01 3.23e+02 angle pdb=" S1 FES A1004 " pdb="FE2 FES A1004 " pdb=" S2 FES A1004 " ideal model delta sigma weight residual 104.33 83.86 20.47 1.14e+00 7.69e-01 3.22e+02 angle pdb=" S1 FES E1004 " pdb="FE1 FES E1004 " pdb=" S2 FES E1004 " ideal model delta sigma weight residual 104.33 83.84 20.49 1.20e+00 6.94e-01 2.91e+02 ... (remaining 35369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.50: 14947 33.50 - 67.00: 347 67.00 - 100.49: 26 100.49 - 133.99: 0 133.99 - 167.49: 4 Dihedral angle restraints: 15324 sinusoidal: 5930 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 90.10 167.49 1 2.00e+01 2.50e-03 4.74e+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 90.16 167.43 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C5' FMN F 601 " pdb=" O5' FMN F 601 " pdb=" P FMN F 601 " pdb=" O1P FMN F 601 " ideal model delta sinusoidal sigma weight residual 75.26 -141.04 -143.70 1 2.00e+01 2.50e-03 4.33e+01 ... (remaining 15321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3853 0.098 - 0.195: 71 0.195 - 0.293: 14 0.293 - 0.390: 6 0.390 - 0.488: 8 Chirality restraints: 3952 Sorted by residual: chirality pdb=" CB VAL A 385 " pdb=" CA VAL A 385 " pdb=" CG1 VAL A 385 " pdb=" CG2 VAL A 385 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 5.95e+00 chirality pdb=" CB VAL E 385 " pdb=" CA VAL E 385 " pdb=" CG1 VAL E 385 " pdb=" CG2 VAL E 385 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 5.93e+00 chirality pdb=" C23 MGD A1002 " pdb=" C14 MGD A1002 " pdb=" N22 MGD A1002 " pdb=" O11 MGD A1002 " both_signs ideal model delta sigma weight residual False 2.33 2.78 -0.45 2.00e-01 2.50e+01 5.16e+00 ... (remaining 3949 not shown) Planarity restraints: 4604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 773 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C ASP A 773 " 0.045 2.00e-02 2.50e+03 pdb=" O ASP A 773 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA A 774 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 773 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.64e+00 pdb=" C ASP E 773 " -0.045 2.00e-02 2.50e+03 pdb=" O ASP E 773 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA E 774 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 222 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.98e+00 pdb=" C SER E 222 " -0.034 2.00e-02 2.50e+03 pdb=" O SER E 222 " 0.013 2.00e-02 2.50e+03 pdb=" N ASP E 223 " 0.011 2.00e-02 2.50e+03 ... (remaining 4601 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 175 2.51 - 3.11: 19390 3.11 - 3.70: 38434 3.70 - 4.30: 57959 4.30 - 4.90: 98824 Nonbonded interactions: 214782 Sorted by model distance: nonbonded pdb=" OG1 THR E 882 " pdb=" O PRO E 937 " model vdw 1.909 3.040 nonbonded pdb=" OG1 THR A 882 " pdb=" O PRO A 937 " model vdw 1.909 3.040 nonbonded pdb=" OG1 THR A 817 " pdb=" O PHE A 821 " model vdw 1.988 3.040 nonbonded pdb=" OG1 THR E 817 " pdb=" O PHE E 821 " model vdw 1.988 3.040 nonbonded pdb=" OE1 GLU E 631 " pdb=" NH2 ARG H 41 " model vdw 2.119 3.120 ... (remaining 214777 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: 4.300 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: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 28.200 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.070 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 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 : 0.013 0.452 25986 Z= 0.702 Angle : 1.362 40.519 35512 Z= 0.778 Chirality : 0.045 0.488 3952 Planarity : 0.004 0.047 4604 Dihedral : 14.548 167.490 9316 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.45 % Favored : 94.37 % Rotamer: Outliers : 1.13 % Allowed : 2.77 % Favored : 96.09 % Cbeta Deviations : 0.07 % 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: -3.82 (0.12), residues: 3302 helix: -1.96 (0.12), residues: 1286 sheet: -2.99 (0.25), residues: 302 loop : -2.95 (0.12), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 384 TYR 0.015 0.001 TYR A 260 PHE 0.009 0.001 PHE A 175 TRP 0.011 0.001 TRP E 780 HIS 0.006 0.001 HIS A 387 Details of bonding type rmsd/Z covalent geometry : bond 0.01030 / 0.56 (25928) covalent geometry : angle 1.16507 / 0.77 (35374) hydrogen bonds : bond 0.15822 / 11.15 ( 950) hydrogen bonds : angle 7.37548 / 5.31 ( 2664) metal coordination : bond 0.12844 / 8.20 ( 56) metal coordination : angle 11.38054 / 7.36 ( 138) Misc. bond : bond 0.45176 / 31.21 ( 2) *********************** 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 569 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 540 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.7607 (mtt) cc_final: 0.7392 (mtt) REVERT: A 601 PHE cc_start: 0.7758 (m-80) cc_final: 0.7447 (m-10) REVERT: A 614 ASP cc_start: 0.6502 (m-30) cc_final: 0.5932 (m-30) REVERT: B 179 ASP cc_start: 0.7196 (m-30) cc_final: 0.6895 (m-30) REVERT: B 227 MET cc_start: 0.8407 (tpp) cc_final: 0.7766 (tpt) REVERT: B 445 ASP cc_start: 0.6869 (m-30) cc_final: 0.6534 (m-30) REVERT: E 78 MET cc_start: 0.7611 (mtt) cc_final: 0.7395 (mtt) REVERT: E 601 PHE cc_start: 0.7748 (m-80) cc_final: 0.7484 (m-10) REVERT: E 614 ASP cc_start: 0.6473 (m-30) cc_final: 0.5909 (m-30) REVERT: F 179 ASP cc_start: 0.7194 (m-30) cc_final: 0.6917 (m-30) REVERT: F 227 MET cc_start: 0.8406 (tpp) cc_final: 0.7766 (tpt) REVERT: F 445 ASP cc_start: 0.6867 (m-30) cc_final: 0.6532 (m-30) outliers start: 29 outliers final: 3 residues processed: 567 average time/residue: 0.2141 time to fit residues: 181.1018 Evaluate side-chains 343 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 340 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain E residue 386 CYS Chi-restraints excluded: chain E residue 892 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 GLN A 96 HIS A 473 ASN A 558 GLN A 584 ASN A 589 GLN A 686 ASN A 690 ASN A 794 HIS A 920 ASN A 930 GLN A 941 GLN B 405 HIS G 91 GLN E 13 GLN E 96 HIS E 387 HIS E 473 ASN E 589 GLN E 686 ASN E 690 ASN E 794 HIS E 920 ASN E 930 GLN E 941 GLN F 405 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.186891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.164957 restraints weight = 27052.426| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 0.98 r_work: 0.3592 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25986 Z= 0.163 Angle : 0.798 23.497 35512 Z= 0.335 Chirality : 0.044 0.217 3952 Planarity : 0.006 0.070 4604 Dihedral : 8.074 173.404 3675 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.51 % Favored : 95.31 % Rotamer: Outliers : 1.76 % Allowed : 10.43 % Favored : 87.81 % 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: -2.32 (0.14), residues: 3302 helix: -0.60 (0.14), residues: 1304 sheet: -2.09 (0.26), residues: 348 loop : -2.21 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 719 TYR 0.021 0.002 TYR E 260 PHE 0.020 0.002 PHE A 728 TRP 0.018 0.001 TRP E 780 HIS 0.006 0.001 HIS F 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (25928) covalent geometry : angle 0.66285 / 0.33 (35374) hydrogen bonds : bond 0.03846 / 2.67 ( 950) hydrogen bonds : angle 5.28231 / 3.77 ( 2664) metal coordination : bond 0.01655 / 0.99 ( 56) metal coordination : angle 7.16202 / 4.88 ( 138) Misc. bond : bond 0.00076 / 0.05 ( 2) *********************** 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 424 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 379 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: A 591 ASN cc_start: 0.6758 (t0) cc_final: 0.6475 (t0) REVERT: A 614 ASP cc_start: 0.7105 (m-30) cc_final: 0.6421 (m-30) REVERT: A 793 MET cc_start: 0.7562 (mmt) cc_final: 0.6730 (ttp) REVERT: A 939 ASP cc_start: 0.7214 (t0) cc_final: 0.6923 (t70) REVERT: B 190 GLU cc_start: 0.6747 (tt0) cc_final: 0.6489 (tt0) REVERT: E 591 ASN cc_start: 0.6810 (t0) cc_final: 0.6524 (t0) REVERT: E 614 ASP cc_start: 0.7075 (m-30) cc_final: 0.6387 (m-30) REVERT: E 793 MET cc_start: 0.7584 (mmt) cc_final: 0.6795 (ttp) outliers start: 45 outliers final: 32 residues processed: 406 average time/residue: 0.2034 time to fit residues: 125.3622 Evaluate side-chains 380 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 348 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 746 HIS Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain G residue 85 MET Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 386 CYS Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 617 ARG Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 746 HIS Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 817 THR Chi-restraints excluded: chain E residue 882 THR Chi-restraints excluded: chain E residue 892 SER Chi-restraints excluded: chain F residue 441 VAL Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain C residue 85 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 279 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 186 optimal weight: 1.9990 chunk 291 optimal weight: 3.9990 chunk 324 optimal weight: 10.0000 chunk 241 optimal weight: 0.0670 chunk 19 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 286 optimal weight: 0.9990 chunk 140 optimal weight: 0.8980 chunk 210 optimal weight: 7.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 ASN E 558 GLN E 779 GLN E 920 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.182743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.161351 restraints weight = 27317.072| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.03 r_work: 0.3541 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25986 Z= 0.123 Angle : 0.717 25.519 35512 Z= 0.295 Chirality : 0.042 0.161 3952 Planarity : 0.005 0.074 4604 Dihedral : 7.737 172.166 3675 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.06 % Favored : 95.88 % Rotamer: Outliers : 2.66 % Allowed : 12.42 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.14), residues: 3302 helix: 0.10 (0.15), residues: 1292 sheet: -1.70 (0.26), residues: 362 loop : -1.86 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 719 TYR 0.019 0.001 TYR A 260 PHE 0.013 0.001 PHE D 16 TRP 0.019 0.001 TRP A 780 HIS 0.002 0.000 HIS E 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (25928) covalent geometry : angle 0.58644 / 0.29 (35374) hydrogen bonds : bond 0.03242 / 2.26 ( 950) hydrogen bonds : angle 4.82864 / 3.43 ( 2664) metal coordination : bond 0.01177 / 0.69 ( 56) metal coordination : angle 6.64784 / 4.36 ( 138) Misc. bond : bond 0.00021 / 0.01 ( 2) *********************** 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 440 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 372 time to evaluate : 0.999 Fit side-chains REVERT: A 522 GLU cc_start: 0.6689 (mt-10) cc_final: 0.6292 (tt0) REVERT: A 591 ASN cc_start: 0.6759 (t0) cc_final: 0.6484 (t0) REVERT: A 746 HIS cc_start: 0.7268 (OUTLIER) cc_final: 0.7039 (p90) REVERT: A 793 MET cc_start: 0.7274 (mmt) cc_final: 0.6691 (ttp) REVERT: A 939 ASP cc_start: 0.7198 (t0) cc_final: 0.6926 (t70) REVERT: B 434 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8172 (ttp80) REVERT: E 522 GLU cc_start: 0.6696 (mt-10) cc_final: 0.6298 (tt0) REVERT: E 591 ASN cc_start: 0.6750 (t0) cc_final: 0.6475 (t0) REVERT: E 746 HIS cc_start: 0.7291 (OUTLIER) cc_final: 0.7048 (p90) REVERT: E 793 MET cc_start: 0.7377 (mmt) cc_final: 0.6756 (ttp) REVERT: F 190 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6734 (mt-10) REVERT: F 434 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8175 (ttp80) outliers start: 68 outliers final: 41 residues processed: 417 average time/residue: 0.2076 time to fit residues: 130.6155 Evaluate side-chains 379 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 333 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 699 SER Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 746 HIS Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain G residue 85 MET Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 617 ARG Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 699 SER Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain E residue 746 HIS Chi-restraints excluded: chain E residue 817 THR Chi-restraints excluded: chain E residue 882 THR Chi-restraints excluded: chain E residue 892 SER Chi-restraints excluded: chain E residue 955 GLU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 65 MET Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 307 HIS Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 434 ARG Chi-restraints excluded: chain F residue 441 VAL Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain C residue 85 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 66 optimal weight: 0.2980 chunk 274 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 284 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 226 optimal weight: 0.0970 chunk 312 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 GLN A 534 GLN A 716 ASN E 534 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.181845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.159091 restraints weight = 26916.757| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.22 r_work: 0.3389 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25986 Z= 0.132 Angle : 0.728 27.815 35512 Z= 0.292 Chirality : 0.042 0.155 3952 Planarity : 0.005 0.076 4604 Dihedral : 7.348 172.296 3674 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.85 % Favored : 95.09 % Rotamer: Outliers : 3.16 % Allowed : 13.48 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.14), residues: 3302 helix: 0.34 (0.15), residues: 1290 sheet: -1.47 (0.26), residues: 376 loop : -1.65 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 719 TYR 0.019 0.001 TYR A 260 PHE 0.013 0.001 PHE A 728 TRP 0.019 0.001 TRP E 780 HIS 0.002 0.001 HIS E 749 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (25928) covalent geometry : angle 0.58068 / 0.29 (35374) hydrogen bonds : bond 0.03158 / 2.20 ( 950) hydrogen bonds : angle 4.61874 / 3.27 ( 2664) metal coordination : bond 0.01211 / 0.72 ( 56) metal coordination : angle 7.05705 / 4.64 ( 138) Misc. bond : bond 0.00144 / 0.10 ( 2) *********************** 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 435 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 354 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 223 ASP cc_start: 0.8466 (m-30) cc_final: 0.8151 (m-30) REVERT: A 317 LYS cc_start: 0.7650 (mtmt) cc_final: 0.7163 (mmmt) REVERT: A 522 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6372 (tt0) REVERT: A 591 ASN cc_start: 0.6891 (t0) cc_final: 0.6601 (t0) REVERT: A 746 HIS cc_start: 0.7317 (OUTLIER) cc_final: 0.6882 (p90) REVERT: A 793 MET cc_start: 0.7472 (mmt) cc_final: 0.6672 (ttp) REVERT: A 939 ASP cc_start: 0.7462 (t0) cc_final: 0.7210 (t70) REVERT: B 235 LYS cc_start: 0.7564 (ptpp) cc_final: 0.7190 (ptpp) REVERT: B 321 ARG cc_start: 0.7536 (mmm160) cc_final: 0.7325 (mmm160) REVERT: B 368 VAL cc_start: 0.8599 (m) cc_final: 0.8333 (t) REVERT: E 15 MET cc_start: 0.7598 (mmt) cc_final: 0.7320 (mmt) REVERT: E 223 ASP cc_start: 0.8500 (m-30) cc_final: 0.8192 (m-30) REVERT: E 317 LYS cc_start: 0.7653 (mtmt) cc_final: 0.7152 (mmmt) REVERT: E 522 GLU cc_start: 0.6839 (mt-10) cc_final: 0.6327 (tt0) REVERT: E 591 ASN cc_start: 0.6867 (t0) cc_final: 0.6558 (t0) REVERT: E 746 HIS cc_start: 0.7368 (OUTLIER) cc_final: 0.6919 (p90) REVERT: E 793 MET cc_start: 0.7576 (mmt) cc_final: 0.6697 (ttp) REVERT: F 45 ILE cc_start: 0.8679 (mm) cc_final: 0.8374 (mm) REVERT: F 190 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.7051 (mt-10) REVERT: F 235 LYS cc_start: 0.7562 (ptpp) cc_final: 0.7193 (ptpp) REVERT: F 264 ASN cc_start: 0.8881 (t0) cc_final: 0.8668 (m-40) REVERT: F 321 ARG cc_start: 0.7490 (mmm160) cc_final: 0.7276 (mmm160) REVERT: F 368 VAL cc_start: 0.8593 (m) cc_final: 0.8336 (t) REVERT: F 434 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8243 (ttp80) outliers start: 81 outliers final: 52 residues processed: 413 average time/residue: 0.1960 time to fit residues: 124.0231 Evaluate side-chains 388 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 332 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 699 SER Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 746 HIS Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 85 MET Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 617 ARG Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 699 SER Chi-restraints excluded: chain E residue 718 VAL Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain E residue 746 HIS Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 817 THR Chi-restraints excluded: chain E residue 882 THR Chi-restraints excluded: chain E residue 892 SER Chi-restraints excluded: chain E residue 955 GLU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 65 MET Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 307 HIS Chi-restraints excluded: chain F residue 390 PHE Chi-restraints excluded: chain F residue 434 ARG Chi-restraints excluded: chain F residue 441 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain H residue 6 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: chunk 168 optimal weight: 1.9990 chunk 253 optimal weight: 6.9990 chunk 255 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 247 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 224 optimal weight: 10.0000 chunk 231 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 534 GLN B 264 ASN E 133 GLN E 534 GLN E 716 ASN E 779 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.174616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.153049 restraints weight = 26871.659| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.23 r_work: 0.3466 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 25986 Z= 0.196 Angle : 0.809 29.659 35512 Z= 0.323 Chirality : 0.045 0.168 3952 Planarity : 0.006 0.077 4604 Dihedral : 7.466 169.924 3674 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.21 % Favored : 94.67 % Rotamer: Outliers : 3.67 % Allowed : 14.30 % Favored : 82.03 % 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: -1.24 (0.14), residues: 3302 helix: 0.29 (0.15), residues: 1298 sheet: -1.47 (0.27), residues: 370 loop : -1.58 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 877 TYR 0.023 0.002 TYR A 260 PHE 0.012 0.001 PHE A 208 TRP 0.018 0.001 TRP E 780 HIS 0.004 0.001 HIS E 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 (25928) covalent geometry : angle 0.64044 / 0.32 (35374) hydrogen bonds : bond 0.03586 / 2.49 ( 950) hydrogen bonds : angle 4.71581 / 3.33 ( 2664) metal coordination : bond 0.01731 / 1.08 ( 56) metal coordination : angle 7.96608 / 5.31 ( 138) Misc. bond : bond 0.00135 / 0.10 ( 2) *********************** 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 423 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 329 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 ASP cc_start: 0.8467 (m-30) cc_final: 0.8123 (m-30) REVERT: A 317 LYS cc_start: 0.7622 (mtmt) cc_final: 0.7348 (mmmt) REVERT: A 522 GLU cc_start: 0.6698 (mt-10) cc_final: 0.6194 (tt0) REVERT: A 682 ASP cc_start: 0.7599 (m-30) cc_final: 0.7151 (m-30) REVERT: A 793 MET cc_start: 0.7278 (mmt) cc_final: 0.6727 (ttp) REVERT: B 45 ILE cc_start: 0.8823 (mm) cc_final: 0.8457 (mm) REVERT: B 235 LYS cc_start: 0.7240 (OUTLIER) cc_final: 0.6974 (ptpp) REVERT: B 264 ASN cc_start: 0.8868 (OUTLIER) cc_final: 0.8612 (m110) REVERT: B 368 VAL cc_start: 0.8678 (m) cc_final: 0.8465 (t) REVERT: E 223 ASP cc_start: 0.8433 (m-30) cc_final: 0.8075 (m-30) REVERT: E 317 LYS cc_start: 0.7615 (mtmt) cc_final: 0.7339 (mmmt) REVERT: E 522 GLU cc_start: 0.6718 (mt-10) cc_final: 0.6229 (tt0) REVERT: E 682 ASP cc_start: 0.7554 (m-30) cc_final: 0.7114 (m-30) REVERT: E 793 MET cc_start: 0.7536 (mmt) cc_final: 0.6855 (ttp) REVERT: F 190 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6886 (mt-10) REVERT: F 235 LYS cc_start: 0.7240 (OUTLIER) cc_final: 0.6976 (ptpp) REVERT: F 368 VAL cc_start: 0.8676 (m) cc_final: 0.8456 (t) outliers start: 94 outliers final: 63 residues processed: 394 average time/residue: 0.2005 time to fit residues: 121.8819 Evaluate side-chains 379 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 312 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 699 SER Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 85 MET Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 617 ARG Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 699 SER Chi-restraints excluded: chain E residue 718 VAL Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain E residue 817 THR Chi-restraints excluded: chain E residue 882 THR Chi-restraints excluded: chain E residue 892 SER Chi-restraints excluded: chain E residue 955 GLU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 65 MET Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 307 HIS Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 390 PHE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain H residue 6 ILE 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: chunk 136 optimal weight: 1.9990 chunk 197 optimal weight: 6.9990 chunk 188 optimal weight: 0.6980 chunk 278 optimal weight: 7.9990 chunk 227 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 310 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 GLN A 133 GLN A 534 GLN A 591 ASN B 264 ASN E 133 GLN E 405 GLN E 534 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.177400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.154548 restraints weight = 26800.640| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.12 r_work: 0.3351 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25986 Z= 0.145 Angle : 0.758 29.136 35512 Z= 0.298 Chirality : 0.043 0.162 3952 Planarity : 0.005 0.082 4604 Dihedral : 7.124 170.313 3674 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.94 % Favored : 95.00 % Rotamer: Outliers : 3.59 % Allowed : 14.45 % Favored : 81.95 % 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: -1.10 (0.14), residues: 3302 helix: 0.44 (0.15), residues: 1296 sheet: -1.35 (0.27), residues: 368 loop : -1.54 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 719 TYR 0.021 0.001 TYR E 260 PHE 0.014 0.001 PHE B 93 TRP 0.019 0.001 TRP E 780 HIS 0.004 0.001 HIS A 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.14 (25928) covalent geometry : angle 0.59386 / 0.30 (35374) hydrogen bonds : bond 0.03243 / 2.26 ( 950) hydrogen bonds : angle 4.61714 / 3.26 ( 2664) metal coordination : bond 0.01312 / 0.79 ( 56) metal coordination : angle 7.58312 / 5.00 ( 138) Misc. bond : bond 0.00033 / 0.02 ( 2) *********************** 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 426 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 334 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 ASP cc_start: 0.8557 (m-30) cc_final: 0.8169 (m-30) REVERT: A 317 LYS cc_start: 0.7538 (mtmt) cc_final: 0.7054 (mmmt) REVERT: A 487 GLU cc_start: 0.6865 (mp0) cc_final: 0.6504 (mp0) REVERT: A 493 ARG cc_start: 0.7466 (tpt90) cc_final: 0.6884 (ttm110) REVERT: A 522 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6476 (tt0) REVERT: A 793 MET cc_start: 0.7455 (mmt) cc_final: 0.6602 (ttp) REVERT: B 45 ILE cc_start: 0.8666 (mm) cc_final: 0.8364 (mm) REVERT: B 235 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7302 (ptpp) REVERT: B 368 VAL cc_start: 0.8674 (m) cc_final: 0.8411 (t) REVERT: E 223 ASP cc_start: 0.8574 (m-30) cc_final: 0.8201 (m-30) REVERT: E 317 LYS cc_start: 0.7564 (mtmt) cc_final: 0.7122 (mmmt) REVERT: E 487 GLU cc_start: 0.6871 (mp0) cc_final: 0.6502 (mp0) REVERT: E 493 ARG cc_start: 0.7482 (tpt90) cc_final: 0.6871 (ttm110) REVERT: E 522 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6471 (tt0) REVERT: E 591 ASN cc_start: 0.7059 (t0) cc_final: 0.6611 (t0) REVERT: E 682 ASP cc_start: 0.7693 (m-30) cc_final: 0.7482 (m-30) REVERT: E 793 MET cc_start: 0.7701 (mmt) cc_final: 0.6738 (ttp) REVERT: F 45 ILE cc_start: 0.8644 (mm) cc_final: 0.8336 (mm) REVERT: F 235 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7280 (ptpp) REVERT: F 368 VAL cc_start: 0.8655 (m) cc_final: 0.8400 (t) outliers start: 92 outliers final: 71 residues processed: 402 average time/residue: 0.1823 time to fit residues: 114.1490 Evaluate side-chains 385 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 312 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 699 SER Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 85 MET Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 457 THR Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 617 ARG Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 699 SER Chi-restraints excluded: chain E residue 718 VAL Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain E residue 741 LEU Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 817 THR Chi-restraints excluded: chain E residue 881 THR Chi-restraints excluded: chain E residue 882 THR Chi-restraints excluded: chain E residue 955 GLU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 65 MET Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 307 HIS Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 390 PHE Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 199 optimal weight: 6.9990 chunk 151 optimal weight: 0.7980 chunk 281 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 310 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 chunk 301 optimal weight: 2.9990 chunk 308 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 GLN A 534 GLN ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN E 133 GLN E 534 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 = 0.176998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.152324 restraints weight = 26837.510| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.27 r_work: 0.3308 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25986 Z= 0.156 Angle : 0.775 29.140 35512 Z= 0.306 Chirality : 0.044 0.167 3952 Planarity : 0.005 0.087 4604 Dihedral : 7.090 169.169 3672 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.21 % Favored : 94.73 % Rotamer: Outliers : 3.63 % Allowed : 14.30 % Favored : 82.07 % 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: -1.04 (0.15), residues: 3302 helix: 0.46 (0.15), residues: 1296 sheet: -1.41 (0.26), residues: 384 loop : -1.45 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 274 TYR 0.021 0.001 TYR E 260 PHE 0.012 0.001 PHE B 93 TRP 0.018 0.001 TRP A 780 HIS 0.004 0.001 HIS A 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (25928) covalent geometry : angle 0.60684 / 0.30 (35374) hydrogen bonds : bond 0.03399 / 2.36 ( 950) hydrogen bonds : angle 4.61423 / 3.25 ( 2664) metal coordination : bond 0.01391 / 0.84 ( 56) metal coordination : angle 7.74885 / 5.10 ( 138) Misc. bond : bond 0.00033 / 0.02 ( 2) *********************** 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 410 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 317 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 ASP cc_start: 0.8655 (m-30) cc_final: 0.8254 (m-30) REVERT: A 317 LYS cc_start: 0.7488 (mtmt) cc_final: 0.6992 (mmmt) REVERT: A 487 GLU cc_start: 0.6894 (mp0) cc_final: 0.6522 (mp0) REVERT: A 522 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6523 (tt0) REVERT: A 793 MET cc_start: 0.7523 (mmt) cc_final: 0.6618 (ttp) REVERT: B 235 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7361 (ptpp) REVERT: B 307 HIS cc_start: 0.7496 (OUTLIER) cc_final: 0.7188 (m-70) REVERT: B 368 VAL cc_start: 0.8729 (m) cc_final: 0.8473 (t) REVERT: E 223 ASP cc_start: 0.8708 (m-30) cc_final: 0.8329 (m-30) REVERT: E 317 LYS cc_start: 0.7527 (mtmt) cc_final: 0.7034 (mmmt) REVERT: E 395 LYS cc_start: 0.7570 (tptt) cc_final: 0.6820 (ttpt) REVERT: E 487 GLU cc_start: 0.6897 (mp0) cc_final: 0.6519 (mp0) REVERT: E 522 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6567 (tt0) REVERT: E 591 ASN cc_start: 0.7129 (t0) cc_final: 0.6657 (t0) REVERT: E 793 MET cc_start: 0.7747 (mmt) cc_final: 0.6750 (ttp) REVERT: F 51 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7723 (mm) REVERT: F 235 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7345 (ptpp) REVERT: F 307 HIS cc_start: 0.7461 (OUTLIER) cc_final: 0.7143 (m-70) REVERT: F 368 VAL cc_start: 0.8728 (m) cc_final: 0.8467 (t) outliers start: 93 outliers final: 73 residues processed: 385 average time/residue: 0.1768 time to fit residues: 105.5331 Evaluate side-chains 389 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 311 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 699 SER Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 85 MET Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 457 THR Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 617 ARG Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 699 SER Chi-restraints excluded: chain E residue 718 VAL Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain E residue 741 LEU Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 817 THR Chi-restraints excluded: chain E residue 881 THR Chi-restraints excluded: chain E residue 882 THR Chi-restraints excluded: chain E residue 955 GLU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 65 MET Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 307 HIS Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 390 PHE Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain H residue 6 ILE 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: chunk 31 optimal weight: 8.9990 chunk 241 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 68 optimal weight: 0.8980 chunk 243 optimal weight: 7.9990 chunk 261 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 319 optimal weight: 5.9990 chunk 276 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 GLN A 473 ASN A 534 GLN ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN E 473 ASN E 534 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.169229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.144839 restraints weight = 27201.040| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.26 r_work: 0.3219 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 25986 Z= 0.319 Angle : 0.970 28.612 35512 Z= 0.397 Chirality : 0.052 0.227 3952 Planarity : 0.006 0.093 4604 Dihedral : 7.475 166.224 3672 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.36 % Favored : 93.52 % Rotamer: Outliers : 3.91 % Allowed : 14.92 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.19 % 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: -0.00 (0.14), residues: 1292 sheet: -1.56 (0.26), residues: 382 loop : -1.62 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 321 TYR 0.026 0.003 TYR E 260 PHE 0.020 0.002 PHE A 208 TRP 0.013 0.002 TRP E 780 HIS 0.007 0.002 HIS F 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00786 / 0.32 (25928) covalent geometry : angle 0.77825 / 0.39 (35374) hydrogen bonds : bond 0.04451 / 3.09 ( 950) hydrogen bonds : angle 5.02759 / 3.55 ( 2664) metal coordination : bond 0.02614 / 1.67 ( 56) metal coordination : angle 9.30898 / 6.29 ( 138) Misc. bond : bond 0.00066 / 0.05 ( 2) *********************** 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 423 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 323 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7575 (mtmt) cc_final: 0.7088 (mmmt) REVERT: A 487 GLU cc_start: 0.6920 (mp0) cc_final: 0.6585 (mp0) REVERT: A 522 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6345 (tt0) REVERT: A 793 MET cc_start: 0.7760 (mmt) cc_final: 0.6776 (ttp) REVERT: B 159 ARG cc_start: 0.7893 (ttm170) cc_final: 0.7596 (mtp180) REVERT: B 235 LYS cc_start: 0.7669 (ptpp) cc_final: 0.7399 (ptpp) REVERT: B 307 HIS cc_start: 0.7551 (OUTLIER) cc_final: 0.7320 (m-70) REVERT: E 317 LYS cc_start: 0.7568 (mtmt) cc_final: 0.7094 (mmmt) REVERT: E 487 GLU cc_start: 0.6892 (mp0) cc_final: 0.6554 (mp0) REVERT: E 522 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6364 (tt0) REVERT: E 793 MET cc_start: 0.7913 (mmt) cc_final: 0.6803 (ttp) REVERT: F 51 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7839 (mm) REVERT: F 159 ARG cc_start: 0.7882 (ttm170) cc_final: 0.7569 (mtp180) REVERT: F 235 LYS cc_start: 0.7656 (ptpp) cc_final: 0.7387 (ptpp) REVERT: F 307 HIS cc_start: 0.7525 (OUTLIER) cc_final: 0.7303 (m-70) outliers start: 100 outliers final: 74 residues processed: 393 average time/residue: 0.1879 time to fit residues: 112.1996 Evaluate side-chains 383 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 306 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 85 MET Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 457 THR Chi-restraints excluded: chain E residue 473 ASN Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 617 ARG Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 718 VAL Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 817 THR Chi-restraints excluded: chain E residue 882 THR Chi-restraints excluded: chain E residue 889 ASP Chi-restraints excluded: chain E residue 955 GLU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 65 MET Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 307 HIS Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 59 VAL 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: chunk 1 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 325 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 182 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 163 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 534 GLN ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN E 473 ASN E 534 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.174959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.149856 restraints weight = 26842.902| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.19 r_work: 0.3309 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 25986 Z= 0.141 Angle : 0.789 28.315 35512 Z= 0.308 Chirality : 0.043 0.178 3952 Planarity : 0.005 0.086 4604 Dihedral : 7.174 166.486 3672 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.42 % Favored : 95.52 % Rotamer: Outliers : 2.89 % Allowed : 16.45 % Favored : 80.66 % 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: -1.08 (0.15), residues: 3302 helix: 0.34 (0.14), residues: 1308 sheet: -1.42 (0.28), residues: 348 loop : -1.42 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 321 TYR 0.021 0.001 TYR A 260 PHE 0.011 0.001 PHE F 390 TRP 0.023 0.001 TRP A 780 HIS 0.003 0.001 HIS A 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (25928) covalent geometry : angle 0.61007 / 0.30 (35374) hydrogen bonds : bond 0.03393 / 2.36 ( 950) hydrogen bonds : angle 4.73247 / 3.33 ( 2664) metal coordination : bond 0.01280 / 0.73 ( 56) metal coordination : angle 8.05547 / 5.35 ( 138) Misc. bond : bond 0.00016 / 0.01 ( 2) *********************** 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 410 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 336 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 ASP cc_start: 0.8608 (m-30) cc_final: 0.8210 (m-30) REVERT: A 317 LYS cc_start: 0.7497 (mtmt) cc_final: 0.7059 (mmmt) REVERT: A 358 CYS cc_start: 0.8290 (m) cc_final: 0.8074 (m) REVERT: A 395 LYS cc_start: 0.7590 (tptt) cc_final: 0.6855 (ttpt) REVERT: A 522 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6366 (tt0) REVERT: A 793 MET cc_start: 0.7599 (mmt) cc_final: 0.6637 (ttp) REVERT: B 159 ARG cc_start: 0.7799 (ttm170) cc_final: 0.7489 (mtp180) REVERT: B 235 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7406 (ptpp) REVERT: G 29 GLN cc_start: 0.8344 (tt0) cc_final: 0.8087 (tt0) REVERT: E 223 ASP cc_start: 0.8603 (m-30) cc_final: 0.8221 (m-30) REVERT: E 317 LYS cc_start: 0.7500 (mtmt) cc_final: 0.7061 (mmmt) REVERT: E 358 CYS cc_start: 0.8267 (m) cc_final: 0.7992 (m) REVERT: E 395 LYS cc_start: 0.7597 (tptt) cc_final: 0.6890 (ttpt) REVERT: E 522 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6389 (tt0) REVERT: E 591 ASN cc_start: 0.7151 (t0) cc_final: 0.6623 (t0) REVERT: E 793 MET cc_start: 0.7772 (mmt) cc_final: 0.6721 (ttp) REVERT: F 45 ILE cc_start: 0.8704 (mm) cc_final: 0.8339 (mm) REVERT: F 159 ARG cc_start: 0.7794 (ttm170) cc_final: 0.7463 (mtp180) REVERT: F 235 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7402 (ptpp) REVERT: C 29 GLN cc_start: 0.8349 (tt0) cc_final: 0.8101 (tt0) outliers start: 74 outliers final: 59 residues processed: 392 average time/residue: 0.1971 time to fit residues: 117.9477 Evaluate side-chains 374 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 313 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 264 ASN 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 85 MET Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 457 THR Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 617 ARG Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 718 VAL Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 817 THR Chi-restraints excluded: chain E residue 882 THR Chi-restraints excluded: chain E residue 955 GLU Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 59 VAL 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: chunk 166 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 266 optimal weight: 9.9990 chunk 78 optimal weight: 0.0970 chunk 93 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 200 optimal weight: 8.9990 chunk 241 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 146 optimal weight: 0.3980 chunk 1 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 534 GLN A 591 ASN B 264 ASN E 534 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.179671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.154195 restraints weight = 26451.250| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.17 r_work: 0.3357 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25986 Z= 0.109 Angle : 0.738 27.806 35512 Z= 0.286 Chirality : 0.042 0.165 3952 Planarity : 0.005 0.087 4604 Dihedral : 6.903 166.863 3672 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.39 % Favored : 95.55 % Rotamer: Outliers : 2.19 % Allowed : 17.30 % Favored : 80.51 % 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: -0.79 (0.15), residues: 3302 helix: 0.68 (0.15), residues: 1292 sheet: -1.38 (0.27), residues: 378 loop : -1.29 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 42 TYR 0.016 0.001 TYR A 260 PHE 0.013 0.001 PHE F 93 TRP 0.024 0.001 TRP E 780 HIS 0.003 0.000 HIS A 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (25928) covalent geometry : angle 0.57180 / 0.28 (35374) hydrogen bonds : bond 0.03001 / 2.08 ( 950) hydrogen bonds : angle 4.55933 / 3.20 ( 2664) metal coordination : bond 0.01005 / 0.55 ( 56) metal coordination : angle 7.50696 / 4.96 ( 138) Misc. bond : bond 0.00022 / 0.02 ( 2) ********************** 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 398 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 342 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 ASP cc_start: 0.8519 (m-30) cc_final: 0.8154 (m-30) REVERT: A 317 LYS cc_start: 0.7446 (mtmt) cc_final: 0.6979 (mmmt) REVERT: A 358 CYS cc_start: 0.8194 (m) cc_final: 0.7931 (m) REVERT: A 395 LYS cc_start: 0.7538 (tptt) cc_final: 0.6841 (ttpt) REVERT: A 522 GLU cc_start: 0.6952 (mt-10) cc_final: 0.6430 (tt0) REVERT: A 617 ARG cc_start: 0.6420 (OUTLIER) cc_final: 0.6010 (ttm170) REVERT: A 793 MET cc_start: 0.7541 (mmt) cc_final: 0.6579 (ttp) REVERT: B 45 ILE cc_start: 0.8674 (mm) cc_final: 0.8357 (mm) REVERT: B 159 ARG cc_start: 0.7768 (ttm170) cc_final: 0.7473 (mtp180) REVERT: B 235 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7515 (ptpp) REVERT: G 29 GLN cc_start: 0.8133 (tt0) cc_final: 0.7926 (tt0) REVERT: E 223 ASP cc_start: 0.8536 (m-30) cc_final: 0.8175 (m-30) REVERT: E 317 LYS cc_start: 0.7440 (mtmt) cc_final: 0.6975 (mmmt) REVERT: E 358 CYS cc_start: 0.8198 (m) cc_final: 0.7925 (m) REVERT: E 395 LYS cc_start: 0.7533 (tptt) cc_final: 0.6846 (ttpt) REVERT: E 405 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8065 (mp10) REVERT: E 522 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6400 (tt0) REVERT: E 591 ASN cc_start: 0.6784 (t0) cc_final: 0.6431 (t0) REVERT: E 617 ARG cc_start: 0.6409 (OUTLIER) cc_final: 0.6014 (ttm170) REVERT: E 793 MET cc_start: 0.7706 (mmt) cc_final: 0.6679 (ttp) REVERT: F 159 ARG cc_start: 0.7788 (ttm170) cc_final: 0.7476 (mtp180) REVERT: F 235 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7469 (ptpp) outliers start: 56 outliers final: 48 residues processed: 381 average time/residue: 0.1838 time to fit residues: 107.1383 Evaluate side-chains 379 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 327 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 264 ASN 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 85 MET Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 572 MET Chi-restraints excluded: chain E residue 617 ARG Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 718 VAL Chi-restraints excluded: chain E residue 817 THR Chi-restraints excluded: chain E residue 882 THR Chi-restraints excluded: chain E residue 955 GLU Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain H residue 59 VAL 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: chunk 39 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 210 optimal weight: 2.9990 chunk 306 optimal weight: 8.9990 chunk 323 optimal weight: 0.9990 chunk 247 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 284 optimal weight: 0.0020 chunk 301 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 overall best weight: 1.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 534 GLN ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN E 534 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.175178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.151091 restraints weight = 26796.250| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.21 r_work: 0.3307 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 25986 Z= 0.169 Angle : 0.794 27.977 35512 Z= 0.312 Chirality : 0.044 0.186 3952 Planarity : 0.005 0.053 4604 Dihedral : 7.037 166.351 3672 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.30 % Favored : 94.64 % Rotamer: Outliers : 2.38 % Allowed : 17.38 % Favored : 80.23 % 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: -0.84 (0.15), residues: 3302 helix: 0.59 (0.15), residues: 1294 sheet: -1.40 (0.26), residues: 394 loop : -1.27 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 321 TYR 0.023 0.002 TYR E 260 PHE 0.012 0.001 PHE E 175 TRP 0.020 0.001 TRP E 780 HIS 0.004 0.001 HIS A 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 (25928) covalent geometry : angle 0.62239 / 0.31 (35374) hydrogen bonds : bond 0.03352 / 2.32 ( 950) hydrogen bonds : angle 4.63061 / 3.26 ( 2664) metal coordination : bond 0.01499 / 0.90 ( 56) metal coordination : angle 7.92602 / 5.30 ( 138) Misc. bond : bond 0.00039 / 0.03 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6789.29 seconds wall clock time: 116 minutes 58.97 seconds (7018.97 seconds total)