Starting phenix.real_space_refine on Fri Sep 19 10:14:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ktr_62563/09_2025/9ktr_62563.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ktr_62563/09_2025/9ktr_62563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ktr_62563/09_2025/9ktr_62563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ktr_62563/09_2025/9ktr_62563.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ktr_62563/09_2025/9ktr_62563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ktr_62563/09_2025/9ktr_62563.map" } resolution = 2.55 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= 0.003 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mo 2 10.26 5 Fe 48 7.16 5 P 14 5.49 5 S 224 5.16 5 C 15750 2.51 5 N 4530 2.21 5 O 4800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25368 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 7222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 951, 7222 Classifications: {'peptide': 951} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 896} Chain: "G" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 477 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "F" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1096 Classifications: {'peptide': 149} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 143} Chain: "H" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 477 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "C" Number of atoms: 3671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3671 Classifications: {'peptide': 496} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 466} Chain: "E" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1096 Classifications: {'peptide': 149} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 143} Chain: "B" Number of atoms: 7222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 951, 7222 Classifications: {'peptide': 951} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 896} Chain: "D" Number of atoms: 3671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3671 Classifications: {'peptide': 496} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 466} Chain: "A" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 130 Ad-hoc single atom residues: {'6MO': 1} Unusual residues: {'2MD': 1, 'FES': 1, 'MGD': 1, 'SF4': 4} Classifications: {'undetermined': 7} Link IDs: {None: 5} Chain breaks: 1 Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAD': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 130 Ad-hoc single atom residues: {'6MO': 1} Unusual residues: {'FES': 1, 'MGD': 2, 'SF4': 4} Classifications: {'undetermined': 7} Link IDs: {None: 5} Chain breaks: 1 Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAD': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 361 SG CYS A 57 70.687 108.178 52.088 1.00 15.24 S ATOM 433 SG CYS A 68 68.165 105.531 50.898 1.00 14.75 S ATOM 458 SG CYS A 71 64.982 107.816 54.934 1.00 15.74 S ATOM 559 SG CYS A 85 67.648 110.100 55.652 1.00 22.96 S ATOM 896 SG CYS A 130 75.525 95.179 47.856 1.00 10.36 S ATOM 839 SG CYS A 121 73.403 90.725 43.692 1.00 17.68 S ATOM 860 SG CYS A 124 79.559 92.371 44.223 1.00 8.57 S ATOM 1327 SG CYS A 185 76.261 105.082 48.927 1.00 10.26 S ATOM 1306 SG CYS A 182 79.064 105.022 43.495 1.00 8.19 S ATOM 1679 SG CYS A 234 81.071 101.245 49.116 1.00 6.53 S ATOM 1652 SG CYS A 230 87.352 104.354 50.828 1.00 13.37 S ATOM 1618 SG CYS A 224 92.701 106.717 50.286 1.00 12.79 S ATOM 1637 SG CYS A 227 90.566 106.780 56.217 1.00 13.65 S ATOM 1381 SG CYS A 192 86.881 109.953 51.519 1.00 59.82 S ATOM 1858 SG CYS A 258 96.339 98.978 65.457 1.00 9.44 S ATOM 2118 SG CYS A 293 96.695 103.853 61.416 1.00 11.55 S ATOM 1881 SG CYS A 261 98.398 104.733 67.452 1.00 14.16 S ATOM 1902 SG CYS A 265 92.488 101.931 66.190 1.00 20.02 S ATOM 8283 SG CYS F 77 66.590 129.403 25.487 1.00 17.03 S ATOM 8319 SG CYS F 82 64.734 130.811 23.283 1.00 25.00 S ATOM 8564 SG CYS F 116 64.299 131.504 30.214 1.00 42.18 S ATOM 8590 SG CYS F 120 62.263 133.181 28.455 1.00 17.92 S ATOM 12451 SG CYS C 429 74.206 58.768 43.321 1.00 9.37 S ATOM 12488 SG CYS C 435 78.869 61.512 39.352 1.00 12.32 S ATOM 12762 SG CYS C 473 79.848 57.253 43.710 1.00 12.93 S ATOM 12468 SG CYS C 432 78.730 63.912 44.182 1.00 8.65 S ATOM 13527 SG CYS E 77 78.489 47.221 25.487 1.00 16.58 S ATOM 13563 SG CYS E 82 80.331 45.947 23.265 1.00 24.38 S ATOM 13808 SG CYS E 116 80.765 45.157 30.233 1.00 42.19 S ATOM 13834 SG CYS E 120 82.847 43.506 28.457 1.00 18.78 S ATOM 14400 SG CYS B 57 74.437 68.448 52.080 1.00 14.81 S ATOM 14472 SG CYS B 68 76.900 71.170 50.898 1.00 13.43 S ATOM 14497 SG CYS B 71 80.112 68.863 54.930 1.00 17.33 S ATOM 14598 SG CYS B 85 77.436 66.596 55.652 1.00 25.49 S ATOM 14935 SG CYS B 130 69.558 81.525 47.857 1.00 9.26 S ATOM 14878 SG CYS B 121 71.682 85.980 43.692 1.00 15.86 S ATOM 14899 SG CYS B 124 65.521 84.322 44.231 1.00 7.41 S ATOM 15366 SG CYS B 185 68.958 71.597 48.965 1.00 9.74 S ATOM 15345 SG CYS B 182 66.006 71.742 43.590 1.00 7.71 S ATOM 15718 SG CYS B 234 63.884 75.387 49.271 1.00 8.89 S ATOM 15391 SG CYS B 188 62.578 69.187 48.360 1.00 7.09 S ATOM 15420 SG CYS B 192 57.745 66.641 52.120 1.00 44.72 S ATOM 15657 SG CYS B 224 52.821 69.604 50.464 1.00 20.66 S ATOM 15676 SG CYS B 227 54.790 70.119 56.110 1.00 13.87 S ATOM 15897 SG CYS B 258 48.755 77.739 65.462 1.00 9.53 S ATOM 16157 SG CYS B 293 48.395 72.877 61.450 1.00 10.96 S ATOM 15920 SG CYS B 261 46.717 72.020 67.446 1.00 13.91 S ATOM 15941 SG CYS B 265 52.864 73.229 66.620 1.00 8.91 S ATOM 24440 SG CYS D 429 70.871 117.935 43.328 1.00 9.68 S ATOM 24477 SG CYS D 435 66.207 115.187 39.353 1.00 12.63 S ATOM 24751 SG CYS D 473 65.229 119.445 43.711 1.00 13.44 S ATOM 24457 SG CYS D 432 66.340 112.789 44.173 1.00 8.61 S Time building chain proxies: 5.82, per 1000 atoms: 0.23 Number of scatterers: 25368 At special positions: 0 Unit cell: (146.01, 177.63, 110.67, 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 224 16.00 P 14 15.00 O 4800 8.00 N 4530 7.00 C 15750 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 753.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A1004 " 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 68 " pdb="FE1 FES A1004 " - pdb=" SG CYS A 57 " pdb=" FES B1004 " pdb="FE2 FES B1004 " - pdb=" SG CYS B 71 " pdb="FE2 FES B1004 " - pdb=" SG CYS B 85 " pdb="FE1 FES B1004 " - pdb=" SG CYS B 68 " pdb="FE1 FES B1004 " - pdb=" SG CYS B 57 " pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 120 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 77 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 82 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 116 " pdb=" FES F 201 " pdb="FE1 FES F 201 " - pdb=" SG CYS F 77 " pdb="FE2 FES F 201 " - pdb=" SG CYS F 120 " pdb="FE1 FES F 201 " - pdb=" SG CYS F 82 " pdb="FE2 FES F 201 " - pdb=" SG CYS F 116 " pdb=" SF4 A1005 " pdb="FE4 SF4 A1005 " - pdb=" ND1 HIS A 117 " pdb="FE2 SF4 A1005 " - pdb=" SG CYS A 121 " pdb="FE1 SF4 A1005 " - pdb=" SG CYS A 130 " pdb="FE3 SF4 A1005 " - pdb=" SG CYS A 124 " pdb=" SF4 A1006 " pdb="FE1 SF4 A1006 " - pdb=" SG CYS A 185 " pdb="FE2 SF4 A1006 " - pdb=" SG CYS A 182 " pdb="FE3 SF4 A1006 " - pdb=" SG CYS A 234 " pdb=" SF4 A1007 " pdb="FE2 SF4 A1007 " - pdb=" SG CYS A 224 " pdb="FE3 SF4 A1007 " - pdb=" SG CYS A 227 " pdb="FE4 SF4 A1007 " - pdb=" SG CYS A 192 " pdb="FE1 SF4 A1007 " - pdb=" SG CYS A 230 " pdb=" SF4 A1008 " pdb="FE4 SF4 A1008 " - pdb=" SG CYS A 265 " pdb="FE3 SF4 A1008 " - pdb=" SG CYS A 261 " pdb="FE1 SF4 A1008 " - pdb=" SG CYS A 258 " pdb="FE2 SF4 A1008 " - pdb=" SG CYS A 293 " pdb=" SF4 B1005 " pdb="FE4 SF4 B1005 " - pdb=" ND1 HIS B 117 " pdb="FE2 SF4 B1005 " - pdb=" SG CYS B 121 " pdb="FE1 SF4 B1005 " - pdb=" SG CYS B 130 " pdb="FE3 SF4 B1005 " - pdb=" SG CYS B 124 " pdb=" SF4 B1006 " pdb="FE1 SF4 B1006 " - pdb=" SG CYS B 185 " pdb="FE2 SF4 B1006 " - pdb=" SG CYS B 182 " pdb="FE3 SF4 B1006 " - pdb=" SG CYS B 234 " pdb="FE4 SF4 B1006 " - pdb=" SG CYS B 188 " pdb=" SF4 B1007 " pdb="FE3 SF4 B1007 " - pdb=" SG CYS B 227 " pdb="FE2 SF4 B1007 " - pdb=" SG CYS B 224 " pdb="FE1 SF4 B1007 " - pdb=" SG CYS B 192 " pdb=" SF4 B1008 " pdb="FE4 SF4 B1008 " - pdb=" SG CYS B 265 " pdb="FE3 SF4 B1008 " - pdb=" SG CYS B 261 " pdb="FE1 SF4 B1008 " - pdb=" SG CYS B 258 " pdb="FE2 SF4 B1008 " - pdb=" SG CYS B 293 " pdb=" SF4 C 603 " pdb="FE1 SF4 C 603 " - pdb=" SG CYS C 429 " pdb="FE2 SF4 C 603 " - pdb=" SG CYS C 435 " pdb="FE3 SF4 C 603 " - pdb=" SG CYS C 473 " pdb="FE4 SF4 C 603 " - pdb=" SG CYS C 432 " pdb=" SF4 D 603 " pdb="FE1 SF4 D 603 " - pdb=" SG CYS D 429 " pdb="FE3 SF4 D 603 " - pdb=" SG CYS D 473 " pdb="FE2 SF4 D 603 " - pdb=" SG CYS D 435 " pdb="FE4 SF4 D 603 " - pdb=" SG CYS D 432 " Number of angles added : 132 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 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: 161 helices and 30 sheets defined 48.0% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 41 through 49 Processing helix chain 'A' and resid 99 through 115 Processing helix chain 'A' and resid 130 through 139 removed outlier: 3.525A pdb=" N GLY A 137 " --> pdb=" O GLN A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 182 Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.515A pdb=" N GLU A 209 " --> pdb=" O ARG A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 293 through 298 Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 326 through 346 removed outlier: 3.601A pdb=" N LEU A 331 " --> pdb=" O TRP A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 373 Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 387 through 398 removed outlier: 3.640A pdb=" N LYS A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 413 Processing helix chain 'A' and resid 422 through 427 Processing helix chain 'A' and resid 427 through 440 Processing helix chain 'A' and resid 472 through 487 Processing helix chain 'A' and resid 491 through 499 Processing helix chain 'A' and resid 500 through 512 Processing helix chain 'A' and resid 513 through 516 Processing helix chain 'A' and resid 517 through 526 removed outlier: 5.058A pdb=" N SER A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) removed outlier: 5.539A 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 550 through 555 Processing helix chain 'A' and resid 558 through 573 Processing helix chain 'A' and resid 591 through 598 Processing helix chain 'A' and resid 615 through 625 Processing helix chain 'A' and resid 635 through 646 Processing helix chain 'A' and resid 657 through 662 Processing helix chain 'A' and resid 664 through 674 Processing helix chain 'A' and resid 687 through 692 Processing helix chain 'A' and resid 700 through 704 Processing helix chain 'A' and resid 729 through 740 Processing helix chain 'A' and resid 749 through 761 removed outlier: 3.927A pdb=" N ILE A 753 " --> pdb=" O HIS A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 765 removed outlier: 3.570A pdb=" N ALA A 765 " --> pdb=" O PRO A 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 762 through 765' Processing helix chain 'A' and resid 768 through 776 Processing helix chain 'A' and resid 839 through 848 removed outlier: 6.067A pdb=" N GLU A 844 " --> pdb=" O ARG A 841 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASN A 845 " --> pdb=" O ARG A 842 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL A 846 " --> pdb=" O THR A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 865 Processing helix chain 'A' and resid 906 through 910 removed outlier: 3.569A pdb=" N VAL A 910 " --> pdb=" O ALA A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 952 Processing helix chain 'G' and resid 5 through 18 Processing helix chain 'G' and resid 23 through 36 Processing helix chain 'G' and resid 37 through 50 Processing helix chain 'G' and resid 56 through 63 Processing helix chain 'G' and resid 64 through 66 No H-bonds generated for 'chain 'G' and resid 64 through 66' Processing helix chain 'F' and resid 4 through 14 Processing helix chain 'F' and resid 20 through 33 Processing helix chain 'F' and resid 39 through 47 Processing helix chain 'F' and resid 50 through 61 removed outlier: 3.519A pdb=" N TYR F 61 " --> pdb=" O VAL F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 85 removed outlier: 3.653A pdb=" N MET F 85 " --> pdb=" O ALA F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 99 Processing helix chain 'F' and resid 119 through 123 removed outlier: 3.512A pdb=" N ALA F 123 " --> pdb=" O CYS F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 150 Processing helix chain 'H' and resid 5 through 18 Processing helix chain 'H' and resid 23 through 36 Processing helix chain 'H' and resid 37 through 50 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 helix chain 'C' and resid 8 through 15 Processing helix chain 'C' and resid 15 through 31 Processing helix chain 'C' and resid 66 through 74 removed outlier: 3.551A pdb=" N VAL C 70 " --> pdb=" O PRO C 67 " (cutoff:3.500A) Proline residue: C 71 - end of helix removed outlier: 3.510A pdb=" N PHE C 74 " --> pdb=" O PRO C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 95 Processing helix chain 'C' and resid 111 through 118 Processing helix chain 'C' and resid 121 through 130 removed outlier: 3.518A pdb=" N ALA C 129 " --> pdb=" O ARG C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 142 Processing helix chain 'C' and resid 153 through 164 Processing helix chain 'C' and resid 183 through 192 Processing helix chain 'C' and resid 192 through 208 removed outlier: 3.929A pdb=" N LEU C 196 " --> pdb=" O ASP C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 237 Processing helix chain 'C' and resid 238 through 244 Processing helix chain 'C' and resid 255 through 259 Processing helix chain 'C' and resid 260 through 269 Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 297 through 302 Processing helix chain 'C' and resid 302 through 310 Processing helix chain 'C' and resid 310 through 316 removed outlier: 3.539A pdb=" N TYR C 314 " --> pdb=" O GLY C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 353 Processing helix chain 'C' and resid 379 through 383 Processing helix chain 'C' and resid 388 through 394 Processing helix chain 'C' and resid 412 through 428 Processing helix chain 'C' and resid 432 through 451 removed outlier: 4.436A pdb=" N VAL C 440 " --> pdb=" O ARG C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 471 removed outlier: 3.934A pdb=" N LEU C 459 " --> pdb=" O ALA C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 479 Processing helix chain 'C' and resid 479 through 490 removed outlier: 3.603A pdb=" N VAL C 483 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE C 487 " --> pdb=" O VAL C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 494 Processing helix chain 'E' and resid 4 through 14 Processing helix chain 'E' and resid 20 through 33 Processing helix chain 'E' and resid 39 through 47 Processing helix chain 'E' and resid 50 through 61 removed outlier: 3.514A pdb=" N TYR E 61 " --> pdb=" O VAL E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 85 Processing helix chain 'E' and resid 86 through 99 Processing helix chain 'E' and resid 119 through 123 removed outlier: 3.512A pdb=" N ALA E 123 " --> pdb=" O CYS E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 150 Processing helix chain 'B' and resid 41 through 49 Processing helix chain 'B' and resid 99 through 115 Processing helix chain 'B' and resid 130 through 139 removed outlier: 3.531A pdb=" N GLY B 137 " --> pdb=" O GLN B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 182 Processing helix chain 'B' and resid 186 through 195 removed outlier: 3.737A pdb=" N GLU B 193 " --> pdb=" O VAL B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 210 removed outlier: 3.514A pdb=" N GLU B 209 " --> pdb=" O ARG B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 293 through 298 Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 328 through 346 Processing helix chain 'B' and resid 359 through 373 Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 387 through 398 removed outlier: 3.651A pdb=" N LYS B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 413 Processing helix chain 'B' and resid 422 through 427 Processing helix chain 'B' and resid 427 through 440 Processing helix chain 'B' and resid 472 through 487 Processing helix chain 'B' and resid 491 through 499 Processing helix chain 'B' and resid 500 through 512 Processing helix chain 'B' and resid 513 through 516 Processing helix chain 'B' and resid 517 through 526 removed outlier: 5.126A pdb=" N SER B 523 " --> pdb=" O GLU B 519 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 542 Processing helix chain 'B' and resid 550 through 555 removed outlier: 3.513A pdb=" N THR B 554 " --> pdb=" O GLY B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 573 Processing helix chain 'B' and resid 591 through 598 Processing helix chain 'B' and resid 615 through 625 Processing helix chain 'B' and resid 635 through 646 Processing helix chain 'B' and resid 657 through 662 Processing helix chain 'B' and resid 664 through 674 Processing helix chain 'B' and resid 687 through 692 Processing helix chain 'B' and resid 700 through 704 Processing helix chain 'B' and resid 729 through 740 Processing helix chain 'B' and resid 749 through 761 removed outlier: 3.923A pdb=" N ILE B 753 " --> pdb=" O HIS B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 765 removed outlier: 3.563A pdb=" N ALA B 765 " --> pdb=" O PRO B 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 762 through 765' Processing helix chain 'B' and resid 768 through 776 Processing helix chain 'B' and resid 839 through 848 removed outlier: 6.080A pdb=" N GLU B 844 " --> pdb=" O ARG B 841 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASN B 845 " --> pdb=" O ARG B 842 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL B 846 " --> pdb=" O THR B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 865 Processing helix chain 'B' and resid 906 through 910 removed outlier: 3.560A pdb=" N VAL B 910 " --> pdb=" O ALA B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 952 Processing helix chain 'D' and resid 8 through 14 Processing helix chain 'D' and resid 15 through 31 Processing helix chain 'D' and resid 44 through 48 removed outlier: 3.541A pdb=" N LEU D 47 " --> pdb=" O MET D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 74 removed outlier: 3.570A pdb=" N VAL D 70 " --> pdb=" O PRO D 67 " (cutoff:3.500A) Proline residue: D 71 - end of helix Processing helix chain 'D' and resid 90 through 95 Processing helix chain 'D' and resid 111 through 118 Processing helix chain 'D' and resid 121 through 130 removed outlier: 3.571A pdb=" N ALA D 129 " --> pdb=" O ARG D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 142 Processing helix chain 'D' and resid 153 through 164 Processing helix chain 'D' and resid 183 through 192 Processing helix chain 'D' and resid 192 through 208 removed outlier: 3.879A pdb=" N LEU D 196 " --> pdb=" O ASP D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 237 Processing helix chain 'D' and resid 238 through 244 Processing helix chain 'D' and resid 255 through 259 Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 297 through 302 Processing helix chain 'D' and resid 302 through 310 Processing helix chain 'D' and resid 310 through 316 removed outlier: 3.510A pdb=" N TYR D 314 " --> pdb=" O GLY D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 353 Processing helix chain 'D' and resid 379 through 385 removed outlier: 4.285A pdb=" N ASP D 384 " --> pdb=" O ALA D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 394 Processing helix chain 'D' and resid 412 through 428 Processing helix chain 'D' and resid 432 through 451 removed outlier: 4.431A pdb=" N VAL D 440 " --> pdb=" O ARG D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 471 removed outlier: 3.917A pdb=" N LEU D 459 " --> pdb=" O ALA D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 479 Processing helix chain 'D' and resid 479 through 490 removed outlier: 3.604A pdb=" N VAL D 483 " --> pdb=" O THR D 479 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE D 487 " --> pdb=" O VAL D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 494 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 37 removed outlier: 9.500A pdb=" N VAL A 95 " --> pdb=" O THR A 26 " (cutoff:3.500A) removed outlier: 6.819A 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 removed outlier: 3.636A pdb=" N GLU A 160 " --> pdb=" O GLN A 157 " (cutoff:3.500A) 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: 6.514A pdb=" N ARG A 272 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LEU A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 323 through 324 removed outlier: 6.685A pdb=" N LEU A 651 " --> pdb=" O ILE A 679 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N HIS A 681 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL A 653 " --> pdb=" O HIS A 681 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 463 through 466 removed outlier: 6.476A pdb=" N LEU A 444 " --> pdb=" O TRP A 464 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N LEU A 466 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL A 446 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ALA A 416 " --> pdb=" O ILE A 445 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL A 447 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL A 418 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 582 " --> pdb=" O ALA A 545 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 604 through 605 removed outlier: 3.666A pdb=" N ARG A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 706 through 709 Processing sheet with id=AB1, first strand: chain 'A' and resid 823 through 828 removed outlier: 4.174A pdb=" N THR A 899 " --> pdb=" O ARG A 853 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ARG A 853 " --> pdb=" O THR A 899 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LEU A 854 " --> pdb=" O THR A 886 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 105 through 106 removed outlier: 6.655A pdb=" N HIS F 72 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N GLU F 112 " --> pdb=" O HIS F 72 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ILE F 74 " --> pdb=" O GLU F 112 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA F 114 " --> pdb=" O ILE F 74 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LEU F 76 " --> pdb=" O ALA F 114 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 35 through 39 removed outlier: 6.194A pdb=" N ILE C 3 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN C 39 " --> pdb=" O ILE C 3 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL C 5 " --> pdb=" O ASN C 39 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LYS C 2 " --> pdb=" O GLU C 54 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY C 85 " --> pdb=" O GLY C 61 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 249 through 251 removed outlier: 7.274A pdb=" N ARG C 250 " --> pdb=" O GLY C 212 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL C 214 " --> pdb=" O ARG C 250 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AB6, first strand: chain 'C' and resid 338 through 343 Processing sheet with id=AB7, first strand: chain 'E' and resid 105 through 106 removed outlier: 6.662A pdb=" N HIS E 72 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N GLU E 112 " --> pdb=" O HIS E 72 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ILE E 74 " --> pdb=" O GLU E 112 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA E 114 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LEU E 76 " --> pdb=" O ALA E 114 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 32 through 37 removed outlier: 9.493A pdb=" N VAL B 95 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR B 28 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 156 through 157 removed outlier: 3.546A pdb=" N GLU B 160 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 175 through 177 Processing sheet with id=AC2, first strand: chain 'B' and resid 202 through 204 Processing sheet with id=AC3, first strand: chain 'B' and resid 252 through 257 removed outlier: 6.508A pdb=" N ARG B 272 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LEU B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 323 through 324 removed outlier: 6.685A pdb=" N LEU B 651 " --> pdb=" O ILE B 679 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N HIS B 681 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL B 653 " --> pdb=" O HIS B 681 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 463 through 466 removed outlier: 6.475A pdb=" N LEU B 444 " --> pdb=" O TRP B 464 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LEU B 466 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B 446 " --> pdb=" O LEU B 466 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ALA B 416 " --> pdb=" O ILE B 445 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL B 447 " --> pdb=" O ALA B 416 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL B 418 " --> pdb=" O VAL B 447 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 582 " --> pdb=" O ALA B 545 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 604 through 605 removed outlier: 3.667A pdb=" N ARG B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 706 through 709 Processing sheet with id=AC8, first strand: chain 'B' and resid 823 through 828 removed outlier: 4.177A pdb=" N THR B 899 " --> pdb=" O ARG B 853 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ARG B 853 " --> pdb=" O THR B 899 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU B 854 " --> pdb=" O THR B 886 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 35 through 39 removed outlier: 6.275A pdb=" N ILE D 3 " --> pdb=" O ARG D 37 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN D 39 " --> pdb=" O ILE D 3 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL D 5 " --> pdb=" O ASN D 39 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LYS D 2 " --> pdb=" O GLU D 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY D 85 " --> pdb=" O GLY D 61 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 246 through 251 removed outlier: 6.595A pdb=" N GLY D 212 " --> pdb=" O GLU D 248 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ARG D 250 " --> pdb=" O GLY D 212 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N VAL D 214 " --> pdb=" O ARG D 250 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 318 through 319 Processing sheet with id=AD3, first strand: chain 'D' and resid 338 through 343 1150 hydrogen bonds defined for protein. 3141 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: 5.32 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 10823 1.43 - 1.65: 14748 1.65 - 1.86: 257 1.86 - 2.07: 0 2.07 - 2.29: 136 Bond restraints: 25964 Sorted by residual: bond pdb=" C12 2MD A1001 " pdb=" C13 2MD A1001 " ideal model delta sigma weight residual 1.529 1.334 0.195 2.00e-02 2.50e+03 9.49e+01 bond pdb=" C3N NAD C 601 " pdb=" C4N NAD C 601 " ideal model delta sigma weight residual 1.390 1.510 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" C3N NAD D 601 " pdb=" C4N NAD D 601 " ideal model delta sigma weight residual 1.390 1.509 -0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" C4N NAD C 601 " pdb=" C5N NAD C 601 " ideal model delta sigma weight residual 1.384 1.500 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" C4N NAD D 601 " pdb=" C5N NAD D 601 " ideal model delta sigma weight residual 1.384 1.500 -0.116 2.00e-02 2.50e+03 3.36e+01 ... (remaining 25959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.15: 35356 4.15 - 8.30: 95 8.30 - 12.45: 9 12.45 - 16.60: 1 16.60 - 20.76: 1 Bond angle restraints: 35462 Sorted by residual: angle pdb=" CA CYS A 192 " pdb=" CB CYS A 192 " pdb=" SG CYS A 192 " ideal model delta sigma weight residual 114.40 135.16 -20.76 2.30e+00 1.89e-01 8.14e+01 angle pdb=" C ARG A 187 " pdb=" N CYS A 188 " pdb=" CA CYS A 188 " ideal model delta sigma weight residual 121.92 111.51 10.41 1.73e+00 3.34e-01 3.62e+01 angle pdb=" N CYS A 192 " pdb=" CA CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sigma weight residual 110.49 101.02 9.47 1.69e+00 3.50e-01 3.14e+01 angle pdb=" C ALA A 191 " pdb=" N CYS A 192 " pdb=" CA CYS A 192 " ideal model delta sigma weight residual 121.54 131.03 -9.49 1.91e+00 2.74e-01 2.47e+01 angle pdb=" C11 2MD A1001 " pdb=" C12 2MD A1001 " pdb=" C13 2MD A1001 " ideal model delta sigma weight residual 107.02 120.75 -13.73 3.00e+00 1.11e-01 2.10e+01 ... (remaining 35457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.87: 14548 27.87 - 55.73: 914 55.73 - 83.60: 115 83.60 - 111.46: 8 111.46 - 139.33: 2 Dihedral angle restraints: 15587 sinusoidal: 6177 harmonic: 9410 Sorted by residual: dihedral pdb=" CA LYS C 278 " pdb=" C LYS C 278 " pdb=" N PRO C 279 " pdb=" CA PRO C 279 " ideal model delta harmonic sigma weight residual 180.00 154.53 25.47 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA GLY D 400 " pdb=" C GLY D 400 " pdb=" N HIS D 401 " pdb=" CA HIS D 401 " ideal model delta harmonic sigma weight residual 180.00 154.56 25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA GLY C 400 " pdb=" C GLY C 400 " pdb=" N HIS C 401 " pdb=" CA HIS C 401 " ideal model delta harmonic sigma weight residual 180.00 154.70 25.30 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 15584 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.477: 3976 0.477 - 0.953: 0 0.953 - 1.430: 0 1.430 - 1.906: 0 1.906 - 2.383: 2 Chirality restraints: 3978 Sorted by residual: chirality pdb=" C12 2MD A1001 " pdb=" C11 2MD A1001 " pdb=" C13 2MD A1001 " pdb=" S12 2MD A1001 " both_signs ideal model delta sigma weight residual False -3.09 -0.71 -2.38 2.00e-01 2.50e+01 1.42e+02 chirality pdb=" C13 2MD A1001 " pdb=" C12 2MD A1001 " pdb=" C14 2MD A1001 " pdb=" S13 2MD A1001 " both_signs ideal model delta sigma weight residual False -2.91 -0.95 -1.96 2.00e-01 2.50e+01 9.62e+01 chirality pdb=" C4' MGD A1002 " pdb=" C3' MGD A1002 " pdb=" C5' MGD A1002 " pdb=" O4' MGD A1002 " both_signs ideal model delta sigma weight residual False -2.53 -2.35 -0.19 2.00e-01 2.50e+01 8.78e-01 ... (remaining 3975 not shown) Planarity restraints: 4618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD C 601 " -0.086 2.00e-02 2.50e+03 7.72e-02 1.19e+02 pdb=" C2N NAD C 601 " 0.158 2.00e-02 2.50e+03 pdb=" C3N NAD C 601 " 0.013 2.00e-02 2.50e+03 pdb=" C4N NAD C 601 " -0.078 2.00e-02 2.50e+03 pdb=" C5N NAD C 601 " 0.069 2.00e-02 2.50e+03 pdb=" C6N NAD C 601 " -0.029 2.00e-02 2.50e+03 pdb=" C7N NAD C 601 " -0.058 2.00e-02 2.50e+03 pdb=" N1N NAD C 601 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD D 601 " 0.073 2.00e-02 2.50e+03 7.27e-02 1.06e+02 pdb=" C2N NAD D 601 " -0.146 2.00e-02 2.50e+03 pdb=" C3N NAD D 601 " -0.013 2.00e-02 2.50e+03 pdb=" C4N NAD D 601 " 0.071 2.00e-02 2.50e+03 pdb=" C5N NAD D 601 " -0.073 2.00e-02 2.50e+03 pdb=" C6N NAD D 601 " 0.040 2.00e-02 2.50e+03 pdb=" C7N NAD D 601 " 0.056 2.00e-02 2.50e+03 pdb=" N1N NAD D 601 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 278 " 0.052 5.00e-02 4.00e+02 7.90e-02 9.99e+00 pdb=" N PRO C 279 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO C 279 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 279 " 0.043 5.00e-02 4.00e+02 ... (remaining 4615 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 71 2.64 - 3.21: 22989 3.21 - 3.77: 43908 3.77 - 4.34: 64435 4.34 - 4.90: 101164 Nonbonded interactions: 232567 Sorted by model distance: nonbonded pdb=" SG CYS A 188 " pdb=" SG CYS A 192 " model vdw 2.076 3.760 nonbonded pdb=" C5' MGD B1002 " pdb=" O3B MGD B1002 " model vdw 2.527 2.752 nonbonded pdb=" O THR C 97 " pdb=" OG1 THR C 97 " model vdw 2.528 3.040 nonbonded pdb=" O THR D 97 " pdb=" OG1 THR D 97 " model vdw 2.528 3.040 nonbonded pdb=" O ARG A 187 " pdb=" CA CYS A 188 " model vdw 2.544 2.776 ... (remaining 232562 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 957 or resid 1002 through 1008)) selection = (chain 'B' and (resid 7 through 957 or resid 1002 through 1008)) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 25.450 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 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 : 0.006 0.525 26018 Z= 0.235 Angle : 1.103 62.322 35594 Z= 0.327 Chirality : 0.064 2.383 3978 Planarity : 0.005 0.079 4618 Dihedral : 17.374 139.330 9579 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.53 % Allowed : 22.67 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.15), residues: 3308 helix: 1.07 (0.14), residues: 1334 sheet: -0.76 (0.24), residues: 412 loop : -0.16 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 410 TYR 0.012 0.001 TYR B 834 PHE 0.013 0.001 PHE B 199 TRP 0.022 0.001 TRP A 780 HIS 0.003 0.001 HIS A 482 Details of bonding type rmsd covalent geometry : bond 0.00398 (25964) covalent geometry : angle 0.63589 (35462) hydrogen bonds : bond 0.14134 ( 1150) hydrogen bonds : angle 6.77684 ( 3141) metal coordination : bond 0.10281 ( 54) metal coordination : angle 14.80577 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 268 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.7521 (p0) cc_final: 0.7133 (p0) outliers start: 39 outliers final: 9 residues processed: 302 average time/residue: 0.7467 time to fit residues: 256.1099 Evaluate side-chains 218 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 209 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain B residue 252 ARG Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain D residue 334 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 GLN F 91 GLN F 129 ASN ** C 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 GLN ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 ASN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.067039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.051080 restraints weight = 50993.825| |-----------------------------------------------------------------------------| r_work (start): 0.2657 rms_B_bonded: 2.26 r_work: 0.2517 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2386 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 26018 Z= 0.296 Angle : 1.117 68.058 35594 Z= 0.325 Chirality : 0.046 0.261 3978 Planarity : 0.005 0.087 4618 Dihedral : 9.263 142.238 4036 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.12 % Allowed : 19.41 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.15), residues: 3308 helix: 1.31 (0.15), residues: 1348 sheet: -0.59 (0.25), residues: 376 loop : -0.20 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 890 TYR 0.015 0.001 TYR B 834 PHE 0.020 0.002 PHE B 333 TRP 0.011 0.001 TRP A 780 HIS 0.004 0.001 HIS E 107 Details of bonding type rmsd covalent geometry : bond 0.00675 (25964) covalent geometry : angle 0.62223 (35462) hydrogen bonds : bond 0.04309 ( 1150) hydrogen bonds : angle 5.41988 ( 3141) metal coordination : bond 0.03051 ( 54) metal coordination : angle 15.24915 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 213 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.9061 (p0) cc_final: 0.8520 (p0) REVERT: A 65 VAL cc_start: 0.9522 (OUTLIER) cc_final: 0.9297 (p) REVERT: A 456 GLU cc_start: 0.9338 (OUTLIER) cc_final: 0.9047 (mm-30) REVERT: A 712 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8804 (tt0) REVERT: A 827 THR cc_start: 0.9425 (m) cc_final: 0.9062 (p) REVERT: A 829 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7765 (mtt-85) REVERT: F 17 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8698 (mtp-110) REVERT: F 63 ASP cc_start: 0.8964 (m-30) cc_final: 0.8556 (m-30) REVERT: F 71 LYS cc_start: 0.9031 (ttpp) cc_final: 0.8756 (ttpp) REVERT: F 95 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8875 (mt-10) REVERT: F 104 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8373 (mt-10) REVERT: C 65 MET cc_start: 0.9128 (mmp) cc_final: 0.8920 (mmm) REVERT: C 89 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.8798 (pp20) REVERT: E 63 ASP cc_start: 0.8957 (m-30) cc_final: 0.8573 (m-30) REVERT: E 71 LYS cc_start: 0.9154 (ttpt) cc_final: 0.8816 (ttpp) REVERT: E 104 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8263 (mt-10) REVERT: E 108 ASP cc_start: 0.8714 (t0) cc_final: 0.8487 (t0) REVERT: B 65 VAL cc_start: 0.9536 (OUTLIER) cc_final: 0.9329 (p) REVERT: B 682 ASP cc_start: 0.9024 (OUTLIER) cc_final: 0.8824 (t70) REVERT: B 712 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8814 (tt0) REVERT: D 190 GLU cc_start: 0.8966 (tt0) cc_final: 0.8569 (mt-10) REVERT: D 264 MET cc_start: 0.9581 (ttp) cc_final: 0.9307 (ttp) outliers start: 105 outliers final: 20 residues processed: 300 average time/residue: 0.7190 time to fit residues: 247.8009 Evaluate side-chains 235 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 206 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 829 ARG Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 904 ASP Chi-restraints excluded: chain F residue 17 ARG Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 682 ASP Chi-restraints excluded: chain B residue 712 GLU Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 832 SER Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 307 optimal weight: 0.8980 chunk 319 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 0.2980 chunk 182 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 221 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 294 optimal weight: 7.9990 chunk 320 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 GLN F 129 ASN C 295 ASN ** C 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 ASN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 906 GLN D 295 ASN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.070096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.054418 restraints weight = 49242.783| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 2.25 r_work: 0.2579 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2447 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26018 Z= 0.122 Angle : 1.008 59.712 35594 Z= 0.274 Chirality : 0.041 0.228 3978 Planarity : 0.004 0.091 4618 Dihedral : 8.739 140.491 4019 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.90 % Allowed : 20.59 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.15), residues: 3308 helix: 1.56 (0.15), residues: 1344 sheet: -0.53 (0.25), residues: 396 loop : -0.04 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 8 TYR 0.012 0.001 TYR B 834 PHE 0.016 0.001 PHE C 419 TRP 0.008 0.001 TRP A 780 HIS 0.004 0.001 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00271 (25964) covalent geometry : angle 0.51962 (35462) hydrogen bonds : bond 0.03516 ( 1150) hydrogen bonds : angle 5.10589 ( 3141) metal coordination : bond 0.01590 ( 54) metal coordination : angle 14.20235 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 222 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.9005 (p0) cc_final: 0.8531 (p0) REVERT: A 65 VAL cc_start: 0.9502 (OUTLIER) cc_final: 0.9284 (p) REVERT: A 79 ARG cc_start: 0.8950 (mtp-110) cc_final: 0.8616 (ptm160) REVERT: A 827 THR cc_start: 0.9347 (m) cc_final: 0.9110 (p) REVERT: F 17 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8744 (mtp-110) REVERT: F 63 ASP cc_start: 0.8985 (m-30) cc_final: 0.8599 (m-30) REVERT: F 71 LYS cc_start: 0.9051 (ttpp) cc_final: 0.8757 (ttpp) REVERT: F 95 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8852 (mt-10) REVERT: F 104 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8378 (mt-10) REVERT: F 108 ASP cc_start: 0.8602 (t0) cc_final: 0.8378 (OUTLIER) REVERT: F 144 ILE cc_start: 0.9355 (mp) cc_final: 0.9125 (mp) REVERT: H 56 ASP cc_start: 0.8342 (t0) cc_final: 0.8131 (t0) REVERT: C 89 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8768 (pp20) REVERT: E 63 ASP cc_start: 0.8964 (m-30) cc_final: 0.8606 (m-30) REVERT: E 71 LYS cc_start: 0.9148 (ttpt) cc_final: 0.8755 (ttpp) REVERT: E 104 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8320 (mt-10) REVERT: E 108 ASP cc_start: 0.8739 (t0) cc_final: 0.8417 (OUTLIER) REVERT: E 144 ILE cc_start: 0.9356 (mp) cc_final: 0.9117 (mp) REVERT: B 807 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8641 (mtt180) REVERT: D 190 GLU cc_start: 0.8952 (tt0) cc_final: 0.8503 (mt-10) REVERT: D 264 MET cc_start: 0.9543 (ttp) cc_final: 0.9292 (ttp) outliers start: 74 outliers final: 22 residues processed: 278 average time/residue: 0.6952 time to fit residues: 222.3156 Evaluate side-chains 229 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 800 ARG Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain F residue 17 ARG Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain B residue 807 ARG Chi-restraints excluded: chain B residue 832 SER Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 934 SER Chi-restraints excluded: chain D residue 334 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 60 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 199 optimal weight: 0.0000 chunk 159 optimal weight: 2.9990 chunk 243 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 272 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 118 optimal weight: 0.0370 overall best weight: 1.3666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 GLN ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 ASN ** C 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 ASN ** C 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 ASN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN D 295 ASN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.069390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.053599 restraints weight = 50231.628| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 2.28 r_work: 0.2564 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2431 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26018 Z= 0.148 Angle : 1.016 61.132 35594 Z= 0.274 Chirality : 0.042 0.228 3978 Planarity : 0.004 0.092 4618 Dihedral : 8.713 141.324 4019 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.82 % Allowed : 21.06 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.15), residues: 3308 helix: 1.62 (0.15), residues: 1356 sheet: -0.44 (0.26), residues: 376 loop : -0.02 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 8 TYR 0.012 0.001 TYR B 834 PHE 0.016 0.001 PHE C 419 TRP 0.007 0.001 TRP A 940 HIS 0.006 0.001 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00336 (25964) covalent geometry : angle 0.52196 (35462) hydrogen bonds : bond 0.03487 ( 1150) hydrogen bonds : angle 4.96804 ( 3141) metal coordination : bond 0.01825 ( 54) metal coordination : angle 14.32028 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 212 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.9004 (p0) cc_final: 0.8576 (p0) REVERT: A 65 VAL cc_start: 0.9513 (OUTLIER) cc_final: 0.9302 (p) REVERT: A 754 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8921 (tpp) REVERT: A 827 THR cc_start: 0.9392 (m) cc_final: 0.9074 (p) REVERT: F 17 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8744 (mtp-110) REVERT: F 41 GLU cc_start: 0.8438 (mp0) cc_final: 0.8191 (mp0) REVERT: F 63 ASP cc_start: 0.8958 (m-30) cc_final: 0.8568 (m-30) REVERT: F 71 LYS cc_start: 0.9106 (ttpp) cc_final: 0.8795 (ttpp) REVERT: F 95 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8912 (mt-10) REVERT: F 104 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8413 (mt-10) REVERT: F 108 ASP cc_start: 0.8697 (t0) cc_final: 0.8418 (OUTLIER) REVERT: H 56 ASP cc_start: 0.8444 (t0) cc_final: 0.8215 (t0) REVERT: C 89 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8762 (pp20) REVERT: E 41 GLU cc_start: 0.8365 (mp0) cc_final: 0.7983 (mp0) REVERT: E 63 ASP cc_start: 0.8963 (m-30) cc_final: 0.8590 (m-30) REVERT: E 71 LYS cc_start: 0.9200 (ttpt) cc_final: 0.8841 (ttpp) REVERT: E 101 LYS cc_start: 0.8837 (mmtm) cc_final: 0.8531 (mmtm) REVERT: E 104 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8358 (mt-10) REVERT: E 108 ASP cc_start: 0.8751 (t0) cc_final: 0.8497 (t0) REVERT: B 754 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8933 (tpp) REVERT: B 807 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8683 (mtt180) REVERT: D 190 GLU cc_start: 0.8947 (tt0) cc_final: 0.8552 (mt-10) outliers start: 72 outliers final: 26 residues processed: 264 average time/residue: 0.7132 time to fit residues: 216.9633 Evaluate side-chains 235 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 800 ARG Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain F residue 17 ARG Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain B residue 807 ARG Chi-restraints excluded: chain B residue 832 SER Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain D residue 334 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 54 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 178 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 327 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 GLN F 129 ASN C 174 ASN C 295 ASN ** C 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 ASN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 906 GLN D 174 ASN D 295 ASN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.067548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.051695 restraints weight = 50655.941| |-----------------------------------------------------------------------------| r_work (start): 0.2666 rms_B_bonded: 2.27 r_work: 0.2525 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2394 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 26018 Z= 0.216 Angle : 1.073 58.430 35594 Z= 0.293 Chirality : 0.043 0.259 3978 Planarity : 0.005 0.095 4618 Dihedral : 8.858 145.513 4019 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.39 % Allowed : 21.41 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.15), residues: 3308 helix: 1.65 (0.15), residues: 1356 sheet: -0.37 (0.26), residues: 388 loop : 0.00 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 79 TYR 0.014 0.001 TYR B 834 PHE 0.019 0.001 PHE D 419 TRP 0.008 0.001 TRP A 940 HIS 0.003 0.001 HIS A 482 Details of bonding type rmsd covalent geometry : bond 0.00495 (25964) covalent geometry : angle 0.56184 (35462) hydrogen bonds : bond 0.03763 ( 1150) hydrogen bonds : angle 4.98801 ( 3141) metal coordination : bond 0.02354 ( 54) metal coordination : angle 15.01454 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 209 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.8995 (mtp-110) cc_final: 0.8786 (ttm110) REVERT: A 829 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7935 (mtt-85) REVERT: F 17 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8781 (mtp-110) REVERT: F 41 GLU cc_start: 0.8503 (mp0) cc_final: 0.8264 (mp0) REVERT: F 63 ASP cc_start: 0.8940 (m-30) cc_final: 0.8525 (m-30) REVERT: F 71 LYS cc_start: 0.9150 (ttpp) cc_final: 0.8910 (ttpp) REVERT: F 95 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8912 (mt-10) REVERT: F 104 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8386 (mt-10) REVERT: H 56 ASP cc_start: 0.8476 (t0) cc_final: 0.8210 (t0) REVERT: C 130 MET cc_start: 0.8905 (mtm) cc_final: 0.8654 (ptp) REVERT: E 41 GLU cc_start: 0.8586 (mp0) cc_final: 0.8338 (mp0) REVERT: E 63 ASP cc_start: 0.8957 (m-30) cc_final: 0.8572 (m-30) REVERT: E 71 LYS cc_start: 0.9222 (ttpt) cc_final: 0.8843 (ttpp) REVERT: E 95 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8701 (mt-10) REVERT: E 101 LYS cc_start: 0.8752 (mmtm) cc_final: 0.8455 (mmtm) REVERT: E 104 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8358 (mt-10) REVERT: E 108 ASP cc_start: 0.8724 (t0) cc_final: 0.8430 (t0) REVERT: B 807 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8729 (mtt180) REVERT: D 190 GLU cc_start: 0.8913 (tt0) cc_final: 0.8551 (mt-10) outliers start: 61 outliers final: 25 residues processed: 254 average time/residue: 0.6771 time to fit residues: 197.0651 Evaluate side-chains 228 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 829 ARG Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain F residue 17 ARG Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 807 ARG Chi-restraints excluded: chain B residue 832 SER Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 334 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 129 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 276 optimal weight: 10.0000 chunk 258 optimal weight: 1.9990 chunk 111 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 217 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 GLN F 129 ASN C 295 ASN ** C 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 ASN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN D 295 ASN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.068736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.052923 restraints weight = 50510.903| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 2.27 r_work: 0.2551 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2419 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26018 Z= 0.153 Angle : 1.048 56.405 35594 Z= 0.281 Chirality : 0.042 0.229 3978 Planarity : 0.004 0.093 4618 Dihedral : 8.746 144.203 4019 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.12 % Allowed : 21.73 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.15), residues: 3308 helix: 1.73 (0.15), residues: 1354 sheet: -0.39 (0.26), residues: 388 loop : 0.03 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 79 TYR 0.012 0.001 TYR B 834 PHE 0.016 0.001 PHE C 419 TRP 0.007 0.001 TRP A 940 HIS 0.003 0.001 HIS A 482 Details of bonding type rmsd covalent geometry : bond 0.00350 (25964) covalent geometry : angle 0.53417 (35462) hydrogen bonds : bond 0.03480 ( 1150) hydrogen bonds : angle 4.91373 ( 3141) metal coordination : bond 0.01827 ( 54) metal coordination : angle 14.81394 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 220 time to evaluate : 0.821 Fit side-chains REVERT: A 261 CYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8658 (p) REVERT: A 754 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8927 (tpp) REVERT: A 827 THR cc_start: 0.9332 (m) cc_final: 0.9066 (p) REVERT: F 17 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8768 (mtp-110) REVERT: F 41 GLU cc_start: 0.8509 (mp0) cc_final: 0.8240 (mp0) REVERT: F 63 ASP cc_start: 0.8965 (m-30) cc_final: 0.8572 (m-30) REVERT: F 95 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8896 (mt-10) REVERT: F 104 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8430 (mt-10) REVERT: F 144 ILE cc_start: 0.9388 (mt) cc_final: 0.9100 (mp) REVERT: H 56 ASP cc_start: 0.8476 (t0) cc_final: 0.8197 (t0) REVERT: C 56 GLU cc_start: 0.9115 (mp0) cc_final: 0.8895 (pm20) REVERT: C 264 MET cc_start: 0.9542 (ttp) cc_final: 0.9331 (ttp) REVERT: E 41 GLU cc_start: 0.8526 (mp0) cc_final: 0.8304 (mp0) REVERT: E 63 ASP cc_start: 0.8960 (m-30) cc_final: 0.8568 (m-30) REVERT: E 71 LYS cc_start: 0.9211 (ttpt) cc_final: 0.8800 (ttpp) REVERT: E 101 LYS cc_start: 0.8776 (mmtm) cc_final: 0.8456 (mmtm) REVERT: E 104 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8351 (mt-10) REVERT: E 108 ASP cc_start: 0.8724 (t0) cc_final: 0.8411 (t0) REVERT: B 79 ARG cc_start: 0.8956 (mtp-110) cc_final: 0.8744 (ttm110) REVERT: B 754 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8935 (tpp) REVERT: D 56 GLU cc_start: 0.9140 (mp0) cc_final: 0.8907 (pm20) REVERT: D 130 MET cc_start: 0.8885 (mtm) cc_final: 0.8679 (ptp) REVERT: D 190 GLU cc_start: 0.8904 (tt0) cc_final: 0.8319 (mt-10) outliers start: 54 outliers final: 26 residues processed: 259 average time/residue: 0.6712 time to fit residues: 199.1517 Evaluate side-chains 221 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain F residue 17 ARG Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 832 SER Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 334 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 272 optimal weight: 3.9990 chunk 204 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 254 optimal weight: 7.9990 chunk 221 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 chunk 219 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 GLN F 129 ASN C 174 ASN C 295 ASN ** C 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 ASN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 ASN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.067034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.051149 restraints weight = 50862.905| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 2.28 r_work: 0.2513 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2382 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 26018 Z= 0.245 Angle : 1.094 55.732 35594 Z= 0.303 Chirality : 0.044 0.252 3978 Planarity : 0.005 0.094 4618 Dihedral : 8.875 147.004 4019 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.04 % Allowed : 21.80 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.15), residues: 3308 helix: 1.70 (0.15), residues: 1354 sheet: -0.39 (0.26), residues: 388 loop : 0.03 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 79 TYR 0.015 0.001 TYR B 834 PHE 0.019 0.001 PHE D 419 TRP 0.007 0.001 TRP A 940 HIS 0.003 0.001 HIS F 72 Details of bonding type rmsd covalent geometry : bond 0.00563 (25964) covalent geometry : angle 0.58233 (35462) hydrogen bonds : bond 0.03778 ( 1150) hydrogen bonds : angle 4.97494 ( 3141) metal coordination : bond 0.02517 ( 54) metal coordination : angle 15.21728 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 191 time to evaluate : 0.972 Fit side-chains REVERT: A 79 ARG cc_start: 0.8988 (mtp-110) cc_final: 0.8783 (ttm110) REVERT: A 261 CYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8653 (p) REVERT: A 754 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.8948 (tpp) REVERT: A 827 THR cc_start: 0.9359 (m) cc_final: 0.9010 (p) REVERT: F 17 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8755 (mtp-110) REVERT: F 41 GLU cc_start: 0.8513 (mp0) cc_final: 0.8259 (mp0) REVERT: F 95 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8899 (mt-10) REVERT: F 104 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8393 (mt-10) REVERT: H 56 ASP cc_start: 0.8513 (t0) cc_final: 0.8225 (t0) REVERT: C 56 GLU cc_start: 0.9119 (mp0) cc_final: 0.8894 (pm20) REVERT: C 130 MET cc_start: 0.8941 (mtm) cc_final: 0.8694 (ptp) REVERT: C 264 MET cc_start: 0.9566 (ttp) cc_final: 0.9364 (ttp) REVERT: E 41 GLU cc_start: 0.8525 (mp0) cc_final: 0.8198 (mp0) REVERT: E 71 LYS cc_start: 0.9211 (ttpt) cc_final: 0.8930 (ttpp) REVERT: E 101 LYS cc_start: 0.8753 (mmtm) cc_final: 0.8398 (mmtm) REVERT: E 104 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8297 (mt-10) REVERT: B 754 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8945 (tpp) REVERT: D 56 GLU cc_start: 0.9132 (mp0) cc_final: 0.8917 (pm20) REVERT: D 130 MET cc_start: 0.8924 (mtm) cc_final: 0.8677 (ptp) REVERT: D 190 GLU cc_start: 0.8889 (tt0) cc_final: 0.8338 (mt-10) outliers start: 52 outliers final: 25 residues processed: 227 average time/residue: 0.7182 time to fit residues: 186.5592 Evaluate side-chains 215 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain F residue 17 ARG Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 832 SER Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 334 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 102 optimal weight: 3.9990 chunk 313 optimal weight: 6.9990 chunk 264 optimal weight: 0.2980 chunk 146 optimal weight: 0.1980 chunk 8 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 chunk 309 optimal weight: 0.6980 chunk 255 optimal weight: 0.9990 chunk 220 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 GLN F 129 ASN C 295 ASN C 329 GLN C 401 HIS E 129 ASN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN D 295 ASN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.070485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.054980 restraints weight = 49849.323| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 2.25 r_work: 0.2601 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 26018 Z= 0.108 Angle : 1.032 55.759 35594 Z= 0.274 Chirality : 0.041 0.198 3978 Planarity : 0.004 0.090 4618 Dihedral : 8.580 139.325 4019 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.80 % Allowed : 22.27 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.15), residues: 3308 helix: 1.71 (0.14), residues: 1368 sheet: -0.51 (0.25), residues: 412 loop : 0.18 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 775 TYR 0.012 0.001 TYR A 834 PHE 0.014 0.001 PHE C 419 TRP 0.008 0.001 TRP A 780 HIS 0.003 0.001 HIS F 72 Details of bonding type rmsd covalent geometry : bond 0.00242 (25964) covalent geometry : angle 0.51992 (35462) hydrogen bonds : bond 0.03177 ( 1150) hydrogen bonds : angle 4.79904 ( 3141) metal coordination : bond 0.01308 ( 54) metal coordination : angle 14.65072 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 211 time to evaluate : 1.048 Fit side-chains REVERT: A 79 ARG cc_start: 0.9025 (mtp-110) cc_final: 0.8818 (ttm110) REVERT: A 261 CYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8734 (p) REVERT: A 754 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8901 (tpp) REVERT: A 827 THR cc_start: 0.9313 (m) cc_final: 0.9099 (p) REVERT: G 6 LEU cc_start: 0.8153 (mt) cc_final: 0.7938 (tp) REVERT: F 17 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8767 (mtp-110) REVERT: F 41 GLU cc_start: 0.8513 (mp0) cc_final: 0.8288 (mp0) REVERT: F 95 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8899 (mt-10) REVERT: F 104 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8396 (mt-10) REVERT: H 56 ASP cc_start: 0.8510 (t0) cc_final: 0.8236 (t0) REVERT: C 56 GLU cc_start: 0.9078 (mp0) cc_final: 0.8846 (pm20) REVERT: E 41 GLU cc_start: 0.8508 (mp0) cc_final: 0.8286 (mp0) REVERT: E 71 LYS cc_start: 0.9181 (ttpt) cc_final: 0.8887 (ttpp) REVERT: E 95 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8389 (mm-30) REVERT: E 101 LYS cc_start: 0.8725 (mmtm) cc_final: 0.8398 (tppt) REVERT: E 104 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8359 (mt-10) REVERT: B 754 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8912 (tpp) REVERT: D 56 GLU cc_start: 0.9111 (mp0) cc_final: 0.8891 (pm20) REVERT: D 190 GLU cc_start: 0.8849 (tt0) cc_final: 0.8158 (mt-10) outliers start: 46 outliers final: 18 residues processed: 244 average time/residue: 0.7168 time to fit residues: 200.9097 Evaluate side-chains 220 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 198 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 800 ARG Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain F residue 17 ARG Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 334 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 112 optimal weight: 0.6980 chunk 170 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 224 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 217 optimal weight: 6.9990 chunk 225 optimal weight: 0.9980 chunk 128 optimal weight: 0.2980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 GLN F 91 GLN F 129 ASN C 295 ASN ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 ASN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN B 405 GLN D 295 ASN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.068827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.053079 restraints weight = 50955.592| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 2.29 r_work: 0.2558 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2427 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26018 Z= 0.164 Angle : 1.060 56.253 35594 Z= 0.290 Chirality : 0.042 0.215 3978 Planarity : 0.004 0.091 4618 Dihedral : 8.668 144.076 4019 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.61 % Allowed : 22.55 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.15), residues: 3308 helix: 1.80 (0.15), residues: 1356 sheet: -0.28 (0.26), residues: 392 loop : 0.12 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 775 TYR 0.012 0.001 TYR A 834 PHE 0.016 0.001 PHE D 419 TRP 0.007 0.001 TRP A 940 HIS 0.004 0.001 HIS F 72 Details of bonding type rmsd covalent geometry : bond 0.00379 (25964) covalent geometry : angle 0.55201 (35462) hydrogen bonds : bond 0.03421 ( 1150) hydrogen bonds : angle 4.83840 ( 3141) metal coordination : bond 0.01865 ( 54) metal coordination : angle 14.87278 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 196 time to evaluate : 1.055 Fit side-chains REVERT: A 79 ARG cc_start: 0.9028 (mtp-110) cc_final: 0.8663 (ptm160) REVERT: A 261 CYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8731 (p) REVERT: A 754 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8937 (tpp) REVERT: A 827 THR cc_start: 0.9362 (m) cc_final: 0.9023 (p) REVERT: A 867 ARG cc_start: 0.8811 (ttm-80) cc_final: 0.8557 (ttm-80) REVERT: G 4 GLU cc_start: 0.6843 (pm20) cc_final: 0.6634 (pm20) REVERT: F 41 GLU cc_start: 0.8528 (mp0) cc_final: 0.8283 (mp0) REVERT: F 95 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8911 (mt-10) REVERT: F 104 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8394 (mt-10) REVERT: H 56 ASP cc_start: 0.8535 (t0) cc_final: 0.8261 (t0) REVERT: C 56 GLU cc_start: 0.9088 (mp0) cc_final: 0.8862 (pm20) REVERT: E 41 GLU cc_start: 0.8499 (mp0) cc_final: 0.8249 (mp0) REVERT: E 71 LYS cc_start: 0.9183 (ttpt) cc_final: 0.8893 (ttpp) REVERT: E 95 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8373 (mm-30) REVERT: E 101 LYS cc_start: 0.8744 (mmtm) cc_final: 0.8384 (tppt) REVERT: E 104 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8397 (mt-10) REVERT: B 754 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8916 (tpp) REVERT: B 867 ARG cc_start: 0.8799 (ttm-80) cc_final: 0.8554 (ttm-80) REVERT: D 56 GLU cc_start: 0.9145 (mp0) cc_final: 0.8925 (pm20) REVERT: D 65 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8699 (mmm) REVERT: D 190 GLU cc_start: 0.8846 (tt0) cc_final: 0.8359 (mt-10) outliers start: 41 outliers final: 21 residues processed: 224 average time/residue: 0.7765 time to fit residues: 198.6875 Evaluate side-chains 216 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain D residue 65 MET Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 334 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 180 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 217 optimal weight: 6.9990 chunk 262 optimal weight: 0.0040 chunk 176 optimal weight: 5.9990 chunk 161 optimal weight: 0.9980 chunk 303 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 253 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 GLN F 129 ASN C 295 ASN ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 ASN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 GLN D 295 ASN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.068034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.052222 restraints weight = 51005.727| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 2.29 r_work: 0.2540 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2410 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 26018 Z= 0.204 Angle : 1.080 56.720 35594 Z= 0.300 Chirality : 0.043 0.244 3978 Planarity : 0.005 0.090 4618 Dihedral : 8.754 146.223 4019 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.25 % Allowed : 23.02 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.15), residues: 3308 helix: 1.77 (0.14), residues: 1358 sheet: -0.26 (0.26), residues: 392 loop : 0.10 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 775 TYR 0.014 0.001 TYR B 834 PHE 0.018 0.001 PHE D 419 TRP 0.007 0.001 TRP A 940 HIS 0.004 0.001 HIS F 72 Details of bonding type rmsd covalent geometry : bond 0.00473 (25964) covalent geometry : angle 0.57311 (35462) hydrogen bonds : bond 0.03591 ( 1150) hydrogen bonds : angle 4.88444 ( 3141) metal coordination : bond 0.02165 ( 54) metal coordination : angle 15.04461 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.981 Fit side-chains REVERT: A 79 ARG cc_start: 0.9024 (mtp-110) cc_final: 0.8665 (ptm160) REVERT: A 261 CYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8673 (p) REVERT: A 754 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8925 (tpp) REVERT: A 867 ARG cc_start: 0.8788 (ttm-80) cc_final: 0.8532 (ttm-80) REVERT: G 4 GLU cc_start: 0.6839 (pm20) cc_final: 0.6530 (pm20) REVERT: F 41 GLU cc_start: 0.8522 (mp0) cc_final: 0.8269 (mp0) REVERT: F 95 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8912 (mt-10) REVERT: F 104 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8344 (mt-10) REVERT: H 56 ASP cc_start: 0.8560 (t0) cc_final: 0.8282 (t0) REVERT: C 56 GLU cc_start: 0.9099 (mp0) cc_final: 0.8869 (pm20) REVERT: C 264 MET cc_start: 0.9582 (ttp) cc_final: 0.9199 (ttm) REVERT: E 41 GLU cc_start: 0.8483 (mp0) cc_final: 0.8229 (mp0) REVERT: E 71 LYS cc_start: 0.9193 (ttpt) cc_final: 0.8908 (ttpp) REVERT: E 95 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8373 (mm-30) REVERT: E 101 LYS cc_start: 0.8721 (mmtm) cc_final: 0.8369 (tppt) REVERT: E 104 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8381 (mt-10) REVERT: B 754 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8929 (tpp) REVERT: B 867 ARG cc_start: 0.8799 (ttm-80) cc_final: 0.8555 (ttm-80) REVERT: D 56 GLU cc_start: 0.9140 (mp0) cc_final: 0.8912 (pm20) REVERT: D 65 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.8808 (mmm) REVERT: D 190 GLU cc_start: 0.8870 (tt0) cc_final: 0.8205 (mt-10) outliers start: 32 outliers final: 20 residues processed: 215 average time/residue: 0.7658 time to fit residues: 188.5491 Evaluate side-chains 211 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain D residue 65 MET Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 334 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 179 optimal weight: 8.9990 chunk 321 optimal weight: 0.0570 chunk 8 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 GLN F 129 ASN C 295 ASN ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 ASN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 ASN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.067398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.051580 restraints weight = 51055.412| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 2.28 r_work: 0.2523 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2393 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 26018 Z= 0.233 Angle : 1.097 57.590 35594 Z= 0.308 Chirality : 0.044 0.242 3978 Planarity : 0.005 0.091 4618 Dihedral : 8.837 148.333 4019 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.18 % Allowed : 23.18 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.15), residues: 3308 helix: 1.76 (0.14), residues: 1354 sheet: -0.28 (0.26), residues: 388 loop : 0.08 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 775 TYR 0.014 0.001 TYR B 834 PHE 0.018 0.001 PHE D 419 TRP 0.008 0.001 TRP G 36 HIS 0.004 0.001 HIS F 72 Details of bonding type rmsd covalent geometry : bond 0.00537 (25964) covalent geometry : angle 0.58972 (35462) hydrogen bonds : bond 0.03738 ( 1150) hydrogen bonds : angle 4.93408 ( 3141) metal coordination : bond 0.02392 ( 54) metal coordination : angle 15.20477 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9672.00 seconds wall clock time: 165 minutes 41.85 seconds (9941.85 seconds total)