Starting phenix.real_space_refine on Mon Jul 6 20:31:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9taj_55748/07_2026/9taj_55748.cif Found real_map, /net/cci-nas-00/data/ceres_data/9taj_55748/07_2026/9taj_55748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9taj_55748/07_2026/9taj_55748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9taj_55748/07_2026/9taj_55748.map" model { file = "/net/cci-nas-00/data/ceres_data/9taj_55748/07_2026/9taj_55748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9taj_55748/07_2026/9taj_55748.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 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 Ca 5 9.91 5 Fe 32 7.16 5 P 19 5.49 5 S 264 5.16 5 C 24665 2.51 5 N 6155 2.21 5 O 7046 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 38186 Number of models: 1 Model: "" Number of chains: 37 Chain: "E" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 146} Chain: "F" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3407 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 413} Chain: "G" Number of atoms: 7027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7027 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 41, 'TRANS': 863} Chain: "I" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1149 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 12, 'TRANS': 132} Chain: "B" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1551 Classifications: {'peptide': 195} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 182} Chain breaks: 3 Chain: "C" Number of atoms: 4760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4760 Classifications: {'peptide': 589} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 551} Chain: "H" Number of atoms: 2404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2404 Classifications: {'peptide': 307} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 292} Chain breaks: 1 Chain: "J" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1226 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "M" Number of atoms: 3964 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 482} Conformer: "B" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 482} bond proxies already assigned to first conformer: 4060 Chain: "A" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 788 Classifications: {'peptide': 98} Link IDs: {'TRANS': 97} Chain breaks: 1 Chain: "L" Number of atoms: 4685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4685 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 18, 'TRANS': 594} Chain: "N" Number of atoms: 3673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3673 Classifications: {'peptide': 485} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 463} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 4 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 28 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'FES': 1, 'SF4': 3} Classifications: {'undetermined': 4} Link IDs: {None: 2} Chain breaks: 3 Chain: "I" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 122 Unusual residues: {'3PE': 2, 'LFA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 140 Unusual residues: {'3PE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 359 Unusual residues: {'3PE': 5, 'CDL': 1, 'TRD': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "N" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 232 Unusual residues: {'3PE': 2, 'LFA': 1, 'TRD': 1, 'UQ8': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "G" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 138 Classifications: {'water': 138} Link IDs: {None: 137} Chain: "I" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "J" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "K" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "M" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "L" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "N" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 647 SG CYS E 92 84.194 66.936 257.370 1.00 48.52 S ATOM 681 SG CYS E 97 85.617 64.605 259.635 1.00 57.56 S ATOM 959 SG CYS E 133 88.014 70.583 257.079 1.00 72.84 S ATOM 985 SG CYS E 137 90.163 68.450 258.324 1.00 59.04 S ATOM 3917 SG CYS F 351 82.779 79.837 240.311 1.00 37.71 S ATOM 3941 SG CYS F 354 85.919 77.162 235.008 1.00 42.62 S ATOM 3961 SG CYS F 357 85.418 73.845 238.828 1.00 47.21 S ATOM 4282 SG CYS F 398 88.880 79.152 240.579 1.00 37.53 S ATOM 6717 SG CYS G 265 60.602 99.480 221.334 1.00 37.65 S ATOM 6432 SG CYS G 230 59.541 99.536 215.061 1.00 49.26 S ATOM 6480 SG CYS G 237 65.286 101.311 216.837 1.00 42.09 S ATOM 6456 SG CYS G 233 60.240 104.959 218.342 1.00 49.10 S ATOM 5811 SG CYS G 153 71.763 78.375 230.999 1.00 49.49 S ATOM 6207 SG CYS G 203 69.550 81.693 225.570 1.00 35.27 S ATOM 5830 SG CYS G 156 75.421 82.206 227.231 1.00 38.54 S ATOM 5859 SG CYS G 159 70.950 84.599 231.095 1.00 35.75 S ATOM 4877 SG CYS G 36 82.630 83.914 227.693 1.00 39.30 S ATOM 4953 SG CYS G 47 82.648 80.617 226.038 1.00 29.41 S ATOM 4979 SG CYS G 50 87.330 82.888 223.762 1.00 41.93 S ATOM 5128 SG CYS G 69 86.918 85.799 226.101 1.00 54.90 S ATOM 5436 SG CYS G 108 65.517 74.981 221.040 1.00 50.82 S ATOM 5416 SG CYS G 105 69.153 70.096 218.420 1.00 36.39 S ATOM 5476 SG CYS G 114 71.251 76.302 219.364 1.00 38.90 S ATOM 11926 SG CYS I 70 60.720 66.764 198.592 1.00 43.28 S ATOM 11950 SG CYS I 74 58.796 66.128 197.717 1.00 66.40 S ATOM 12193 SG CYS I 102 64.022 61.929 197.454 1.00 44.05 S ATOM 12168 SG CYS I 99 57.613 61.299 196.451 1.00 38.91 S ATOM 12211 SG CYS I 105 60.137 61.517 202.329 1.00 48.13 S ATOM 11903 SG CYS I 66 58.799 66.466 206.765 1.00 43.36 S ATOM 11881 SG CYS I 63 61.452 67.522 212.392 1.00 33.11 S ATOM 12240 SG CYS I 109 60.539 61.804 210.925 1.00 44.02 S ATOM 11863 SG CYS I 60 55.123 65.709 211.732 1.00 35.64 S ATOM 13849 SG CYS B 158 62.047 60.225 189.222 1.00 44.57 S ATOM 13632 SG CYS B 129 61.419 63.923 185.086 1.00 43.03 S ATOM 13189 SG CYS B 64 59.117 57.802 184.105 1.00 57.89 S ATOM 13183 SG CYS B 63 65.465 58.824 183.817 1.00 61.19 S Time building chain proxies: 8.25, per 1000 atoms: 0.22 Number of scatterers: 38186 At special positions: 0 Unit cell: (129.525, 149.325, 287.925, 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) Fe 32 26.01 Ca 5 19.99 S 264 16.00 P 19 15.00 O 7046 8.00 N 6155 7.00 C 24665 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: 3.52 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb=" FES G1003 " pdb="FE2 FES G1003 " - pdb=" SG CYS G 50 " pdb="FE1 FES G1003 " - pdb=" SG CYS G 47 " pdb="FE2 FES G1003 " - pdb=" SG CYS G 69 " pdb="FE1 FES G1003 " - pdb=" SG CYS G 36 " pdb=" SF4 B 301 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 64 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 63 " pdb=" SF4 F 502 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 354 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 351 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 398 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 357 " pdb=" SF4 G1001 " pdb="FE4 SF4 G1001 " - pdb=" SG CYS G 233 " pdb="FE1 SF4 G1001 " - pdb=" SG CYS G 265 " pdb="FE3 SF4 G1001 " - pdb=" SG CYS G 237 " pdb="FE2 SF4 G1001 " - pdb=" SG CYS G 230 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 156 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 159 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 153 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 203 " pdb=" SF4 G1007 " pdb="FE1 SF4 G1007 " - pdb=" NE2 HIS G 101 " pdb="FE2 SF4 G1007 " - pdb=" SG CYS G 108 " pdb="FE3 SF4 G1007 " - pdb=" SG CYS G 105 " pdb="FE4 SF4 G1007 " - pdb=" SG CYS G 114 " pdb=" SF4 I 202 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 99 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 70 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 102 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 105 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 74 " pdb=" SF4 I 203 " pdb="FE2 SF4 I 203 " - pdb=" SG CYS I 63 " pdb="FE4 SF4 I 203 " - pdb=" SG CYS I 60 " pdb="FE3 SF4 I 203 " - pdb=" SG CYS I 109 " pdb="FE1 SF4 I 203 " - pdb=" SG CYS I 66 " Number of angles added : 96 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8590 Finding SS restraints... Secondary structure from input PDB file: 221 helices and 28 sheets defined 61.3% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'E' and resid 15 through 26 Processing helix chain 'E' and resid 27 through 29 No H-bonds generated for 'chain 'E' and resid 27 through 29' Processing helix chain 'E' and resid 31 through 34 Processing helix chain 'E' and resid 35 through 48 Processing helix chain 'E' and resid 51 through 53 No H-bonds generated for 'chain 'E' and resid 51 through 53' Processing helix chain 'E' and resid 54 through 63 removed outlier: 4.869A pdb=" N ASP E 60 " --> pdb=" O HIS E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 76 removed outlier: 3.554A pdb=" N VAL E 69 " --> pdb=" O PRO E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 101 Processing helix chain 'E' and resid 101 through 113 removed outlier: 4.046A pdb=" N ILE E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 140 Processing helix chain 'E' and resid 154 through 156 No H-bonds generated for 'chain 'E' and resid 154 through 156' Processing helix chain 'E' and resid 157 through 162 Processing helix chain 'E' and resid 163 through 165 No H-bonds generated for 'chain 'E' and resid 163 through 165' Processing helix chain 'F' and resid 25 through 32 Processing helix chain 'F' and resid 35 through 43 Processing helix chain 'F' and resid 46 through 58 Processing helix chain 'F' and resid 68 through 75 removed outlier: 3.718A pdb=" N LEU F 75 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 108 removed outlier: 3.982A pdb=" N LEU F 103 " --> pdb=" O TYR F 99 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU F 104 " --> pdb=" O LYS F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 124 removed outlier: 3.787A pdb=" N LEU F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 153 Processing helix chain 'F' and resid 177 through 181 Processing helix chain 'F' and resid 182 through 191 removed outlier: 3.714A pdb=" N ILE F 187 " --> pdb=" O GLU F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 212 Processing helix chain 'F' and resid 219 through 232 removed outlier: 3.882A pdb=" N VAL F 225 " --> pdb=" O THR F 221 " (cutoff:3.500A) Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 232 through 238 removed outlier: 3.601A pdb=" N TYR F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 277 removed outlier: 3.636A pdb=" N TYR F 277 " --> pdb=" O ILE F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 305 Processing helix chain 'F' and resid 310 through 317 Processing helix chain 'F' and resid 334 through 349 Processing helix chain 'F' and resid 354 through 373 removed outlier: 3.601A pdb=" N LEU F 361 " --> pdb=" O CYS F 357 " (cutoff:3.500A) Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 379 through 391 removed outlier: 3.559A pdb=" N ARG F 389 " --> pdb=" O GLU F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 405 Processing helix chain 'F' and resid 405 through 415 Processing helix chain 'F' and resid 415 through 421 removed outlier: 3.613A pdb=" N PHE F 419 " --> pdb=" O PHE F 415 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 28 Processing helix chain 'G' and resid 83 through 99 Processing helix chain 'G' and resid 104 through 108 Processing helix chain 'G' and resid 114 through 124 Processing helix chain 'G' and resid 150 through 153 Processing helix chain 'G' and resid 157 through 164 Processing helix chain 'G' and resid 177 through 181 removed outlier: 3.898A pdb=" N VAL G 181 " --> pdb=" O HIS G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 198 through 203 Processing helix chain 'G' and resid 211 through 216 removed outlier: 3.624A pdb=" N GLU G 215 " --> pdb=" O LYS G 211 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ARG G 216 " --> pdb=" O THR G 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 211 through 216' Processing helix chain 'G' and resid 219 through 223 Processing helix chain 'G' and resid 265 through 271 Processing helix chain 'G' and resid 272 through 277 Processing helix chain 'G' and resid 296 through 309 Processing helix chain 'G' and resid 323 through 335 Processing helix chain 'G' and resid 344 through 361 Processing helix chain 'G' and resid 368 through 374 Processing helix chain 'G' and resid 383 through 388 Processing helix chain 'G' and resid 388 through 400 removed outlier: 3.555A pdb=" N ALA G 392 " --> pdb=" O GLY G 388 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN G 397 " --> pdb=" O LEU G 393 " (cutoff:3.500A) Processing helix chain 'G' and resid 400 through 410 removed outlier: 3.596A pdb=" N ARG G 404 " --> pdb=" O LYS G 400 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 425 Processing helix chain 'G' and resid 452 through 468 Processing helix chain 'G' and resid 478 through 494 removed outlier: 3.590A pdb=" N LYS G 484 " --> pdb=" O GLU G 480 " (cutoff:3.500A) Processing helix chain 'G' and resid 508 through 525 removed outlier: 3.987A pdb=" N ILE G 512 " --> pdb=" O SER G 508 " (cutoff:3.500A) Processing helix chain 'G' and resid 539 through 547 Processing helix chain 'G' and resid 550 through 560 Processing helix chain 'G' and resid 578 through 587 Processing helix chain 'G' and resid 614 through 618 removed outlier: 3.727A pdb=" N SER G 618 " --> pdb=" O PHE G 615 " (cutoff:3.500A) Processing helix chain 'G' and resid 649 through 664 Processing helix chain 'G' and resid 670 through 682 Processing helix chain 'G' and resid 683 through 691 removed outlier: 4.942A pdb=" N GLY G 687 " --> pdb=" O GLU G 684 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS G 689 " --> pdb=" O ALA G 686 " (cutoff:3.500A) Processing helix chain 'G' and resid 763 through 771 removed outlier: 3.877A pdb=" N GLN G 771 " --> pdb=" O ASN G 768 " (cutoff:3.500A) Processing helix chain 'G' and resid 826 through 831 Proline residue: G 831 - end of helix Processing helix chain 'G' and resid 832 through 837 removed outlier: 4.174A pdb=" N ARG G 836 " --> pdb=" O VAL G 832 " (cutoff:3.500A) Processing helix chain 'G' and resid 845 through 853 Processing helix chain 'G' and resid 894 through 898 Processing helix chain 'I' and resid 64 through 70 Processing helix chain 'I' and resid 103 through 108 Processing helix chain 'I' and resid 126 through 129 Processing helix chain 'I' and resid 133 through 137 Processing helix chain 'I' and resid 149 through 153 Processing helix chain 'B' and resid 37 through 52 removed outlier: 4.459A pdb=" N LEU B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ASN B 43 " --> pdb=" O MET B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 70 removed outlier: 3.837A pdb=" N VAL B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET B 68 " --> pdb=" O CYS B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 106 through 117 removed outlier: 3.666A pdb=" N MET B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 133 Processing helix chain 'B' and resid 144 through 148 removed outlier: 3.532A pdb=" N PHE B 148 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 178 removed outlier: 3.734A pdb=" N TYR B 165 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET B 170 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 204 through 210 removed outlier: 3.590A pdb=" N ALA B 210 " --> pdb=" O GLY B 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 34 removed outlier: 3.607A pdb=" N GLY C 27 " --> pdb=" O ASP C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 66 Processing helix chain 'C' and resid 133 through 146 removed outlier: 3.705A pdb=" N TYR C 137 " --> pdb=" O ASN C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 195 removed outlier: 3.788A pdb=" N LEU C 185 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET C 194 " --> pdb=" O GLN C 190 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU C 195 " --> pdb=" O ASP C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 205 Processing helix chain 'C' and resid 211 through 215 removed outlier: 3.532A pdb=" N ASP C 214 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 228 removed outlier: 3.579A pdb=" N HIS C 228 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 261 removed outlier: 3.921A pdb=" N GLU C 261 " --> pdb=" O GLU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 274 removed outlier: 3.503A pdb=" N THR C 272 " --> pdb=" O TYR C 268 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP C 273 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG C 274 " --> pdb=" O PRO C 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 268 through 274' Processing helix chain 'C' and resid 280 through 296 removed outlier: 4.009A pdb=" N GLU C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 300 through 331 removed outlier: 3.540A pdb=" N ASP C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 354 Processing helix chain 'C' and resid 375 through 385 Processing helix chain 'C' and resid 386 through 401 removed outlier: 3.858A pdb=" N ARG C 390 " --> pdb=" O TRP C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 408 Processing helix chain 'C' and resid 415 through 422 Processing helix chain 'C' and resid 426 through 431 Processing helix chain 'C' and resid 437 through 442 Processing helix chain 'C' and resid 446 through 450 removed outlier: 3.667A pdb=" N ASN C 449 " --> pdb=" O GLY C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 487 removed outlier: 4.330A pdb=" N LYS C 470 " --> pdb=" O ARG C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 509 Processing helix chain 'C' and resid 511 through 524 Processing helix chain 'C' and resid 563 through 572 removed outlier: 4.037A pdb=" N ALA C 567 " --> pdb=" O THR C 563 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN C 570 " --> pdb=" O PHE C 566 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE C 572 " --> pdb=" O HIS C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 577 removed outlier: 3.566A pdb=" N ARG C 577 " --> pdb=" O PRO C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 592 removed outlier: 4.251A pdb=" N ASP C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 600 Processing helix chain 'H' and resid 7 through 39 removed outlier: 3.694A pdb=" N LEU H 13 " --> pdb=" O ILE H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 69 removed outlier: 3.737A pdb=" N LEU H 60 " --> pdb=" O GLY H 56 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL H 61 " --> pdb=" O SER H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 93 Proline residue: H 87 - end of helix Processing helix chain 'H' and resid 95 through 101 removed outlier: 3.751A pdb=" N ILE H 100 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 125 removed outlier: 3.875A pdb=" N PHE H 119 " --> pdb=" O GLY H 115 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU H 120 " --> pdb=" O ILE H 116 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU H 125 " --> pdb=" O MET H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 137 removed outlier: 3.935A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER H 137 " --> pdb=" O ALA H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 158 Processing helix chain 'H' and resid 159 through 164 removed outlier: 3.917A pdb=" N LEU H 164 " --> pdb=" O LEU H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 172 Processing helix chain 'H' and resid 175 through 182 Processing helix chain 'H' and resid 192 through 207 Processing helix chain 'H' and resid 230 through 257 removed outlier: 3.517A pdb=" N PHE H 234 " --> pdb=" O SER H 230 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY H 235 " --> pdb=" O GLY H 231 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 285 Processing helix chain 'H' and resid 286 through 288 No H-bonds generated for 'chain 'H' and resid 286 through 288' Processing helix chain 'H' and resid 293 through 304 removed outlier: 3.654A pdb=" N GLY H 301 " --> pdb=" O VAL H 297 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TRP H 302 " --> pdb=" O MET H 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 305 through 325 removed outlier: 3.582A pdb=" N GLN H 325 " --> pdb=" O LEU H 321 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 21 removed outlier: 3.542A pdb=" N TYR J 6 " --> pdb=" O GLU J 2 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS J 8 " --> pdb=" O ALA J 4 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR J 21 " --> pdb=" O LEU J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 47 Processing helix chain 'J' and resid 48 through 59 removed outlier: 3.595A pdb=" N ILE J 56 " --> pdb=" O GLY J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 75 Processing helix chain 'J' and resid 79 through 84 Processing helix chain 'J' and resid 85 through 89 Processing helix chain 'J' and resid 93 through 113 removed outlier: 3.734A pdb=" N GLY J 113 " --> pdb=" O TYR J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 134 Processing helix chain 'J' and resid 137 through 158 removed outlier: 3.520A pdb=" N SER J 145 " --> pdb=" O VAL J 141 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET J 146 " --> pdb=" O GLU J 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 25 removed outlier: 3.597A pdb=" N ARG K 25 " --> pdb=" O GLY K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 54 Processing helix chain 'K' and resid 56 through 88 Processing helix chain 'K' and resid 91 through 96 removed outlier: 3.905A pdb=" N SER K 96 " --> pdb=" O ASP K 93 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 20 Proline residue: M 10 - end of helix Processing helix chain 'M' and resid 21 through 24 Processing helix chain 'M' and resid 27 through 50 Processing helix chain 'M' and resid 84 through 105 removed outlier: 3.614A pdb=" N LEU M 89 " --> pdb=" O GLY M 85 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET M 90 " --> pdb=" O LEU M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 133 removed outlier: 3.551A pdb=" N PHE M 116 " --> pdb=" O TYR M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 144 Processing helix chain 'M' and resid 146 through 157 Processing helix chain 'M' and resid 168 through 201 removed outlier: 3.718A pdb=" N SER M 181 " --> pdb=" O TYR M 177 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY M 182 " --> pdb=" O THR M 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 235 removed outlier: 3.727A pdb=" N ALA M 230 " --> pdb=" O GLY M 226 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS M 234 " --> pdb=" O ALA M 230 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 251 removed outlier: 3.939A pdb=" N ASP M 246 " --> pdb=" O GLY M 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 255 through 260 Processing helix chain 'M' and resid 265 through 275 removed outlier: 3.858A pdb=" N TYR M 269 " --> pdb=" O LYS M 265 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 286 Processing helix chain 'M' and resid 286 through 308 Processing helix chain 'M' and resid 310 through 331 removed outlier: 3.665A pdb=" N SER M 319 " --> pdb=" O ILE M 315 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL M 320 " --> pdb=" O ALA M 316 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE M 325 " --> pdb=" O SER M 321 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL M 326 " --> pdb=" O HIS M 322 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR M 331 " --> pdb=" O LEU M 327 " (cutoff:3.500A) Processing helix chain 'M' and resid 334 through 367 Processing helix chain 'M' and resid 370 through 374 Processing helix chain 'M' and resid 376 through 380 Processing helix chain 'M' and resid 383 through 396 Processing helix chain 'M' and resid 402 through 416 removed outlier: 4.146A pdb=" N GLN M 416 " --> pdb=" O PHE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 418 through 427 removed outlier: 3.771A pdb=" N PHE M 427 " --> pdb=" O VAL M 423 " (cutoff:3.500A) Processing helix chain 'M' and resid 427 through 445 removed outlier: 3.777A pdb=" N PHE M 431 " --> pdb=" O PHE M 427 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE M 445 " --> pdb=" O HIS M 441 " (cutoff:3.500A) Processing helix chain 'M' and resid 450 through 455 removed outlier: 3.560A pdb=" N SER M 454 " --> pdb=" O GLN M 451 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN M 455 " --> pdb=" O ILE M 452 " (cutoff:3.500A) Processing helix chain 'M' and resid 461 through 481 Processing helix chain 'M' and resid 482 through 489 Processing helix chain 'M' and resid 489 through 502 Processing helix chain 'A' and resid 8 through 36 removed outlier: 3.684A pdb=" N CYS A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY A 34 " --> pdb=" O MET A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 90 removed outlier: 3.515A pdb=" N VAL A 71 " --> pdb=" O LYS A 67 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 72 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 120 removed outlier: 6.148A pdb=" N TRP A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N VAL A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 22 Proline residue: L 11 - end of helix removed outlier: 3.910A pdb=" N ARG L 22 " --> pdb=" O LEU L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 56 removed outlier: 3.822A pdb=" N VAL L 38 " --> pdb=" O GLY L 34 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY L 56 " --> pdb=" O PHE L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 107 removed outlier: 3.997A pdb=" N TRP L 105 " --> pdb=" O MET L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 132 Processing helix chain 'L' and resid 135 through 155 removed outlier: 3.570A pdb=" N GLY L 142 " --> pdb=" O LEU L 138 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY L 155 " --> pdb=" O TYR L 151 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 193 removed outlier: 3.573A pdb=" N GLY L 164 " --> pdb=" O ASP L 160 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY L 177 " --> pdb=" O VAL L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 208 Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 212 through 230 removed outlier: 3.508A pdb=" N MET L 216 " --> pdb=" O ASN L 212 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY L 228 " --> pdb=" O GLY L 224 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS L 229 " --> pdb=" O GLY L 225 " (cutoff:3.500A) Processing helix chain 'L' and resid 240 through 245 removed outlier: 4.098A pdb=" N MET L 243 " --> pdb=" O ALA L 240 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA L 244 " --> pdb=" O ASP L 241 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY L 245 " --> pdb=" O ALA L 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 240 through 245' Processing helix chain 'L' and resid 246 through 256 Processing helix chain 'L' and resid 258 through 269 removed outlier: 4.239A pdb=" N GLY L 262 " --> pdb=" O MET L 258 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL L 263 " --> pdb=" O VAL L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 269 through 275 removed outlier: 3.715A pdb=" N MET L 275 " --> pdb=" O GLY L 271 " (cutoff:3.500A) Processing helix chain 'L' and resid 276 through 299 Processing helix chain 'L' and resid 303 through 325 Processing helix chain 'L' and resid 327 through 353 removed outlier: 3.866A pdb=" N ALA L 343 " --> pdb=" O ALA L 339 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER L 351 " --> pdb=" O LEU L 347 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL L 352 " --> pdb=" O ALA L 348 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE L 353 " --> pdb=" O SER L 349 " (cutoff:3.500A) Processing helix chain 'L' and resid 354 through 360 removed outlier: 6.445A pdb=" N HIS L 357 " --> pdb=" O LEU L 354 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN L 360 " --> pdb=" O HIS L 357 " (cutoff:3.500A) Processing helix chain 'L' and resid 367 through 372 removed outlier: 4.024A pdb=" N SER L 371 " --> pdb=" O GLY L 367 " (cutoff:3.500A) Processing helix chain 'L' and resid 374 through 387 removed outlier: 3.898A pdb=" N CYS L 378 " --> pdb=" O LEU L 374 " (cutoff:3.500A) Processing helix chain 'L' and resid 393 through 409 removed outlier: 4.038A pdb=" N PHE L 397 " --> pdb=" O THR L 393 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE L 402 " --> pdb=" O SER L 398 " (cutoff:3.500A) Processing helix chain 'L' and resid 411 through 437 removed outlier: 3.531A pdb=" N MET L 432 " --> pdb=" O TYR L 428 " (cutoff:3.500A) Processing helix chain 'L' and resid 454 through 465 removed outlier: 3.521A pdb=" N THR L 465 " --> pdb=" O LEU L 461 " (cutoff:3.500A) Processing helix chain 'L' and resid 466 through 471 removed outlier: 3.646A pdb=" N ILE L 471 " --> pdb=" O GLY L 468 " (cutoff:3.500A) Processing helix chain 'L' and resid 489 through 496 Processing helix chain 'L' and resid 497 through 512 Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 525 through 537 removed outlier: 3.643A pdb=" N ASN L 537 " --> pdb=" O THR L 533 " (cutoff:3.500A) Processing helix chain 'L' and resid 540 through 549 Processing helix chain 'L' and resid 549 through 560 Processing helix chain 'L' and resid 563 through 570 Processing helix chain 'L' and resid 570 through 584 Processing helix chain 'L' and resid 590 through 613 Processing helix chain 'N' and resid 6 through 11 removed outlier: 4.022A pdb=" N ALA N 10 " --> pdb=" O GLN N 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 11 through 31 Processing helix chain 'N' and resid 33 through 51 Processing helix chain 'N' and resid 51 through 59 Processing helix chain 'N' and resid 70 through 97 removed outlier: 3.518A pdb=" N LEU N 75 " --> pdb=" O GLY N 71 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR N 76 " --> pdb=" O PHE N 72 " (cutoff:3.500A) Proline residue: N 93 - end of helix removed outlier: 4.363A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 121 removed outlier: 3.736A pdb=" N LEU N 107 " --> pdb=" O ASP N 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 144 Proline residue: N 138 - end of helix removed outlier: 3.822A pdb=" N GLY N 141 " --> pdb=" O LEU N 137 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY N 144 " --> pdb=" O PHE N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 182 Processing helix chain 'N' and resid 185 through 189 Processing helix chain 'N' and resid 200 through 218 removed outlier: 3.572A pdb=" N PHE N 216 " --> pdb=" O VAL N 212 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS N 217 " --> pdb=" O GLY N 213 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 234 Processing helix chain 'N' and resid 235 through 261 removed outlier: 4.151A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 Processing helix chain 'N' and resid 266 through 288 removed outlier: 3.855A pdb=" N ASN N 285 " --> pdb=" O ILE N 281 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA N 288 " --> pdb=" O GLY N 284 " (cutoff:3.500A) Processing helix chain 'N' and resid 293 through 315 removed outlier: 3.547A pdb=" N ILE N 303 " --> pdb=" O GLY N 299 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER N 304 " --> pdb=" O TYR N 300 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY N 307 " --> pdb=" O ILE N 303 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR N 308 " --> pdb=" O SER N 304 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU N 309 " --> pdb=" O HIS N 305 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA N 312 " --> pdb=" O TYR N 308 " (cutoff:3.500A) Processing helix chain 'N' and resid 321 through 348 removed outlier: 3.584A pdb=" N GLY N 327 " --> pdb=" O MET N 323 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL N 328 " --> pdb=" O GLU N 324 " (cutoff:3.500A) Processing helix chain 'N' and resid 364 through 368 Processing helix chain 'N' and resid 369 through 384 Processing helix chain 'N' and resid 389 through 405 Processing helix chain 'N' and resid 407 through 431 removed outlier: 4.110A pdb=" N TYR N 423 " --> pdb=" O ALA N 419 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR N 424 " --> pdb=" O ILE N 420 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL N 428 " --> pdb=" O TYR N 424 " (cutoff:3.500A) Processing helix chain 'N' and resid 447 through 470 Processing helix chain 'N' and resid 471 through 481 Processing sheet with id=AA1, first strand: chain 'E' and resid 126 through 131 Processing sheet with id=AA2, first strand: chain 'F' and resid 168 through 174 removed outlier: 6.479A pdb=" N GLY F 128 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N HIS F 172 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE F 130 " --> pdb=" O HIS F 172 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLY F 174 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU F 132 " --> pdb=" O GLY F 174 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG F 133 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 260 through 265 removed outlier: 3.631A pdb=" N PHE F 252 " --> pdb=" O GLY F 260 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA F 326 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLY F 251 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ALA F 328 " --> pdb=" O GLY F 251 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER F 253 " --> pdb=" O ALA F 328 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ASP F 330 " --> pdb=" O SER F 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 12 through 14 removed outlier: 3.925A pdb=" N THR G 77 " --> pdb=" O THR G 5 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE G 78 " --> pdb=" O TYR G 55 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 146 through 148 Processing sheet with id=AA6, first strand: chain 'G' and resid 173 through 175 Processing sheet with id=AA7, first strand: chain 'G' and resid 224 through 225 Processing sheet with id=AA8, first strand: chain 'G' and resid 224 through 225 removed outlier: 8.002A pdb=" N ASN G 238 " --> pdb=" O ASN G 253 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ASN G 253 " --> pdb=" O ASN G 238 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N SER G 240 " --> pdb=" O ILE G 251 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ILE G 251 " --> pdb=" O SER G 240 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY G 242 " --> pdb=" O ARG G 249 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 292 through 294 removed outlier: 6.177A pdb=" N VAL G 566 " --> pdb=" O MET G 593 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL G 595 " --> pdb=" O VAL G 566 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL G 568 " --> pdb=" O VAL G 595 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE G 315 " --> pdb=" O VAL G 567 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LEU G 569 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE G 317 " --> pdb=" O LEU G 569 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N TYR G 340 " --> pdb=" O VAL G 314 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLY G 316 " --> pdb=" O TYR G 340 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 447 through 450 removed outlier: 3.765A pdb=" N TRP G 447 " --> pdb=" O LEU G 431 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA G 376 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ILE G 501 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU G 378 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N GLY G 503 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N LEU G 380 " --> pdb=" O GLY G 503 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 620 through 623 Processing sheet with id=AB3, first strand: chain 'G' and resid 704 through 705 removed outlier: 6.568A pdb=" N LEU G 704 " --> pdb=" O THR G 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'G' and resid 873 through 875 removed outlier: 5.729A pdb=" N ILE G 842 " --> pdb=" O GLU G 874 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ARG G 813 " --> pdb=" O VAL G 884 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU G 886 " --> pdb=" O ARG G 813 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA G 815 " --> pdb=" O LEU G 886 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 860 through 862 Processing sheet with id=AB6, first strand: chain 'I' and resid 48 through 50 Processing sheet with id=AB7, first strand: chain 'I' and resid 75 through 81 removed outlier: 4.097A pdb=" N PHE I 91 " --> pdb=" O GLN I 78 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ALA I 80 " --> pdb=" O PRO I 89 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 22 through 25 Processing sheet with id=AB9, first strand: chain 'B' and resid 56 through 60 removed outlier: 3.565A pdb=" N VAL B 97 " --> pdb=" O TYR B 57 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N MET B 96 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N MET B 126 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL B 98 " --> pdb=" O MET B 126 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 153 " --> pdb=" O VAL B 123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 38 through 41 removed outlier: 4.301A pdb=" N VAL C 49 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ALA C 116 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE C 96 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N SER C 97 " --> pdb=" O GLY C 79 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLY C 79 " --> pdb=" O SER C 97 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N PHE C 99 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU C 77 " --> pdb=" O PHE C 99 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N HIS C 101 " --> pdb=" O PHE C 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 123 through 125 removed outlier: 6.603A pdb=" N VAL C 124 " --> pdb=" O ASP C 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 232 through 238 removed outlier: 7.192A pdb=" N ARG C 232 " --> pdb=" O PRO C 247 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL C 234 " --> pdb=" O CYS C 245 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N CYS C 245 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN C 236 " --> pdb=" O VAL C 243 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 363 through 364 Processing sheet with id=AC5, first strand: chain 'C' and resid 531 through 539 removed outlier: 3.841A pdb=" N GLY C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 65 through 67 removed outlier: 3.862A pdb=" N SER M 65 " --> pdb=" O ILE M 83 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 70 through 72 Processing sheet with id=AC8, first strand: chain 'L' and resid 60 through 62 Processing sheet with id=AC9, first strand: chain 'L' and resid 66 through 70 Processing sheet with id=AD1, first strand: chain 'N' and resid 61 through 63 removed outlier: 3.531A pdb=" N MET N 67 " --> pdb=" O VAL N 63 " (cutoff:3.500A) 2005 hydrogen bonds defined for protein. 5705 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: 8.70 Time building geometry restraints manager: 4.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 15539 1.40 - 1.62: 22601 1.62 - 1.84: 439 1.84 - 2.06: 0 2.06 - 2.28: 92 Bond restraints: 38671 Sorted by residual: bond pdb=" C3 UQ8 N 502 " pdb=" C4 UQ8 N 502 " ideal model delta sigma weight residual 1.339 1.480 -0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" C3 UQ8 N 503 " pdb=" C4 UQ8 N 503 " ideal model delta sigma weight residual 1.339 1.479 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C1 UQ8 N 502 " pdb=" C6 UQ8 N 502 " ideal model delta sigma weight residual 1.345 1.481 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" C1 UQ8 N 503 " pdb=" C6 UQ8 N 503 " ideal model delta sigma weight residual 1.345 1.479 -0.134 2.00e-02 2.50e+03 4.50e+01 bond pdb=" C4 FMN F 501 " pdb=" C4A FMN F 501 " ideal model delta sigma weight residual 1.485 1.384 0.101 2.00e-02 2.50e+03 2.53e+01 ... (remaining 38666 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 51762 2.54 - 5.08: 482 5.08 - 7.62: 73 7.62 - 10.16: 19 10.16 - 12.70: 4 Bond angle restraints: 52340 Sorted by residual: angle pdb=" C ILE H 74 " pdb=" N PRO H 75 " pdb=" CA PRO H 75 " ideal model delta sigma weight residual 119.84 125.44 -5.60 1.25e+00 6.40e-01 2.01e+01 angle pdb=" N VAL C 336 " pdb=" CA VAL C 336 " pdb=" C VAL C 336 " ideal model delta sigma weight residual 112.12 108.51 3.61 8.40e-01 1.42e+00 1.85e+01 angle pdb=" OB3 CDL L 703 " pdb=" PB2 CDL L 703 " pdb=" OB4 CDL L 703 " ideal model delta sigma weight residual 121.80 109.10 12.70 3.00e+00 1.11e-01 1.79e+01 angle pdb=" OB2 CDL L 703 " pdb=" PB2 CDL L 703 " pdb=" OB5 CDL L 703 " ideal model delta sigma weight residual 96.70 109.29 -12.59 3.00e+00 1.11e-01 1.76e+01 angle pdb=" OA3 CDL L 703 " pdb=" PA1 CDL L 703 " pdb=" OA4 CDL L 703 " ideal model delta sigma weight residual 121.92 109.47 12.45 3.00e+00 1.11e-01 1.72e+01 ... (remaining 52335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.00: 21910 34.00 - 68.00: 970 68.00 - 102.00: 66 102.00 - 136.00: 10 136.00 - 170.00: 1 Dihedral angle restraints: 22957 sinusoidal: 9529 harmonic: 13428 Sorted by residual: dihedral pdb=" O21 3PE M 602 " pdb=" C2 3PE M 602 " pdb=" C3 3PE M 602 " pdb=" O31 3PE M 602 " ideal model delta sinusoidal sigma weight residual 60.47 -109.53 170.00 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CA LEU C 237 " pdb=" C LEU C 237 " pdb=" N ASP C 238 " pdb=" CA ASP C 238 " ideal model delta harmonic sigma weight residual 180.00 158.20 21.80 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" C16 UQ8 N 503 " pdb=" C17 UQ8 N 503 " pdb=" C18 UQ8 N 503 " pdb=" C19 UQ8 N 503 " ideal model delta sinusoidal sigma weight residual 112.06 -126.26 -121.68 1 3.00e+01 1.11e-03 1.63e+01 ... (remaining 22954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 4043 0.037 - 0.074: 1341 0.074 - 0.111: 342 0.111 - 0.148: 56 0.148 - 0.184: 2 Chirality restraints: 5784 Sorted by residual: chirality pdb=" CG LEU B 42 " pdb=" CB LEU B 42 " pdb=" CD1 LEU B 42 " pdb=" CD2 LEU B 42 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" CA PHE H 69 " pdb=" N PHE H 69 " pdb=" C PHE H 69 " pdb=" CB PHE H 69 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.14e-01 chirality pdb=" CA PHE H 238 " pdb=" N PHE H 238 " pdb=" C PHE H 238 " pdb=" CB PHE H 238 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.04e-01 ... (remaining 5781 not shown) Planarity restraints: 6512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 122 " -0.019 2.00e-02 2.50e+03 3.98e-02 1.58e+01 pdb=" C ALA A 122 " 0.069 2.00e-02 2.50e+03 pdb=" O ALA A 122 " -0.027 2.00e-02 2.50e+03 pdb=" N LEU A 123 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER L 497 " 0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C SER L 497 " -0.057 2.00e-02 2.50e+03 pdb=" O SER L 497 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY L 498 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE L 372 " -0.042 5.00e-02 4.00e+02 6.52e-02 6.81e+00 pdb=" N PRO L 373 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO L 373 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO L 373 " -0.036 5.00e-02 4.00e+02 ... (remaining 6509 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 10364 2.81 - 3.33: 36350 3.33 - 3.86: 66340 3.86 - 4.38: 81929 4.38 - 4.90: 136683 Nonbonded interactions: 331666 Sorted by model distance: nonbonded pdb=" OE2 GLU G 649 " pdb="CA CA G1004 " model vdw 2.291 3.250 nonbonded pdb="CA CA E 202 " pdb=" O HOH E 303 " model vdw 2.311 3.250 nonbonded pdb=" OG SER B 53 " pdb=" OD1 ASP H 63 " model vdw 2.321 3.040 nonbonded pdb=" OD2 ASP G 619 " pdb="CA CA G1004 " model vdw 2.420 3.250 nonbonded pdb=" O ASP C 238 " pdb=" OD1 ASP C 238 " model vdw 2.436 3.040 ... (remaining 331661 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.47 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: 30.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.810 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 41.450 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 38708 Z= 0.170 Angle : 0.712 36.771 52436 Z= 0.287 Chirality : 0.039 0.184 5784 Planarity : 0.004 0.065 6512 Dihedral : 17.676 170.001 14367 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.84 % Favored : 96.12 % Rotamer: Outliers : 1.54 % Allowed : 17.88 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.12), residues: 4663 helix: 1.42 (0.10), residues: 2563 sheet: -0.06 (0.31), residues: 309 loop : -0.57 (0.15), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 80 TYR 0.022 0.001 TYR M 435 PHE 0.023 0.001 PHE L 341 TRP 0.014 0.001 TRP L 143 HIS 0.007 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 (38671) covalent geometry : angle 0.59911 / 0.29 (52340) hydrogen bonds : bond 0.17229 / 11.51 ( 2003) hydrogen bonds : angle 6.09459 / 4.31 ( 5705) metal coordination : bond 0.01223 / 0.72 ( 37) metal coordination : angle 9.00355 / 5.90 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 810 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 415 PHE cc_start: 0.7210 (m-80) cc_final: 0.6230 (m-80) REVERT: B 7 ARG cc_start: 0.7445 (mtm-85) cc_final: 0.6799 (ptp90) REVERT: B 20 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7085 (mm-40) REVERT: B 86 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6773 (tp) REVERT: B 92 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8435 (mp10) REVERT: C 327 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.7186 (tt) REVERT: C 328 GLN cc_start: 0.6924 (mm-40) cc_final: 0.6443 (mt0) REVERT: C 329 ASP cc_start: 0.5955 (p0) cc_final: 0.5665 (m-30) REVERT: H 59 GLN cc_start: 0.7751 (tt0) cc_final: 0.6998 (mm-40) REVERT: H 64 MET cc_start: 0.7686 (mmt) cc_final: 0.7486 (mmm) REVERT: H 325 GLN cc_start: 0.5364 (mt0) cc_final: 0.5112 (pt0) REVERT: M 303 TRP cc_start: 0.8548 (OUTLIER) cc_final: 0.7730 (m-90) REVERT: M 403 ASN cc_start: 0.7672 (m110) cc_final: 0.7435 (m-40) REVERT: A 125 TRP cc_start: 0.5726 (OUTLIER) cc_final: 0.5396 (m100) REVERT: N 482 MET cc_start: 0.7983 (tpp) cc_final: 0.7768 (ttt) outliers start: 59 outliers final: 9 residues processed: 851 average time/residue: 0.6547 time to fit residues: 687.9399 Evaluate side-chains 448 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 433 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain A residue 125 TRP Chi-restraints excluded: chain N residue 253 VAL Chi-restraints excluded: chain N residue 430 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 0.8980 chunk 455 optimal weight: 0.9980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 238 ASN F 341 ASN F 386 GLN G 218 ASN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 397 GLN ** G 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 793 ASN G 867 ASN I 64 ASN I 168 ASN ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN C 167 HIS C 283 ASN ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 HIS K 82 GLN M 206 ASN L 2 ASN ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.092931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.067744 restraints weight = 110038.278| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.91 r_work: 0.3017 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 38708 Z= 0.151 Angle : 0.740 35.735 52436 Z= 0.306 Chirality : 0.042 0.298 5784 Planarity : 0.004 0.051 6512 Dihedral : 12.607 167.555 6061 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.45 % Allowed : 22.09 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.13), residues: 4663 helix: 1.57 (0.10), residues: 2596 sheet: 0.07 (0.31), residues: 307 loop : -0.44 (0.15), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 19 TYR 0.022 0.002 TYR M 435 PHE 0.031 0.002 PHE H 256 TRP 0.014 0.001 TRP H 260 HIS 0.012 0.001 HIS C 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (38671) covalent geometry : angle 0.61098 / 0.30 (52340) hydrogen bonds : bond 0.04407 / 2.91 ( 2003) hydrogen bonds : angle 4.73094 / 3.35 ( 5705) metal coordination : bond 0.01378 / 0.84 ( 37) metal coordination : angle 9.77401 / 6.49 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 471 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 ARG cc_start: 0.8256 (mtm-85) cc_final: 0.8015 (mtm180) REVERT: F 331 HIS cc_start: 0.8359 (p-80) cc_final: 0.7975 (p90) REVERT: G 888 MET cc_start: 0.8828 (tpp) cc_final: 0.8531 (tpp) REVERT: I 126 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8382 (mtmm) REVERT: B 7 ARG cc_start: 0.7708 (mtm-85) cc_final: 0.5958 (mtm-85) REVERT: B 63 CYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8828 (p) REVERT: B 92 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8402 (mp10) REVERT: B 106 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.7397 (ttm) REVERT: B 166 MET cc_start: 0.7574 (tpt) cc_final: 0.7352 (tpt) REVERT: B 174 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8449 (mp0) REVERT: B 219 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7872 (mm-30) REVERT: C 73 MET cc_start: 0.6788 (tpp) cc_final: 0.6323 (tpp) REVERT: C 112 MET cc_start: 0.8073 (tpp) cc_final: 0.7840 (mmm) REVERT: C 160 MET cc_start: 0.8779 (mmt) cc_final: 0.8270 (tpt) REVERT: C 257 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8489 (mm-30) REVERT: C 328 GLN cc_start: 0.6356 (mm-40) cc_final: 0.5788 (mt0) REVERT: C 407 ARG cc_start: 0.6639 (mtt180) cc_final: 0.6422 (mtt-85) REVERT: H 59 GLN cc_start: 0.7764 (tt0) cc_final: 0.7341 (mm-40) REVERT: H 63 ASP cc_start: 0.9071 (m-30) cc_final: 0.8832 (m-30) REVERT: H 64 MET cc_start: 0.7873 (mmt) cc_final: 0.7616 (mmm) REVERT: H 71 GLU cc_start: 0.7684 (tt0) cc_final: 0.7350 (tp30) REVERT: H 165 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8484 (tpp) REVERT: H 228 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7858 (tt0) REVERT: H 241 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8417 (tm-30) REVERT: H 286 ARG cc_start: 0.8584 (tpt-90) cc_final: 0.8283 (tpt90) REVERT: H 293 ARG cc_start: 0.8420 (mtp180) cc_final: 0.8192 (ptt180) REVERT: H 294 TYR cc_start: 0.7193 (t80) cc_final: 0.6878 (t80) REVERT: H 296 GLN cc_start: 0.9055 (mt0) cc_final: 0.8473 (mt0) REVERT: H 325 GLN cc_start: 0.6463 (mt0) cc_final: 0.5731 (pt0) REVERT: J 73 MET cc_start: 0.8730 (ptm) cc_final: 0.8395 (ptm) REVERT: J 161 GLU cc_start: 0.7101 (mp0) cc_final: 0.6850 (mp0) REVERT: K 99 ARG cc_start: 0.8560 (mmm160) cc_final: 0.8326 (mmm160) REVERT: M 107 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8716 (mmtm) REVERT: M 150 MET cc_start: 0.8795 (tpp) cc_final: 0.8541 (mmm) REVERT: M 235 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.7334 (ttm) REVERT: M 303 TRP cc_start: 0.9305 (OUTLIER) cc_final: 0.8458 (m-10) REVERT: M 371 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8369 (mtm) REVERT: M 373 MET cc_start: 0.8488 (mpp) cc_final: 0.7817 (mtp) REVERT: M 374 MET cc_start: 0.8840 (mtt) cc_final: 0.8594 (mpt) REVERT: M 398 MET cc_start: 0.8816 (tpp) cc_final: 0.8472 (tpp) REVERT: A 30 MET cc_start: 0.7531 (mtt) cc_final: 0.7206 (mtp) REVERT: A 61 ARG cc_start: 0.6455 (ttt-90) cc_final: 0.6159 (ptt-90) REVERT: A 67 LYS cc_start: 0.8944 (ptmt) cc_final: 0.8413 (ptpt) REVERT: A 73 MET cc_start: 0.9113 (tmm) cc_final: 0.8820 (tmm) REVERT: L 88 MET cc_start: 0.8197 (mmm) cc_final: 0.7914 (mmm) REVERT: L 139 MET cc_start: 0.9438 (OUTLIER) cc_final: 0.9127 (tpp) REVERT: L 183 PHE cc_start: 0.8753 (m-80) cc_final: 0.8456 (m-80) REVERT: L 216 MET cc_start: 0.8049 (pp-130) cc_final: 0.7746 (ppp) REVERT: L 233 LEU cc_start: 0.8739 (tt) cc_final: 0.8203 (mp) REVERT: L 436 VAL cc_start: 0.9163 (t) cc_final: 0.8851 (m) REVERT: L 460 LEU cc_start: 0.8681 (tp) cc_final: 0.8409 (tp) REVERT: N 150 LYS cc_start: 0.8807 (mmtm) cc_final: 0.8311 (mtpm) REVERT: N 200 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7520 (tm-30) outliers start: 171 outliers final: 39 residues processed: 587 average time/residue: 0.6100 time to fit residues: 444.0690 Evaluate side-chains 454 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 401 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 405 VAL Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 855 ASN Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain H residue 304 ILE Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 107 LYS Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 149 CYS Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 239 LEU Chi-restraints excluded: chain L residue 321 LEU Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 361 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 307 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 410 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 258 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 chunk 208 optimal weight: 0.9990 chunk 387 optimal weight: 6.9990 chunk 365 optimal weight: 0.9980 chunk 414 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 ASN G 54 GLN ** G 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 482 GLN G 655 HIS I 168 ASN B 22 GLN B 58 ASN C 319 HIS ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 308 GLN M 403 ASN M 416 GLN ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 ASN ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 121 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.089470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.064830 restraints weight = 109547.866| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.78 r_work: 0.2948 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 38708 Z= 0.207 Angle : 0.777 38.510 52436 Z= 0.314 Chirality : 0.044 0.321 5784 Planarity : 0.004 0.050 6512 Dihedral : 12.343 161.574 6043 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.61 % Allowed : 21.91 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.13), residues: 4663 helix: 1.57 (0.10), residues: 2594 sheet: -0.06 (0.31), residues: 306 loop : -0.49 (0.15), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 19 TYR 0.022 0.002 TYR M 435 PHE 0.026 0.002 PHE L 341 TRP 0.020 0.001 TRP A 125 HIS 0.006 0.001 HIS K 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (38671) covalent geometry : angle 0.62442 / 0.31 (52340) hydrogen bonds : bond 0.04458 / 2.94 ( 2003) hydrogen bonds : angle 4.61944 / 3.27 ( 5705) metal coordination : bond 0.02060 / 1.27 ( 37) metal coordination : angle 10.83871 / 7.22 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 423 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 111 LYS cc_start: 0.9190 (mtmm) cc_final: 0.8882 (pptt) REVERT: E 112 LYS cc_start: 0.8943 (tttt) cc_final: 0.8670 (tttt) REVERT: E 125 ARG cc_start: 0.8344 (ttt-90) cc_final: 0.8039 (ttt-90) REVERT: F 247 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.7344 (t) REVERT: G 98 MET cc_start: 0.9220 (mmt) cc_final: 0.8814 (mmt) REVERT: G 249 ARG cc_start: 0.9278 (OUTLIER) cc_final: 0.7510 (mtt180) REVERT: G 385 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8794 (t) REVERT: G 670 GLN cc_start: 0.6353 (OUTLIER) cc_final: 0.5717 (tm-30) REVERT: G 859 ARG cc_start: 0.8883 (mtp-110) cc_final: 0.8450 (ttm-80) REVERT: G 888 MET cc_start: 0.8798 (tpp) cc_final: 0.8497 (tpp) REVERT: B 23 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7966 (pm20) REVERT: B 63 CYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8923 (p) REVERT: B 92 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8364 (mp10) REVERT: B 106 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7483 (ttm) REVERT: B 174 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8507 (mp0) REVERT: C 73 MET cc_start: 0.7033 (tpp) cc_final: 0.6554 (tpp) REVERT: C 112 MET cc_start: 0.8077 (tpp) cc_final: 0.7726 (tpp) REVERT: C 160 MET cc_start: 0.8761 (mmt) cc_final: 0.8263 (tpt) REVERT: C 328 GLN cc_start: 0.6380 (mm-40) cc_final: 0.5780 (tt0) REVERT: C 532 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7836 (mm-30) REVERT: H 64 MET cc_start: 0.8061 (mmt) cc_final: 0.7840 (mmm) REVERT: H 71 GLU cc_start: 0.8041 (tt0) cc_final: 0.7545 (tp30) REVERT: H 111 ASP cc_start: 0.8510 (t0) cc_final: 0.8291 (t0) REVERT: H 148 ARG cc_start: 0.8807 (ttm-80) cc_final: 0.8213 (ttp-170) REVERT: H 157 GLU cc_start: 0.9212 (OUTLIER) cc_final: 0.8480 (tm-30) REVERT: H 165 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8725 (tpp) REVERT: H 214 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7890 (mm-40) REVERT: H 228 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8020 (tt0) REVERT: H 241 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8467 (tm-30) REVERT: H 286 ARG cc_start: 0.8640 (tpt-90) cc_final: 0.8376 (tpt90) REVERT: H 293 ARG cc_start: 0.8349 (mtp180) cc_final: 0.7926 (ptt90) REVERT: H 325 GLN cc_start: 0.6322 (mt0) cc_final: 0.5416 (pt0) REVERT: J 161 GLU cc_start: 0.7343 (mp0) cc_final: 0.7111 (mp0) REVERT: M 107 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8736 (mmtm) REVERT: M 235 MET cc_start: 0.7581 (ttm) cc_final: 0.7361 (ttm) REVERT: M 303 TRP cc_start: 0.9344 (OUTLIER) cc_final: 0.8540 (m-10) REVERT: M 371 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8677 (mtm) REVERT: M 373 MET cc_start: 0.8579 (mpp) cc_final: 0.8347 (mpp) REVERT: M 398 MET cc_start: 0.8914 (tpp) cc_final: 0.8527 (tpp) REVERT: M 460 MET cc_start: 0.8629 (ptp) cc_final: 0.8303 (ppp) REVERT: M 465 LEU cc_start: 0.9202 (tp) cc_final: 0.8888 (tp) REVERT: A 30 MET cc_start: 0.7730 (mtt) cc_final: 0.7430 (mtp) REVERT: A 61 ARG cc_start: 0.6656 (ttt-90) cc_final: 0.6244 (ptt-90) REVERT: A 67 LYS cc_start: 0.9011 (ptmt) cc_final: 0.8549 (ptpt) REVERT: A 73 MET cc_start: 0.9130 (tmm) cc_final: 0.8730 (tmm) REVERT: L 139 MET cc_start: 0.9429 (OUTLIER) cc_final: 0.9201 (tpp) REVERT: L 216 MET cc_start: 0.8057 (pp-130) cc_final: 0.7806 (ppp) REVERT: L 233 LEU cc_start: 0.8755 (tt) cc_final: 0.8120 (mp) REVERT: L 275 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7214 (mtt) REVERT: L 276 THR cc_start: 0.6482 (t) cc_final: 0.6241 (t) REVERT: L 286 VAL cc_start: 0.9289 (t) cc_final: 0.8987 (t) REVERT: L 319 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7691 (mpp) REVERT: L 430 PHE cc_start: 0.8592 (m-80) cc_final: 0.7740 (m-80) REVERT: L 436 VAL cc_start: 0.9144 (t) cc_final: 0.8844 (m) REVERT: L 460 LEU cc_start: 0.8731 (tp) cc_final: 0.8412 (tp) REVERT: L 598 MET cc_start: 0.9345 (OUTLIER) cc_final: 0.9030 (mtm) REVERT: N 150 LYS cc_start: 0.8871 (mmtm) cc_final: 0.8590 (mtpm) REVERT: N 200 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7439 (tm-30) REVERT: N 347 MET cc_start: 0.9067 (mmm) cc_final: 0.8852 (tpp) outliers start: 177 outliers final: 66 residues processed: 543 average time/residue: 0.6626 time to fit residues: 447.2804 Evaluate side-chains 460 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 374 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 249 ARG Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 475 ASP Chi-restraints excluded: chain G residue 504 THR Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain G residue 670 GLN Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 790 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 532 GLU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 141 TYR Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 107 LYS Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 149 CYS Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 319 MET Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain L residue 610 MET Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 430 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 74 optimal weight: 0.9980 chunk 271 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 314 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 426 optimal weight: 0.8980 chunk 254 optimal weight: 0.9990 chunk 457 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 chunk 351 optimal weight: 0.9990 chunk 374 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN B 58 ASN ** C 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 487 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.090063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.065217 restraints weight = 127765.399| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.01 r_work: 0.2953 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 38708 Z= 0.148 Angle : 0.736 36.554 52436 Z= 0.294 Chirality : 0.042 0.248 5784 Planarity : 0.004 0.051 6512 Dihedral : 12.060 157.597 6043 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.80 % Allowed : 23.03 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.13), residues: 4663 helix: 1.69 (0.10), residues: 2574 sheet: -0.12 (0.31), residues: 306 loop : -0.47 (0.15), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 19 TYR 0.024 0.001 TYR C 414 PHE 0.027 0.001 PHE J 3 TRP 0.013 0.001 TRP C 376 HIS 0.007 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (38671) covalent geometry : angle 0.59430 / 0.29 (52340) hydrogen bonds : bond 0.04009 / 2.65 ( 2003) hydrogen bonds : angle 4.47358 / 3.17 ( 5705) metal coordination : bond 0.01449 / 0.88 ( 37) metal coordination : angle 10.14874 / 6.80 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 411 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 111 LYS cc_start: 0.9182 (mtmm) cc_final: 0.8900 (pptt) REVERT: E 112 LYS cc_start: 0.8929 (tttt) cc_final: 0.8614 (tttt) REVERT: E 125 ARG cc_start: 0.8339 (ttt-90) cc_final: 0.8056 (ttt-90) REVERT: F 247 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.7491 (t) REVERT: G 98 MET cc_start: 0.9231 (mmt) cc_final: 0.8960 (mmt) REVERT: G 319 SER cc_start: 0.8404 (OUTLIER) cc_final: 0.8139 (m) REVERT: G 385 THR cc_start: 0.9194 (OUTLIER) cc_final: 0.8771 (t) REVERT: G 844 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7960 (mm) REVERT: G 888 MET cc_start: 0.8727 (tpp) cc_final: 0.8490 (tpp) REVERT: I 126 LYS cc_start: 0.8702 (mtmm) cc_final: 0.8436 (mttt) REVERT: B 7 ARG cc_start: 0.7645 (mtm-85) cc_final: 0.6939 (mtm-85) REVERT: B 63 CYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8928 (p) REVERT: B 92 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8457 (mp10) REVERT: B 106 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7452 (ttm) REVERT: B 174 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8515 (mp0) REVERT: B 178 LYS cc_start: 0.8129 (mtpt) cc_final: 0.7512 (tttt) REVERT: C 73 MET cc_start: 0.7015 (tpp) cc_final: 0.6527 (tpp) REVERT: C 112 MET cc_start: 0.8090 (tpp) cc_final: 0.7870 (tpp) REVERT: C 160 MET cc_start: 0.8769 (mmt) cc_final: 0.8305 (tpt) REVERT: C 328 GLN cc_start: 0.6412 (mm-40) cc_final: 0.5797 (tt0) REVERT: C 532 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7860 (mm-30) REVERT: H 59 GLN cc_start: 0.8087 (tt0) cc_final: 0.7763 (mm-40) REVERT: H 63 ASP cc_start: 0.9258 (m-30) cc_final: 0.9058 (m-30) REVERT: H 64 MET cc_start: 0.8112 (mmt) cc_final: 0.7887 (mmm) REVERT: H 71 GLU cc_start: 0.8018 (tt0) cc_final: 0.7561 (tp30) REVERT: H 148 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8190 (tpt-90) REVERT: H 157 GLU cc_start: 0.9256 (OUTLIER) cc_final: 0.8569 (tm-30) REVERT: H 165 MET cc_start: 0.8965 (mmp) cc_final: 0.8632 (tpp) REVERT: H 214 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7869 (mm-40) REVERT: H 227 ILE cc_start: 0.8557 (tp) cc_final: 0.8162 (pp) REVERT: H 241 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8512 (tm-30) REVERT: H 286 ARG cc_start: 0.8681 (tpt-90) cc_final: 0.8368 (tpt90) REVERT: H 293 ARG cc_start: 0.8311 (mtp180) cc_final: 0.7855 (ptt90) REVERT: H 325 GLN cc_start: 0.6362 (mt0) cc_final: 0.5488 (pt0) REVERT: J 69 PHE cc_start: 0.9266 (OUTLIER) cc_final: 0.8920 (t80) REVERT: M 150 MET cc_start: 0.8924 (tpp) cc_final: 0.8703 (mmm) REVERT: M 303 TRP cc_start: 0.9337 (OUTLIER) cc_final: 0.8568 (m-10) REVERT: M 371 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8440 (mtm) REVERT: M 373 MET cc_start: 0.8579 (mpp) cc_final: 0.8329 (mpp) REVERT: M 374 MET cc_start: 0.8911 (mtt) cc_final: 0.8585 (mpt) REVERT: M 460 MET cc_start: 0.8525 (ptp) cc_final: 0.8311 (ppp) REVERT: M 465 LEU cc_start: 0.9205 (tp) cc_final: 0.8866 (tp) REVERT: A 30 MET cc_start: 0.7723 (mtt) cc_final: 0.7439 (mtp) REVERT: A 67 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8587 (ptpt) REVERT: A 73 MET cc_start: 0.9129 (tmm) cc_final: 0.8722 (tmm) REVERT: L 119 TYR cc_start: 0.8888 (m-10) cc_final: 0.8484 (m-80) REVERT: L 216 MET cc_start: 0.8109 (pp-130) cc_final: 0.7794 (ppp) REVERT: L 233 LEU cc_start: 0.8750 (tt) cc_final: 0.8300 (mp) REVERT: L 305 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7996 (pptt) REVERT: L 319 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7687 (mpp) REVERT: L 430 PHE cc_start: 0.8557 (m-80) cc_final: 0.7673 (m-80) REVERT: L 436 VAL cc_start: 0.9173 (t) cc_final: 0.8834 (m) REVERT: L 460 LEU cc_start: 0.8825 (tp) cc_final: 0.8490 (tp) REVERT: N 150 LYS cc_start: 0.8847 (mmtm) cc_final: 0.8535 (mtpm) REVERT: N 191 LYS cc_start: 0.8959 (ttmm) cc_final: 0.8736 (ttpp) REVERT: N 200 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7550 (tm-30) REVERT: N 347 MET cc_start: 0.9045 (mmm) cc_final: 0.8813 (tpp) REVERT: N 371 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8097 (pt) outliers start: 146 outliers final: 57 residues processed: 509 average time/residue: 0.6598 time to fit residues: 415.4639 Evaluate side-chains 454 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 378 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 319 SER Chi-restraints excluded: chain G residue 355 LEU Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 405 GLU Chi-restraints excluded: chain G residue 475 ASP Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 790 THR Chi-restraints excluded: chain G residue 844 LEU Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 532 GLU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 141 TYR Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 470 LEU Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 149 CYS Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 305 LYS Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 319 MET Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain L residue 610 MET Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 371 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 445 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 371 optimal weight: 4.9990 chunk 288 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 309 optimal weight: 0.6980 chunk 419 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 411 optimal weight: 0.9980 chunk 370 optimal weight: 2.9990 chunk 432 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 GLN B 58 ASN B 92 GLN ** C 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 403 ASN ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 404 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.090411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.066045 restraints weight = 108900.696| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.75 r_work: 0.2975 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 38708 Z= 0.133 Angle : 0.723 35.508 52436 Z= 0.288 Chirality : 0.041 0.195 5784 Planarity : 0.004 0.057 6512 Dihedral : 11.759 152.564 6043 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.75 % Allowed : 23.32 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.13), residues: 4663 helix: 1.74 (0.10), residues: 2572 sheet: -0.03 (0.30), residues: 308 loop : -0.47 (0.15), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 19 TYR 0.026 0.001 TYR C 414 PHE 0.030 0.001 PHE J 3 TRP 0.018 0.001 TRP C 376 HIS 0.007 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (38671) covalent geometry : angle 0.58299 / 0.29 (52340) hydrogen bonds : bond 0.03802 / 2.51 ( 2003) hydrogen bonds : angle 4.38013 / 3.10 ( 5705) metal coordination : bond 0.01266 / 0.77 ( 37) metal coordination : angle 10.01149 / 6.79 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 417 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 111 LYS cc_start: 0.9156 (mtmm) cc_final: 0.8900 (mtmm) REVERT: E 125 ARG cc_start: 0.8306 (ttt-90) cc_final: 0.8017 (ttt-90) REVERT: F 105 MET cc_start: 0.7767 (mtp) cc_final: 0.7279 (mtm) REVERT: F 247 THR cc_start: 0.8396 (OUTLIER) cc_final: 0.7514 (t) REVERT: F 333 ILE cc_start: 0.7217 (mm) cc_final: 0.6916 (tp) REVERT: G 98 MET cc_start: 0.9233 (mmt) cc_final: 0.8952 (mmt) REVERT: G 150 MET cc_start: 0.9034 (mmm) cc_final: 0.8716 (tpp) REVERT: G 385 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8767 (t) REVERT: G 522 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9067 (mm) REVERT: G 533 MET cc_start: 0.9309 (mmm) cc_final: 0.8341 (mmm) REVERT: G 599 ARG cc_start: 0.8337 (ttm-80) cc_final: 0.8076 (tpp80) REVERT: G 844 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7936 (mm) REVERT: G 859 ARG cc_start: 0.8776 (mtp-110) cc_final: 0.8343 (tpp80) REVERT: G 888 MET cc_start: 0.8691 (tpp) cc_final: 0.8481 (tpp) REVERT: I 126 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8422 (mttt) REVERT: B 7 ARG cc_start: 0.7501 (mtm-85) cc_final: 0.6967 (mtm-85) REVERT: B 39 MET cc_start: 0.8220 (pmm) cc_final: 0.8017 (pmm) REVERT: B 63 CYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8843 (p) REVERT: B 92 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8583 (pm20) REVERT: B 106 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7390 (ttm) REVERT: B 174 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8493 (mp0) REVERT: B 178 LYS cc_start: 0.8102 (mtpt) cc_final: 0.7560 (tttt) REVERT: C 73 MET cc_start: 0.7010 (tpp) cc_final: 0.6436 (tpp) REVERT: C 112 MET cc_start: 0.8044 (tpp) cc_final: 0.7796 (tpp) REVERT: C 142 TRP cc_start: 0.8194 (OUTLIER) cc_final: 0.7014 (t-100) REVERT: C 160 MET cc_start: 0.8721 (mmt) cc_final: 0.8257 (tpt) REVERT: C 328 GLN cc_start: 0.6460 (mm-40) cc_final: 0.5824 (mt0) REVERT: C 532 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7881 (mm-30) REVERT: C 561 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8284 (p) REVERT: H 32 MET cc_start: 0.6786 (OUTLIER) cc_final: 0.6470 (mtm) REVERT: H 59 GLN cc_start: 0.8103 (tt0) cc_final: 0.7823 (mm-40) REVERT: H 71 GLU cc_start: 0.7975 (tt0) cc_final: 0.7571 (tp30) REVERT: H 79 ASP cc_start: 0.7568 (t0) cc_final: 0.7188 (t0) REVERT: H 157 GLU cc_start: 0.9290 (tm-30) cc_final: 0.8926 (tm-30) REVERT: H 165 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8578 (mmm) REVERT: H 241 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8563 (tm-30) REVERT: H 296 GLN cc_start: 0.9033 (mt0) cc_final: 0.8500 (mt0) REVERT: H 325 GLN cc_start: 0.6291 (mt0) cc_final: 0.5438 (pt0) REVERT: J 69 PHE cc_start: 0.9246 (OUTLIER) cc_final: 0.8914 (t80) REVERT: J 82 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8371 (pp20) REVERT: J 142 GLU cc_start: 0.9128 (OUTLIER) cc_final: 0.8898 (mp0) REVERT: J 146 MET cc_start: 0.8948 (mpp) cc_final: 0.8680 (mpp) REVERT: M 150 MET cc_start: 0.8871 (tpp) cc_final: 0.8646 (mmm) REVERT: M 303 TRP cc_start: 0.9331 (OUTLIER) cc_final: 0.8547 (m-10) REVERT: M 371 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8622 (mtm) REVERT: M 398 MET cc_start: 0.9229 (mmm) cc_final: 0.8263 (tpp) REVERT: M 465 LEU cc_start: 0.9210 (tp) cc_final: 0.8847 (tp) REVERT: A 30 MET cc_start: 0.7682 (mtt) cc_final: 0.7413 (mtp) REVERT: A 67 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8797 (pttm) REVERT: A 73 MET cc_start: 0.9118 (tmm) cc_final: 0.8679 (tmm) REVERT: L 4 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8883 (tm) REVERT: L 139 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8864 (tpp) REVERT: L 216 MET cc_start: 0.8149 (pp-130) cc_final: 0.7817 (ppp) REVERT: L 305 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7969 (pptt) REVERT: L 319 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7764 (mpp) REVERT: L 400 ASP cc_start: 0.9126 (t70) cc_final: 0.8911 (m-30) REVERT: L 425 THR cc_start: 0.9094 (p) cc_final: 0.8866 (t) REVERT: L 430 PHE cc_start: 0.8496 (m-80) cc_final: 0.7471 (m-80) REVERT: L 436 VAL cc_start: 0.9162 (t) cc_final: 0.8846 (m) REVERT: L 460 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8495 (tp) REVERT: L 598 MET cc_start: 0.9303 (OUTLIER) cc_final: 0.8985 (mtm) REVERT: N 150 LYS cc_start: 0.8833 (mmtm) cc_final: 0.8501 (mtpm) REVERT: N 197 MET cc_start: 0.7377 (ptm) cc_final: 0.7080 (ptm) REVERT: N 200 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7570 (tm-30) REVERT: N 371 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8083 (pt) outliers start: 144 outliers final: 65 residues processed: 523 average time/residue: 0.6565 time to fit residues: 426.4064 Evaluate side-chains 462 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 370 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 355 LEU Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 405 GLU Chi-restraints excluded: chain G residue 475 ASP Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain G residue 522 LEU Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 790 THR Chi-restraints excluded: chain G residue 844 LEU Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 142 TRP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 532 GLU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 141 TYR Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 470 LEU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 149 CYS Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 305 LYS Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 319 MET Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 460 LEU Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain L residue 610 MET Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 371 ILE Chi-restraints excluded: chain N residue 430 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 79 optimal weight: 0.4980 chunk 335 optimal weight: 1.9990 chunk 220 optimal weight: 0.9990 chunk 188 optimal weight: 0.0670 chunk 125 optimal weight: 0.9990 chunk 221 optimal weight: 3.9990 chunk 269 optimal weight: 4.9990 chunk 168 optimal weight: 8.9990 chunk 371 optimal weight: 1.9990 chunk 347 optimal weight: 0.4980 chunk 418 optimal weight: 8.9990 overall best weight: 0.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 142 ASN ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 ASN B 58 ASN ** C 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.090778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.065082 restraints weight = 126610.832| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.96 r_work: 0.2987 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 38708 Z= 0.123 Angle : 0.725 34.780 52436 Z= 0.291 Chirality : 0.041 0.320 5784 Planarity : 0.004 0.064 6512 Dihedral : 11.524 148.450 6042 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.67 % Allowed : 24.17 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.13), residues: 4663 helix: 1.77 (0.10), residues: 2576 sheet: 0.06 (0.31), residues: 305 loop : -0.41 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 19 TYR 0.027 0.001 TYR C 414 PHE 0.033 0.001 PHE L 183 TRP 0.023 0.001 TRP C 376 HIS 0.006 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (38671) covalent geometry : angle 0.59467 / 0.29 (52340) hydrogen bonds : bond 0.03685 / 2.44 ( 2003) hydrogen bonds : angle 4.35513 / 3.09 ( 5705) metal coordination : bond 0.01055 / 0.63 ( 37) metal coordination : angle 9.72934 / 6.57 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 409 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 111 LYS cc_start: 0.9130 (mtmm) cc_final: 0.8928 (mtmm) REVERT: E 125 ARG cc_start: 0.8311 (ttt-90) cc_final: 0.8051 (ttt-90) REVERT: F 105 MET cc_start: 0.7773 (mtp) cc_final: 0.7270 (mtm) REVERT: F 247 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.7591 (t) REVERT: G 98 MET cc_start: 0.9212 (mmp) cc_final: 0.8925 (mmt) REVERT: G 150 MET cc_start: 0.9002 (mmm) cc_final: 0.8695 (tpp) REVERT: G 319 SER cc_start: 0.8290 (p) cc_final: 0.8038 (m) REVERT: G 385 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8765 (t) REVERT: G 522 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9078 (mm) REVERT: G 533 MET cc_start: 0.9264 (mmm) cc_final: 0.8314 (mmm) REVERT: G 859 ARG cc_start: 0.8774 (mtp-110) cc_final: 0.8404 (tpp80) REVERT: I 126 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8417 (mttt) REVERT: B 7 ARG cc_start: 0.7470 (mtm-85) cc_final: 0.6640 (mtm-85) REVERT: B 23 GLU cc_start: 0.8312 (pt0) cc_final: 0.7808 (pm20) REVERT: B 39 MET cc_start: 0.8249 (pmm) cc_final: 0.8016 (pmm) REVERT: B 50 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8606 (mtt180) REVERT: B 92 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8553 (mp10) REVERT: B 106 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7451 (ttm) REVERT: B 174 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8512 (mp0) REVERT: B 178 LYS cc_start: 0.8061 (mtpt) cc_final: 0.7566 (tttt) REVERT: C 73 MET cc_start: 0.7004 (tpp) cc_final: 0.6437 (tpp) REVERT: C 112 MET cc_start: 0.8060 (tpp) cc_final: 0.7811 (tpp) REVERT: C 142 TRP cc_start: 0.8224 (OUTLIER) cc_final: 0.7043 (t-100) REVERT: C 160 MET cc_start: 0.8728 (mmt) cc_final: 0.8288 (tpt) REVERT: C 328 GLN cc_start: 0.6453 (mm-40) cc_final: 0.5749 (mt0) REVERT: C 333 MET cc_start: 0.4186 (mtt) cc_final: 0.3652 (mtp) REVERT: C 469 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8222 (mm) REVERT: C 532 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7932 (mm-30) REVERT: C 561 VAL cc_start: 0.8631 (OUTLIER) cc_final: 0.8232 (p) REVERT: H 71 GLU cc_start: 0.8029 (tt0) cc_final: 0.7652 (tp30) REVERT: H 73 TRP cc_start: 0.8235 (t60) cc_final: 0.7927 (t60) REVERT: H 148 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8071 (ttp-170) REVERT: H 157 GLU cc_start: 0.9291 (OUTLIER) cc_final: 0.8848 (tm-30) REVERT: H 165 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8563 (mmm) REVERT: H 228 GLU cc_start: 0.8439 (tp30) cc_final: 0.8155 (tp30) REVERT: H 241 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8465 (tm-30) REVERT: H 325 GLN cc_start: 0.6221 (mt0) cc_final: 0.5430 (pt0) REVERT: J 69 PHE cc_start: 0.9240 (OUTLIER) cc_final: 0.8928 (t80) REVERT: J 82 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8280 (pp20) REVERT: J 142 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8890 (mp0) REVERT: J 146 MET cc_start: 0.8969 (mpp) cc_final: 0.8699 (mpp) REVERT: M 150 MET cc_start: 0.8821 (tpp) cc_final: 0.8614 (mmm) REVERT: M 303 TRP cc_start: 0.9337 (OUTLIER) cc_final: 0.8525 (m-10) REVERT: M 371 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8389 (mtm) REVERT: M 373 MET cc_start: 0.8639 (mpp) cc_final: 0.7876 (mtp) REVERT: M 374 MET cc_start: 0.8980 (mtt) cc_final: 0.8691 (mpt) REVERT: M 460 MET cc_start: 0.8559 (ppp) cc_final: 0.8034 (pmm) REVERT: A 67 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8826 (ptpt) REVERT: A 73 MET cc_start: 0.9158 (tmm) cc_final: 0.8754 (tmm) REVERT: L 3 MET cc_start: 0.7602 (mmt) cc_final: 0.7385 (mmm) REVERT: L 4 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8919 (tm) REVERT: L 119 TYR cc_start: 0.8860 (m-10) cc_final: 0.8397 (m-80) REVERT: L 139 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8826 (tpp) REVERT: L 216 MET cc_start: 0.8121 (pp-130) cc_final: 0.7809 (ppp) REVERT: L 233 LEU cc_start: 0.8590 (tt) cc_final: 0.8007 (mp) REVERT: L 276 THR cc_start: 0.6420 (t) cc_final: 0.5617 (t) REVERT: L 305 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.8061 (pptt) REVERT: L 319 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7764 (mpp) REVERT: L 430 PHE cc_start: 0.8446 (m-80) cc_final: 0.7335 (m-80) REVERT: L 436 VAL cc_start: 0.9055 (t) cc_final: 0.8800 (m) REVERT: L 454 SER cc_start: 0.8453 (OUTLIER) cc_final: 0.8024 (t) REVERT: L 460 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8512 (tp) REVERT: L 568 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8444 (tmm) REVERT: N 150 LYS cc_start: 0.8829 (mmtm) cc_final: 0.8480 (mtpm) REVERT: N 197 MET cc_start: 0.7410 (ptm) cc_final: 0.7132 (ptm) REVERT: N 200 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7588 (tm-30) REVERT: N 371 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8067 (pt) outliers start: 141 outliers final: 61 residues processed: 508 average time/residue: 0.6162 time to fit residues: 392.9130 Evaluate side-chains 460 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 370 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 355 LEU Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 405 GLU Chi-restraints excluded: chain G residue 475 ASP Chi-restraints excluded: chain G residue 522 LEU Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 142 TRP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 532 GLU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 141 TYR Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain K residue 26 ARG Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 149 CYS Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 305 LYS Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 319 MET Chi-restraints excluded: chain L residue 454 SER Chi-restraints excluded: chain L residue 460 LEU Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 371 ILE Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain N residue 457 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 163 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 110 optimal weight: 0.0270 chunk 114 optimal weight: 0.3980 chunk 219 optimal weight: 3.9990 chunk 301 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 153 optimal weight: 0.8980 chunk 259 optimal weight: 10.0000 chunk 314 optimal weight: 0.6980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN ** C 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.091171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.066443 restraints weight = 122893.359| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.92 r_work: 0.2999 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 38708 Z= 0.118 Angle : 0.748 34.156 52436 Z= 0.297 Chirality : 0.041 0.346 5784 Planarity : 0.004 0.070 6512 Dihedral : 11.329 145.453 6041 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.38 % Allowed : 24.75 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.13), residues: 4663 helix: 1.78 (0.10), residues: 2572 sheet: 0.11 (0.30), residues: 305 loop : -0.37 (0.15), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG E 19 TYR 0.028 0.001 TYR C 414 PHE 0.038 0.001 PHE L 183 TRP 0.026 0.001 TRP C 376 HIS 0.006 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (38671) covalent geometry : angle 0.61071 / 0.29 (52340) hydrogen bonds : bond 0.03641 / 2.39 ( 2003) hydrogen bonds : angle 4.35450 / 3.09 ( 5705) metal coordination : bond 0.00934 / 0.56 ( 37) metal coordination : angle 10.12715 / 6.65 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 414 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 111 LYS cc_start: 0.9132 (mtmm) cc_final: 0.8830 (mtmt) REVERT: E 125 ARG cc_start: 0.8311 (ttt-90) cc_final: 0.8077 (ttt-90) REVERT: F 247 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.7609 (t) REVERT: F 333 ILE cc_start: 0.7250 (OUTLIER) cc_final: 0.6417 (pp) REVERT: F 335 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8251 (ptp) REVERT: G 150 MET cc_start: 0.8936 (mmm) cc_final: 0.8658 (tpp) REVERT: G 319 SER cc_start: 0.8288 (p) cc_final: 0.8031 (m) REVERT: G 385 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8776 (t) REVERT: G 522 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9105 (mm) REVERT: G 533 MET cc_start: 0.9169 (mmm) cc_final: 0.8312 (mmm) REVERT: G 859 ARG cc_start: 0.8755 (mtp-110) cc_final: 0.8164 (tpp80) REVERT: I 126 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8491 (mttt) REVERT: B 7 ARG cc_start: 0.7381 (mtm-85) cc_final: 0.6441 (mtm-85) REVERT: B 23 GLU cc_start: 0.8411 (pt0) cc_final: 0.7886 (pm20) REVERT: B 39 MET cc_start: 0.8287 (pmm) cc_final: 0.8041 (pmm) REVERT: B 50 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8613 (mtt180) REVERT: B 92 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8529 (pm20) REVERT: B 106 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7579 (ttm) REVERT: B 174 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8525 (mp0) REVERT: B 178 LYS cc_start: 0.8136 (mtpt) cc_final: 0.7586 (tttt) REVERT: C 73 MET cc_start: 0.6992 (tpp) cc_final: 0.6482 (tpp) REVERT: C 142 TRP cc_start: 0.8336 (OUTLIER) cc_final: 0.7110 (t-100) REVERT: C 160 MET cc_start: 0.8746 (mmt) cc_final: 0.8332 (tpt) REVERT: C 187 LYS cc_start: 0.8089 (mmtm) cc_final: 0.7390 (tppt) REVERT: C 328 GLN cc_start: 0.6505 (mm-40) cc_final: 0.5800 (mt0) REVERT: C 333 MET cc_start: 0.4483 (mtt) cc_final: 0.3883 (mtp) REVERT: C 532 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7945 (mm-30) REVERT: C 561 VAL cc_start: 0.8604 (OUTLIER) cc_final: 0.8205 (p) REVERT: H 71 GLU cc_start: 0.8056 (tt0) cc_final: 0.7689 (mm-30) REVERT: H 79 ASP cc_start: 0.7796 (t0) cc_final: 0.7269 (t0) REVERT: H 148 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8099 (ttp-170) REVERT: H 157 GLU cc_start: 0.9210 (OUTLIER) cc_final: 0.8818 (tm-30) REVERT: H 165 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8555 (mmm) REVERT: H 228 GLU cc_start: 0.8385 (tp30) cc_final: 0.8140 (tp30) REVERT: H 241 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8518 (tm-30) REVERT: H 286 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8291 (tpt90) REVERT: H 325 GLN cc_start: 0.6238 (mt0) cc_final: 0.5454 (pt0) REVERT: J 69 PHE cc_start: 0.9264 (OUTLIER) cc_final: 0.8998 (t80) REVERT: J 73 MET cc_start: 0.8768 (ptm) cc_final: 0.8561 (ttt) REVERT: K 99 ARG cc_start: 0.8553 (mmm160) cc_final: 0.8158 (mmm160) REVERT: M 303 TRP cc_start: 0.9365 (OUTLIER) cc_final: 0.8609 (m-10) REVERT: M 371 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8641 (mtm) REVERT: M 373 MET cc_start: 0.8649 (mpp) cc_final: 0.7914 (mtp) REVERT: M 460 MET cc_start: 0.8544 (ppp) cc_final: 0.8226 (pmm) REVERT: M 465 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8624 (mt) REVERT: A 67 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8830 (ptpt) REVERT: A 73 MET cc_start: 0.9184 (tmm) cc_final: 0.8767 (tmm) REVERT: L 3 MET cc_start: 0.7542 (mmt) cc_final: 0.7337 (mmm) REVERT: L 4 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8947 (tm) REVERT: L 119 TYR cc_start: 0.8848 (m-10) cc_final: 0.8459 (m-80) REVERT: L 139 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8783 (tpp) REVERT: L 143 TRP cc_start: 0.8781 (t-100) cc_final: 0.8573 (t-100) REVERT: L 146 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8682 (m) REVERT: L 216 MET cc_start: 0.8174 (pp-130) cc_final: 0.7822 (ppp) REVERT: L 233 LEU cc_start: 0.8584 (tt) cc_final: 0.8008 (mp) REVERT: L 305 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8013 (pptt) REVERT: L 319 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7774 (mpp) REVERT: L 430 PHE cc_start: 0.8429 (m-80) cc_final: 0.7287 (m-80) REVERT: L 436 VAL cc_start: 0.8995 (t) cc_final: 0.8754 (m) REVERT: L 460 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8353 (tp) REVERT: L 568 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8365 (tmm) REVERT: N 96 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8209 (mt-10) REVERT: N 150 LYS cc_start: 0.8835 (mmtm) cc_final: 0.8535 (mtpm) REVERT: N 197 MET cc_start: 0.7506 (ptm) cc_final: 0.7248 (ptm) REVERT: N 200 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7668 (tm-30) REVERT: N 371 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8127 (pt) outliers start: 130 outliers final: 57 residues processed: 505 average time/residue: 0.6293 time to fit residues: 395.5237 Evaluate side-chains 463 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 375 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 475 ASP Chi-restraints excluded: chain G residue 522 LEU Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 142 TRP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 532 GLU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 141 TYR Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain H residue 286 ARG Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain K residue 26 ARG Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 437 LEU Chi-restraints excluded: chain M residue 465 LEU Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 149 CYS Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 279 VAL Chi-restraints excluded: chain L residue 296 PHE Chi-restraints excluded: chain L residue 305 LYS Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 319 MET Chi-restraints excluded: chain L residue 460 LEU Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 371 ILE Chi-restraints excluded: chain N residue 457 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 9 optimal weight: 10.0000 chunk 252 optimal weight: 4.9990 chunk 198 optimal weight: 0.6980 chunk 372 optimal weight: 2.9990 chunk 442 optimal weight: 2.9990 chunk 357 optimal weight: 10.0000 chunk 446 optimal weight: 0.7980 chunk 167 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 221 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.090706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.066089 restraints weight = 104112.472| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.79 r_work: 0.2996 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 38708 Z= 0.136 Angle : 0.771 35.210 52436 Z= 0.306 Chirality : 0.042 0.242 5784 Planarity : 0.004 0.076 6512 Dihedral : 11.224 142.567 6041 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.33 % Allowed : 25.24 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.13), residues: 4663 helix: 1.77 (0.10), residues: 2573 sheet: 0.15 (0.31), residues: 305 loop : -0.41 (0.15), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG E 19 TYR 0.026 0.001 TYR L 428 PHE 0.047 0.001 PHE L 183 TRP 0.021 0.001 TRP C 376 HIS 0.006 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (38671) covalent geometry : angle 0.63534 / 0.30 (52340) hydrogen bonds : bond 0.03704 / 2.44 ( 2003) hydrogen bonds : angle 4.35963 / 3.09 ( 5705) metal coordination : bond 0.01259 / 0.76 ( 37) metal coordination : angle 10.22795 / 6.75 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 394 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 111 LYS cc_start: 0.9128 (mtmm) cc_final: 0.8808 (mtmt) REVERT: E 125 ARG cc_start: 0.8315 (ttt-90) cc_final: 0.8066 (ttt-90) REVERT: F 247 THR cc_start: 0.8410 (OUTLIER) cc_final: 0.7580 (t) REVERT: F 335 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8087 (ptp) REVERT: G 98 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8797 (mmt) REVERT: G 150 MET cc_start: 0.9012 (mmm) cc_final: 0.8698 (tpp) REVERT: G 319 SER cc_start: 0.8289 (p) cc_final: 0.8030 (m) REVERT: G 385 THR cc_start: 0.9172 (OUTLIER) cc_final: 0.8757 (t) REVERT: G 522 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9046 (mm) REVERT: G 533 MET cc_start: 0.9178 (mmm) cc_final: 0.8233 (mmm) REVERT: I 126 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8415 (mttt) REVERT: B 7 ARG cc_start: 0.7373 (mtm-85) cc_final: 0.6410 (mtm-85) REVERT: B 23 GLU cc_start: 0.8330 (pt0) cc_final: 0.7805 (pm20) REVERT: B 39 MET cc_start: 0.8265 (pmm) cc_final: 0.8012 (pmm) REVERT: B 50 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8612 (mtt180) REVERT: B 69 VAL cc_start: 0.8257 (OUTLIER) cc_final: 0.8039 (m) REVERT: B 92 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8647 (mp10) REVERT: B 174 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8504 (mp0) REVERT: B 178 LYS cc_start: 0.8066 (mtpt) cc_final: 0.7644 (tttt) REVERT: C 73 MET cc_start: 0.6983 (tpp) cc_final: 0.6458 (tpp) REVERT: C 142 TRP cc_start: 0.8211 (OUTLIER) cc_final: 0.7036 (t-100) REVERT: C 160 MET cc_start: 0.8700 (mmt) cc_final: 0.8301 (tpt) REVERT: C 187 LYS cc_start: 0.8086 (mmtm) cc_final: 0.7395 (tppt) REVERT: C 328 GLN cc_start: 0.6661 (mm-40) cc_final: 0.5894 (tt0) REVERT: C 333 MET cc_start: 0.4386 (mtt) cc_final: 0.3813 (mtp) REVERT: C 532 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7951 (mm-30) REVERT: C 543 ILE cc_start: 0.6035 (OUTLIER) cc_final: 0.5726 (mp) REVERT: C 561 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8230 (p) REVERT: H 71 GLU cc_start: 0.7988 (tt0) cc_final: 0.7551 (mm-30) REVERT: H 148 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8049 (ttp-170) REVERT: H 157 GLU cc_start: 0.9299 (OUTLIER) cc_final: 0.8877 (tm-30) REVERT: H 165 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8121 (mmm) REVERT: H 241 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8597 (tm-30) REVERT: H 286 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8286 (tpt90) REVERT: H 325 GLN cc_start: 0.6308 (mt0) cc_final: 0.5350 (pt0) REVERT: J 69 PHE cc_start: 0.9218 (OUTLIER) cc_final: 0.8964 (t80) REVERT: K 94 SER cc_start: 0.8822 (m) cc_final: 0.8340 (p) REVERT: K 99 ARG cc_start: 0.8567 (mmm160) cc_final: 0.8173 (mmm160) REVERT: M 303 TRP cc_start: 0.9335 (OUTLIER) cc_final: 0.8628 (m-10) REVERT: M 371 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8334 (mtm) REVERT: M 373 MET cc_start: 0.8618 (mpp) cc_final: 0.7852 (mtp) REVERT: M 374 MET cc_start: 0.8938 (mtt) cc_final: 0.8391 (ptp) REVERT: M 460 MET cc_start: 0.8525 (ppp) cc_final: 0.8239 (pmm) REVERT: M 465 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8670 (mt) REVERT: A 63 ARG cc_start: 0.5677 (tpp-160) cc_final: 0.5441 (tpm170) REVERT: A 67 LYS cc_start: 0.9161 (ptmt) cc_final: 0.8764 (ptpt) REVERT: A 73 MET cc_start: 0.9209 (tmm) cc_final: 0.8732 (tmm) REVERT: L 4 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8999 (tm) REVERT: L 119 TYR cc_start: 0.8847 (m-10) cc_final: 0.8482 (m-80) REVERT: L 127 MET cc_start: 0.9359 (tpp) cc_final: 0.9123 (tpt) REVERT: L 139 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8703 (tpp) REVERT: L 143 TRP cc_start: 0.8796 (t-100) cc_final: 0.8524 (t-100) REVERT: L 216 MET cc_start: 0.8122 (pp-130) cc_final: 0.7829 (ppp) REVERT: L 233 LEU cc_start: 0.8592 (tt) cc_final: 0.7996 (mp) REVERT: L 305 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7974 (pptt) REVERT: L 319 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7687 (mmt) REVERT: L 430 PHE cc_start: 0.8461 (m-80) cc_final: 0.7343 (m-80) REVERT: L 436 VAL cc_start: 0.9043 (t) cc_final: 0.8823 (m) REVERT: L 460 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8504 (tp) REVERT: L 568 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8415 (tmm) REVERT: N 6 GLN cc_start: 0.8030 (pm20) cc_final: 0.7802 (pp30) REVERT: N 96 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8120 (mt-10) REVERT: N 150 LYS cc_start: 0.8800 (mmtm) cc_final: 0.8477 (mtpm) REVERT: N 197 MET cc_start: 0.7480 (ptm) cc_final: 0.7209 (ptm) REVERT: N 200 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7606 (tm-30) REVERT: N 371 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.8059 (pt) outliers start: 128 outliers final: 64 residues processed: 483 average time/residue: 0.6345 time to fit residues: 380.8217 Evaluate side-chains 466 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 372 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain G residue 98 MET Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 355 LEU Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 405 GLU Chi-restraints excluded: chain G residue 475 ASP Chi-restraints excluded: chain G residue 522 LEU Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 790 THR Chi-restraints excluded: chain G residue 855 ASN Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 142 TRP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 532 GLU Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 141 TYR Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 286 ARG Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain K residue 26 ARG Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 465 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 149 CYS Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 305 LYS Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 319 MET Chi-restraints excluded: chain L residue 454 SER Chi-restraints excluded: chain L residue 460 LEU Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 371 ILE Chi-restraints excluded: chain N residue 430 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 238 optimal weight: 0.8980 chunk 340 optimal weight: 0.0570 chunk 235 optimal weight: 4.9990 chunk 242 optimal weight: 4.9990 chunk 424 optimal weight: 3.9990 chunk 234 optimal weight: 0.9980 chunk 157 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 257 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 247 optimal weight: 2.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 44 GLN ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN C 252 HIS M 159 HIS M 403 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.091008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.064969 restraints weight = 140891.772| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.20 r_work: 0.2973 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 38708 Z= 0.132 Angle : 0.785 35.068 52436 Z= 0.313 Chirality : 0.042 0.382 5784 Planarity : 0.004 0.079 6512 Dihedral : 11.118 140.907 6040 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.76 % Allowed : 25.87 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.13), residues: 4663 helix: 1.73 (0.10), residues: 2573 sheet: 0.07 (0.30), residues: 314 loop : -0.39 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG E 19 TYR 0.024 0.001 TYR C 414 PHE 0.045 0.001 PHE G 328 TRP 0.018 0.001 TRP C 376 HIS 0.006 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (38671) covalent geometry : angle 0.64863 / 0.31 (52340) hydrogen bonds : bond 0.03719 / 2.45 ( 2003) hydrogen bonds : angle 4.39318 / 3.12 ( 5705) metal coordination : bond 0.01178 / 0.72 ( 37) metal coordination : angle 10.33515 / 6.80 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 383 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 112 LYS cc_start: 0.8879 (tttt) cc_final: 0.8136 (mmmm) REVERT: F 247 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.7579 (t) REVERT: F 281 MET cc_start: 0.5341 (OUTLIER) cc_final: 0.4642 (mpp) REVERT: F 335 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8136 (ptp) REVERT: G 98 MET cc_start: 0.9252 (OUTLIER) cc_final: 0.8830 (mmt) REVERT: G 150 MET cc_start: 0.8997 (mmm) cc_final: 0.8701 (tpp) REVERT: G 319 SER cc_start: 0.8340 (p) cc_final: 0.8085 (m) REVERT: G 343 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8871 (mp) REVERT: G 385 THR cc_start: 0.9153 (OUTLIER) cc_final: 0.8765 (t) REVERT: G 522 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9087 (mm) REVERT: G 533 MET cc_start: 0.9188 (mmm) cc_final: 0.8299 (mmm) REVERT: I 126 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8503 (mttt) REVERT: B 7 ARG cc_start: 0.7398 (mtm-85) cc_final: 0.6424 (mtm-85) REVERT: B 23 GLU cc_start: 0.8358 (pt0) cc_final: 0.7836 (pm20) REVERT: B 39 MET cc_start: 0.8277 (pmm) cc_final: 0.8014 (pmm) REVERT: B 50 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8637 (mtt180) REVERT: B 92 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8593 (pm20) REVERT: B 106 MET cc_start: 0.8066 (mtp) cc_final: 0.7826 (ttm) REVERT: B 174 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8556 (mp0) REVERT: B 178 LYS cc_start: 0.8171 (mtpt) cc_final: 0.7614 (tttt) REVERT: C 73 MET cc_start: 0.6995 (tpp) cc_final: 0.6475 (tpp) REVERT: C 142 TRP cc_start: 0.8308 (OUTLIER) cc_final: 0.7108 (t-100) REVERT: C 160 MET cc_start: 0.8730 (mmt) cc_final: 0.8349 (tpt) REVERT: C 187 LYS cc_start: 0.8097 (mmtm) cc_final: 0.7410 (tppt) REVERT: C 328 GLN cc_start: 0.6697 (mm-40) cc_final: 0.5900 (tt0) REVERT: C 333 MET cc_start: 0.4284 (mtt) cc_final: 0.3696 (mtp) REVERT: C 356 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8298 (t80) REVERT: C 532 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7968 (mm-30) REVERT: C 543 ILE cc_start: 0.6084 (OUTLIER) cc_final: 0.5764 (mp) REVERT: C 561 VAL cc_start: 0.8608 (OUTLIER) cc_final: 0.8138 (p) REVERT: H 71 GLU cc_start: 0.8042 (tt0) cc_final: 0.7653 (mm-30) REVERT: H 148 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8024 (ttp-170) REVERT: H 157 GLU cc_start: 0.9245 (OUTLIER) cc_final: 0.8864 (tm-30) REVERT: H 165 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8121 (mmm) REVERT: H 209 ARG cc_start: 0.7989 (mmm-85) cc_final: 0.7570 (mmm-85) REVERT: H 228 GLU cc_start: 0.8319 (tp30) cc_final: 0.7756 (tm-30) REVERT: H 241 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8622 (tm-30) REVERT: H 286 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8300 (tpt90) REVERT: H 325 GLN cc_start: 0.6330 (mt0) cc_final: 0.5359 (pt0) REVERT: J 69 PHE cc_start: 0.9252 (OUTLIER) cc_final: 0.9011 (t80) REVERT: K 94 SER cc_start: 0.8849 (m) cc_final: 0.8389 (p) REVERT: K 99 ARG cc_start: 0.8582 (mmm160) cc_final: 0.8267 (mmm160) REVERT: M 303 TRP cc_start: 0.9370 (OUTLIER) cc_final: 0.8548 (m-10) REVERT: M 371 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8337 (mtm) REVERT: M 373 MET cc_start: 0.8611 (mpp) cc_final: 0.7865 (mtp) REVERT: M 374 MET cc_start: 0.8899 (mtt) cc_final: 0.8399 (ptp) REVERT: M 460 MET cc_start: 0.8543 (ppp) cc_final: 0.8300 (pmm) REVERT: M 465 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8659 (mt) REVERT: A 67 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8832 (pttm) REVERT: A 73 MET cc_start: 0.9210 (tmm) cc_final: 0.8764 (tmm) REVERT: L 4 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9054 (tm) REVERT: L 216 MET cc_start: 0.8137 (pp-130) cc_final: 0.7800 (ppp) REVERT: L 233 LEU cc_start: 0.8611 (tt) cc_final: 0.8011 (mp) REVERT: L 305 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8013 (pptt) REVERT: L 319 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7511 (mmt) REVERT: L 436 VAL cc_start: 0.9015 (t) cc_final: 0.8814 (m) REVERT: L 460 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8511 (tp) REVERT: L 568 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8376 (tmm) REVERT: N 6 GLN cc_start: 0.8083 (pm20) cc_final: 0.7856 (pp30) REVERT: N 96 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8185 (mt-10) REVERT: N 150 LYS cc_start: 0.8825 (mmtm) cc_final: 0.8509 (mtpm) REVERT: N 197 MET cc_start: 0.7490 (ptm) cc_final: 0.7237 (ptm) REVERT: N 200 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7721 (tm-30) REVERT: N 371 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8094 (pt) outliers start: 106 outliers final: 58 residues processed: 459 average time/residue: 0.6335 time to fit residues: 360.8160 Evaluate side-chains 453 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 363 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain G residue 98 MET Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 405 GLU Chi-restraints excluded: chain G residue 522 LEU Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 790 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 142 TRP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 532 GLU Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 286 ARG Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain K residue 26 ARG Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 465 LEU Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 149 CYS Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 305 LYS Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 319 MET Chi-restraints excluded: chain L residue 460 LEU Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 371 ILE Chi-restraints excluded: chain N residue 430 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 155 optimal weight: 0.3980 chunk 370 optimal weight: 0.7980 chunk 438 optimal weight: 2.9990 chunk 420 optimal weight: 0.7980 chunk 215 optimal weight: 0.9990 chunk 232 optimal weight: 0.0470 chunk 17 optimal weight: 0.8980 chunk 357 optimal weight: 9.9990 chunk 383 optimal weight: 10.0000 chunk 76 optimal weight: 0.4980 chunk 121 optimal weight: 0.0020 overall best weight: 0.3486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.092264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.066517 restraints weight = 110865.742| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.02 r_work: 0.3018 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 38708 Z= 0.115 Angle : 0.779 33.245 52436 Z= 0.312 Chirality : 0.042 0.393 5784 Planarity : 0.004 0.081 6512 Dihedral : 10.861 139.120 6040 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.50 % Allowed : 26.33 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.13), residues: 4663 helix: 1.76 (0.10), residues: 2570 sheet: 0.17 (0.31), residues: 309 loop : -0.37 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG E 19 TYR 0.037 0.001 TYR L 428 PHE 0.056 0.001 PHE L 183 TRP 0.026 0.001 TRP L 143 HIS 0.007 0.001 HIS G 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (38671) covalent geometry : angle 0.65094 / 0.31 (52340) hydrogen bonds : bond 0.03541 / 2.33 ( 2003) hydrogen bonds : angle 4.36766 / 3.10 ( 5705) metal coordination : bond 0.00846 / 0.51 ( 37) metal coordination : angle 10.04202 / 6.69 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 409 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 111 LYS cc_start: 0.9169 (mtmm) cc_final: 0.8902 (mtmm) REVERT: E 112 LYS cc_start: 0.8833 (tttt) cc_final: 0.8168 (mmtp) REVERT: F 247 THR cc_start: 0.8379 (OUTLIER) cc_final: 0.7610 (t) REVERT: F 256 VAL cc_start: 0.5920 (OUTLIER) cc_final: 0.5595 (p) REVERT: F 335 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.8113 (ptp) REVERT: G 98 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8762 (mmt) REVERT: G 150 MET cc_start: 0.8893 (mmm) cc_final: 0.8623 (tpp) REVERT: G 319 SER cc_start: 0.8333 (p) cc_final: 0.8092 (m) REVERT: G 385 THR cc_start: 0.9147 (OUTLIER) cc_final: 0.8755 (t) REVERT: G 522 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9056 (mm) REVERT: G 533 MET cc_start: 0.9136 (mmm) cc_final: 0.8274 (mmm) REVERT: G 888 MET cc_start: 0.8868 (tpp) cc_final: 0.8660 (tpp) REVERT: I 126 LYS cc_start: 0.8675 (mtmm) cc_final: 0.8449 (mttt) REVERT: B 7 ARG cc_start: 0.7386 (mtm-85) cc_final: 0.6359 (mtm-85) REVERT: B 19 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7134 (tp) REVERT: B 23 GLU cc_start: 0.8322 (pt0) cc_final: 0.7803 (pm20) REVERT: B 39 MET cc_start: 0.8226 (pmm) cc_final: 0.7882 (pmm) REVERT: B 41 LYS cc_start: 0.8935 (mmmm) cc_final: 0.8072 (mtmt) REVERT: B 50 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8635 (mtt180) REVERT: B 92 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8625 (pm20) REVERT: B 119 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7771 (tm-30) REVERT: B 170 MET cc_start: 0.8676 (mmm) cc_final: 0.7682 (mtt) REVERT: B 174 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8514 (mp0) REVERT: B 178 LYS cc_start: 0.8088 (mtpt) cc_final: 0.7650 (tttt) REVERT: C 73 MET cc_start: 0.6951 (tpp) cc_final: 0.6398 (tpp) REVERT: C 142 TRP cc_start: 0.8318 (OUTLIER) cc_final: 0.7225 (t-100) REVERT: C 160 MET cc_start: 0.8729 (mmt) cc_final: 0.8361 (tpt) REVERT: C 187 LYS cc_start: 0.8118 (mmtm) cc_final: 0.7429 (tppt) REVERT: C 328 GLN cc_start: 0.6616 (mm-40) cc_final: 0.5857 (mt0) REVERT: C 333 MET cc_start: 0.4361 (mtt) cc_final: 0.3818 (mtp) REVERT: C 356 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.8088 (t80) REVERT: C 532 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7916 (mm-30) REVERT: C 561 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8127 (p) REVERT: H 71 GLU cc_start: 0.7925 (tt0) cc_final: 0.7580 (mm-30) REVERT: H 148 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7963 (ttp-170) REVERT: H 157 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.8837 (tm-30) REVERT: H 209 ARG cc_start: 0.8059 (mmm-85) cc_final: 0.7553 (mmm-85) REVERT: H 241 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8661 (tm-30) REVERT: H 286 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8311 (tpt90) REVERT: H 325 GLN cc_start: 0.6295 (mt0) cc_final: 0.5367 (pt0) REVERT: J 69 PHE cc_start: 0.9231 (OUTLIER) cc_final: 0.9010 (t80) REVERT: K 62 TYR cc_start: 0.9032 (t80) cc_final: 0.8787 (t80) REVERT: K 94 SER cc_start: 0.8749 (m) cc_final: 0.8281 (p) REVERT: K 99 ARG cc_start: 0.8571 (mmm160) cc_final: 0.8321 (mmm160) REVERT: M 123 ILE cc_start: 0.9301 (mt) cc_final: 0.9033 (mp) REVERT: M 303 TRP cc_start: 0.9352 (OUTLIER) cc_final: 0.8595 (m-10) REVERT: M 322 HIS cc_start: 0.8886 (m170) cc_final: 0.8651 (m170) REVERT: M 371 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8437 (mtm) REVERT: M 373 MET cc_start: 0.8600 (mpp) cc_final: 0.7840 (mtp) REVERT: M 374 MET cc_start: 0.8924 (mtt) cc_final: 0.8468 (ptp) REVERT: M 460 MET cc_start: 0.8521 (ppp) cc_final: 0.8320 (pmm) REVERT: M 465 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8623 (mt) REVERT: A 67 LYS cc_start: 0.9163 (ptmt) cc_final: 0.8816 (pttm) REVERT: A 73 MET cc_start: 0.9189 (tmm) cc_final: 0.8734 (tmm) REVERT: L 4 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.9003 (tm) REVERT: L 119 TYR cc_start: 0.8859 (m-10) cc_final: 0.8532 (m-80) REVERT: L 127 MET cc_start: 0.9314 (tpp) cc_final: 0.9035 (tpt) REVERT: L 216 MET cc_start: 0.8056 (pp-130) cc_final: 0.7723 (ppp) REVERT: L 233 LEU cc_start: 0.8566 (tt) cc_final: 0.7969 (mp) REVERT: L 305 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7957 (pptt) REVERT: L 319 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7608 (mmt) REVERT: L 460 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8561 (tp) REVERT: L 568 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8290 (tmm) REVERT: N 96 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8123 (mt-10) REVERT: N 150 LYS cc_start: 0.8757 (mmtm) cc_final: 0.8436 (mtpm) REVERT: N 197 MET cc_start: 0.7474 (ptm) cc_final: 0.7235 (ptm) REVERT: N 200 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7672 (tm-30) REVERT: N 321 MET cc_start: 0.8580 (ptp) cc_final: 0.8352 (pmm) REVERT: N 482 MET cc_start: 0.7270 (tpt) cc_final: 0.6953 (tpt) outliers start: 96 outliers final: 49 residues processed: 478 average time/residue: 0.6264 time to fit residues: 372.3126 Evaluate side-chains 457 residues out of total 3841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 381 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain G residue 98 MET Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 355 LEU Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 522 LEU Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain G residue 790 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 142 TRP Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 532 GLU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain H residue 286 ARG Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain K residue 26 ARG Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 465 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 305 LYS Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 319 MET Chi-restraints excluded: chain L residue 460 LEU Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 430 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 65 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 288 optimal weight: 0.7980 chunk 237 optimal weight: 0.9990 chunk 247 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 340 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 64 optimal weight: 0.3980 chunk 407 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN C 328 GLN H 170 GLN ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 403 ASN ** L 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.090915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.066052 restraints weight = 139475.443| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.24 r_work: 0.2979 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 38708 Z= 0.138 Angle : 0.804 34.961 52436 Z= 0.322 Chirality : 0.042 0.401 5784 Planarity : 0.004 0.084 6512 Dihedral : 10.845 138.142 6040 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.42 % Allowed : 26.65 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.13), residues: 4663 helix: 1.71 (0.10), residues: 2577 sheet: 0.27 (0.31), residues: 301 loop : -0.35 (0.15), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG E 19 TYR 0.020 0.001 TYR M 435 PHE 0.053 0.001 PHE G 328 TRP 0.021 0.001 TRP L 143 HIS 0.012 0.001 HIS N 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (38671) covalent geometry : angle 0.66999 / 0.32 (52340) hydrogen bonds : bond 0.03705 / 2.43 ( 2003) hydrogen bonds : angle 4.42415 / 3.14 ( 5705) metal coordination : bond 0.01228 / 0.74 ( 37) metal coordination : angle 10.39017 / 6.85 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16148.74 seconds wall clock time: 275 minutes 9.01 seconds (16509.01 seconds total)