Starting phenix.real_space_refine on Sat Jul 4 16:48:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9een_47959/07_2026/9een_47959.cif Found real_map, /net/cci-nas-00/data/ceres_data/9een_47959/07_2026/9een_47959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9een_47959/07_2026/9een_47959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9een_47959/07_2026/9een_47959.map" model { file = "/net/cci-nas-00/data/ceres_data/9een_47959/07_2026/9een_47959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9een_47959/07_2026/9een_47959.cif" } resolution = 3.85 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= 0.000 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 Zn 6 6.06 5 P 42 5.49 5 Mg 6 5.21 5 S 84 5.16 5 C 13488 2.51 5 N 3768 2.21 5 O 4212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.02s 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: 21606 Number of models: 1 Model: "" Number of chains: 24 Chain: "L" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1118 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 135} Chain: "H" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1118 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 135} Chain: "J" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1118 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 135} Chain: "D" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1118 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 135} Chain: "E" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1118 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 135} Chain: "I" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1118 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 135} Chain: "A" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2415 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 297} Chain: "B" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2415 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 297} Chain: "C" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2415 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 297} Chain: "F" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2415 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 297} Chain: "G" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2415 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 297} Chain: "K" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2415 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 297} Chain: "L" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 1, ' ZN': 1, 'CTP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 1, ' ZN': 1, 'CTP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 1, ' ZN': 1, 'CTP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 1, ' ZN': 1, 'CTP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 1, ' ZN': 1, 'CTP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 1, ' ZN': 1, 'CTP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {' CP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {' CP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {' CP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {' CP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {' CP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {' CP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 777 SG CYS L 109 102.345 59.902 50.069 1.00134.08 S ATOM 812 SG CYS L 114 99.980 57.734 48.411 1.00139.61 S ATOM 993 SG CYS L 138 103.555 59.002 46.597 1.00143.00 S ATOM 1020 SG CYS L 141 100.386 61.121 47.034 1.00142.59 S ATOM 1895 SG CYS H 109 79.339 90.171 65.525 1.00111.72 S ATOM 1930 SG CYS H 114 77.473 87.568 67.510 1.00121.54 S ATOM 2111 SG CYS H 138 79.570 90.417 69.428 1.00116.95 S ATOM 2138 SG CYS H 141 81.197 87.595 67.657 1.00116.56 S ATOM 3013 SG CYS J 109 91.597 36.419 65.309 1.00121.46 S ATOM 3048 SG CYS J 114 91.304 39.809 67.079 1.00122.30 S ATOM 3229 SG CYS J 138 92.113 36.477 69.216 1.00112.38 S ATOM 3256 SG CYS J 141 88.756 37.145 67.740 1.00117.97 S ATOM 4131 SG CYS D 109 55.074 87.179 49.164 1.00121.41 S ATOM 4166 SG CYS D 114 58.189 86.177 47.211 1.00128.75 S ATOM 4347 SG CYS D 138 55.121 87.804 45.343 1.00125.69 S ATOM 4374 SG CYS D 141 55.029 84.287 46.628 1.00119.10 S ATOM 5249 SG CYS E 109 40.332 52.100 65.807 1.00127.15 S ATOM 5284 SG CYS E 114 43.305 51.227 68.095 1.00133.58 S ATOM 5465 SG CYS E 138 39.611 52.208 69.658 1.00113.92 S ATOM 5492 SG CYS E 141 41.695 54.875 68.070 1.00110.77 S ATOM 6367 SG CYS I 109 54.254 33.209 49.266 1.00116.65 S ATOM 6402 SG CYS I 114 53.855 36.042 46.909 1.00130.95 S ATOM 6583 SG CYS I 138 54.094 32.281 45.459 1.00119.66 S ATOM 6610 SG CYS I 141 57.012 34.211 46.880 1.00121.26 S Time building chain proxies: 5.37, per 1000 atoms: 0.25 Number of scatterers: 21606 At special positions: 0 Unit cell: (147.522, 141.108, 115.452, 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) Zn 6 29.99 S 84 16.00 P 42 15.00 Mg 6 11.99 O 4212 8.00 N 3768 7.00 C 13488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 933.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 141 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 114 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 138 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 109 " pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 141 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 109 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 138 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 114 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 141 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 109 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 114 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 138 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 141 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 109 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 138 " pdb=" ZN J 201 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 141 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 109 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 114 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 138 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 109 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 141 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 114 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 138 " Number of angles added : 36 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5184 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 26 sheets defined 42.1% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'L' and resid 25 through 34 removed outlier: 3.581A pdb=" N LYS L 34 " --> pdb=" O LEU L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 78 removed outlier: 3.512A pdb=" N VAL L 71 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU L 76 " --> pdb=" O ASP L 72 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR L 77 " --> pdb=" O GLN L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 119 removed outlier: 3.853A pdb=" N ALA L 118 " --> pdb=" O CYS L 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 153 removed outlier: 3.689A pdb=" N VAL L 150 " --> pdb=" O SER L 146 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN L 153 " --> pdb=" O VAL L 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 33 removed outlier: 3.636A pdb=" N PHE H 33 " --> pdb=" O LEU H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 78 removed outlier: 3.775A pdb=" N LEU H 76 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR H 77 " --> pdb=" O GLN H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 118 removed outlier: 3.972A pdb=" N HIS H 117 " --> pdb=" O CYS H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 153 removed outlier: 3.551A pdb=" N VAL H 150 " --> pdb=" O SER H 146 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN H 153 " --> pdb=" O VAL H 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 33 Processing helix chain 'J' and resid 67 through 78 removed outlier: 3.901A pdb=" N LEU J 76 " --> pdb=" O ASP J 72 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR J 77 " --> pdb=" O GLN J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 118 removed outlier: 3.616A pdb=" N HIS J 117 " --> pdb=" O CYS J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 153 Processing helix chain 'D' and resid 25 through 33 removed outlier: 3.616A pdb=" N LEU D 29 " --> pdb=" O ILE D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 78 removed outlier: 3.993A pdb=" N LEU D 76 " --> pdb=" O ASP D 72 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TYR D 77 " --> pdb=" O GLN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 118 Processing helix chain 'D' and resid 146 through 153 removed outlier: 3.573A pdb=" N VAL D 150 " --> pdb=" O SER D 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 32 Processing helix chain 'E' and resid 67 through 78 removed outlier: 3.672A pdb=" N LEU E 76 " --> pdb=" O ASP E 72 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR E 77 " --> pdb=" O GLN E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 118 removed outlier: 3.738A pdb=" N HIS E 117 " --> pdb=" O CYS E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 153 removed outlier: 3.748A pdb=" N ASN E 153 " --> pdb=" O VAL E 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 33 Processing helix chain 'I' and resid 67 through 78 removed outlier: 3.850A pdb=" N LEU I 76 " --> pdb=" O ASP I 72 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR I 77 " --> pdb=" O GLN I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 118 Processing helix chain 'I' and resid 147 through 153 Processing helix chain 'A' and resid 16 through 33 Processing helix chain 'A' and resid 53 through 66 Processing helix chain 'A' and resid 79 through 85 Processing helix chain 'A' and resid 87 through 97 removed outlier: 3.714A pdb=" N THR A 91 " --> pdb=" O THR A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 118 Processing helix chain 'A' and resid 134 through 150 Processing helix chain 'A' and resid 166 through 178 Processing helix chain 'A' and resid 189 through 193 removed outlier: 3.537A pdb=" N ALA A 193 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.612A pdb=" N LEU A 199 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 220 removed outlier: 3.943A pdb=" N VAL A 218 " --> pdb=" O SER A 214 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA A 220 " --> pdb=" O GLU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 245 removed outlier: 3.989A pdb=" N ALA A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.502A pdb=" N HIS A 255 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 280 Processing helix chain 'A' and resid 284 through 304 removed outlier: 3.792A pdb=" N ILE A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 33 Processing helix chain 'B' and resid 53 through 66 Processing helix chain 'B' and resid 79 through 85 Processing helix chain 'B' and resid 87 through 97 removed outlier: 3.715A pdb=" N THR B 91 " --> pdb=" O THR B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 118 Processing helix chain 'B' and resid 134 through 150 Processing helix chain 'B' and resid 166 through 178 Processing helix chain 'B' and resid 189 through 193 removed outlier: 3.537A pdb=" N ALA B 193 " --> pdb=" O ASP B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 removed outlier: 3.610A pdb=" N LEU B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 220 removed outlier: 3.943A pdb=" N VAL B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 245 removed outlier: 3.989A pdb=" N ALA B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 removed outlier: 3.502A pdb=" N HIS B 255 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 280 Processing helix chain 'B' and resid 284 through 304 removed outlier: 3.791A pdb=" N ILE B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 33 Processing helix chain 'C' and resid 53 through 66 Processing helix chain 'C' and resid 79 through 85 Processing helix chain 'C' and resid 87 through 97 removed outlier: 3.713A pdb=" N THR C 91 " --> pdb=" O THR C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 118 Processing helix chain 'C' and resid 134 through 150 Processing helix chain 'C' and resid 166 through 178 Processing helix chain 'C' and resid 189 through 193 removed outlier: 3.538A pdb=" N ALA C 193 " --> pdb=" O ASP C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 removed outlier: 3.611A pdb=" N LEU C 199 " --> pdb=" O PRO C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 220 removed outlier: 3.943A pdb=" N VAL C 218 " --> pdb=" O SER C 214 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA C 220 " --> pdb=" O GLU C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 245 removed outlier: 3.989A pdb=" N ALA C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.501A pdb=" N HIS C 255 " --> pdb=" O SER C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 280 Processing helix chain 'C' and resid 284 through 304 removed outlier: 3.791A pdb=" N ILE C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE C 294 " --> pdb=" O GLY C 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 33 Processing helix chain 'F' and resid 53 through 66 Processing helix chain 'F' and resid 79 through 85 Processing helix chain 'F' and resid 87 through 97 removed outlier: 3.713A pdb=" N THR F 91 " --> pdb=" O THR F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 118 Processing helix chain 'F' and resid 134 through 150 Processing helix chain 'F' and resid 166 through 178 Processing helix chain 'F' and resid 189 through 193 removed outlier: 3.537A pdb=" N ALA F 193 " --> pdb=" O ASP F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 206 removed outlier: 3.609A pdb=" N LEU F 199 " --> pdb=" O PRO F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 220 removed outlier: 3.943A pdb=" N VAL F 218 " --> pdb=" O SER F 214 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA F 220 " --> pdb=" O GLU F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 245 removed outlier: 3.989A pdb=" N ALA F 245 " --> pdb=" O ALA F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 255 removed outlier: 3.503A pdb=" N HIS F 255 " --> pdb=" O SER F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 280 Processing helix chain 'F' and resid 284 through 304 removed outlier: 3.791A pdb=" N ILE F 293 " --> pdb=" O ALA F 289 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE F 294 " --> pdb=" O GLY F 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 33 Processing helix chain 'G' and resid 53 through 66 Processing helix chain 'G' and resid 79 through 85 Processing helix chain 'G' and resid 87 through 97 removed outlier: 3.715A pdb=" N THR G 91 " --> pdb=" O THR G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 118 Processing helix chain 'G' and resid 134 through 150 Processing helix chain 'G' and resid 166 through 178 Processing helix chain 'G' and resid 189 through 193 removed outlier: 3.537A pdb=" N ALA G 193 " --> pdb=" O ASP G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 removed outlier: 3.612A pdb=" N LEU G 199 " --> pdb=" O PRO G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 220 removed outlier: 3.943A pdb=" N VAL G 218 " --> pdb=" O SER G 214 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA G 220 " --> pdb=" O GLU G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 236 through 245 removed outlier: 3.990A pdb=" N ALA G 245 " --> pdb=" O ALA G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 255 removed outlier: 3.501A pdb=" N HIS G 255 " --> pdb=" O SER G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 274 through 280 Processing helix chain 'G' and resid 284 through 304 removed outlier: 3.792A pdb=" N ILE G 293 " --> pdb=" O ALA G 289 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE G 294 " --> pdb=" O GLY G 290 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 33 Processing helix chain 'K' and resid 53 through 66 Processing helix chain 'K' and resid 79 through 85 Processing helix chain 'K' and resid 87 through 97 removed outlier: 3.714A pdb=" N THR K 91 " --> pdb=" O THR K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 118 Processing helix chain 'K' and resid 134 through 150 Processing helix chain 'K' and resid 166 through 178 Processing helix chain 'K' and resid 189 through 193 removed outlier: 3.537A pdb=" N ALA K 193 " --> pdb=" O ASP K 190 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 206 removed outlier: 3.610A pdb=" N LEU K 199 " --> pdb=" O PRO K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 214 through 220 removed outlier: 3.944A pdb=" N VAL K 218 " --> pdb=" O SER K 214 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA K 220 " --> pdb=" O GLU K 216 " (cutoff:3.500A) Processing helix chain 'K' and resid 236 through 245 removed outlier: 3.990A pdb=" N ALA K 245 " --> pdb=" O ALA K 241 " (cutoff:3.500A) Processing helix chain 'K' and resid 250 through 255 removed outlier: 3.502A pdb=" N HIS K 255 " --> pdb=" O SER K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 274 through 280 Processing helix chain 'K' and resid 284 through 304 removed outlier: 3.791A pdb=" N ILE K 293 " --> pdb=" O ALA K 289 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE K 294 " --> pdb=" O GLY K 290 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 42 through 49 removed outlier: 3.633A pdb=" N ASN L 47 " --> pdb=" O LYS L 56 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LYS L 56 " --> pdb=" O ASN L 47 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ASP L 57 " --> pdb=" O HIS L 20 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N HIS L 20 " --> pdb=" O ASP L 57 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP L 19 " --> pdb=" O THR L 82 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ARG L 85 " --> pdb=" O VAL L 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 103 through 104 removed outlier: 3.781A pdb=" N ILE L 103 " --> pdb=" O PHE L 125 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP L 133 " --> pdb=" O ARG L 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 48 through 50 removed outlier: 6.779A pdb=" N ASP H 57 " --> pdb=" O HIS H 20 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N HIS H 20 " --> pdb=" O ASP H 57 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ARG H 85 " --> pdb=" O VAL H 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 42 through 44 removed outlier: 5.146A pdb=" N ILE D 44 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LYS D 60 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU D 46 " --> pdb=" O LEU D 58 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N LEU D 58 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ASP D 57 " --> pdb=" O HIS D 20 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N HIS D 20 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY D 15 " --> pdb=" O ILE D 86 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG D 85 " --> pdb=" O VAL D 92 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 103 through 104 removed outlier: 3.631A pdb=" N ALA H 126 " --> pdb=" O LYS H 137 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 42 through 44 removed outlier: 4.572A pdb=" N GLY J 15 " --> pdb=" O ILE J 86 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG J 85 " --> pdb=" O VAL J 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 48 through 50 Processing sheet with id=AA8, first strand: chain 'J' and resid 126 through 130 removed outlier: 3.571A pdb=" N LYS J 143 " --> pdb=" O CYS J 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 103 through 104 removed outlier: 3.530A pdb=" N ILE D 103 " --> pdb=" O PHE D 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 42 through 44 Processing sheet with id=AB2, first strand: chain 'E' and resid 42 through 44 removed outlier: 6.289A pdb=" N ASP E 57 " --> pdb=" O HIS E 20 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N HIS E 20 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ASP E 87 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N VAL E 91 " --> pdb=" O ASP E 87 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 103 through 104 removed outlier: 3.845A pdb=" N ILE E 103 " --> pdb=" O PHE E 125 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE E 125 " --> pdb=" O ILE E 103 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 43 through 49 removed outlier: 5.873A pdb=" N LYS I 56 " --> pdb=" O ASN I 47 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ASP I 57 " --> pdb=" O HIS I 20 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N HIS I 20 " --> pdb=" O ASP I 57 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY I 15 " --> pdb=" O ILE I 86 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP I 19 " --> pdb=" O THR I 82 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG I 85 " --> pdb=" O VAL I 92 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 103 through 104 Processing sheet with id=AB6, first strand: chain 'A' and resid 69 through 73 removed outlier: 3.688A pdb=" N ALA A 101 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG A 105 " --> pdb=" O CYS A 47 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE A 102 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 209 through 212 removed outlier: 6.902A pdb=" N VAL A 157 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE A 187 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N MET A 159 " --> pdb=" O ILE A 187 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N HIS A 156 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N TYR A 226 " --> pdb=" O HIS A 156 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ALA A 158 " --> pdb=" O TYR A 226 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU A 225 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 69 through 73 removed outlier: 3.687A pdb=" N ALA B 101 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG B 105 " --> pdb=" O CYS B 47 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE B 102 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 209 through 212 removed outlier: 6.902A pdb=" N VAL B 157 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE B 187 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N MET B 159 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N HIS B 156 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N TYR B 226 " --> pdb=" O HIS B 156 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA B 158 " --> pdb=" O TYR B 226 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 225 " --> pdb=" O LEU B 264 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 69 through 73 removed outlier: 3.687A pdb=" N ALA C 101 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG C 105 " --> pdb=" O CYS C 47 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE C 102 " --> pdb=" O LEU C 125 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 209 through 212 removed outlier: 6.902A pdb=" N VAL C 157 " --> pdb=" O TYR C 185 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE C 187 " --> pdb=" O VAL C 157 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N MET C 159 " --> pdb=" O ILE C 187 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N HIS C 156 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N TYR C 226 " --> pdb=" O HIS C 156 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ALA C 158 " --> pdb=" O TYR C 226 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU C 225 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 69 through 73 removed outlier: 3.687A pdb=" N ALA F 101 " --> pdb=" O VAL F 43 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG F 105 " --> pdb=" O CYS F 47 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE F 102 " --> pdb=" O LEU F 125 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 209 through 212 removed outlier: 6.902A pdb=" N VAL F 157 " --> pdb=" O TYR F 185 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE F 187 " --> pdb=" O VAL F 157 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N MET F 159 " --> pdb=" O ILE F 187 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N HIS F 156 " --> pdb=" O ILE F 224 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N TYR F 226 " --> pdb=" O HIS F 156 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA F 158 " --> pdb=" O TYR F 226 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU F 225 " --> pdb=" O LEU F 264 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 69 through 73 removed outlier: 3.687A pdb=" N ALA G 101 " --> pdb=" O VAL G 43 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG G 105 " --> pdb=" O CYS G 47 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE G 102 " --> pdb=" O LEU G 125 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 209 through 212 removed outlier: 6.901A pdb=" N VAL G 157 " --> pdb=" O TYR G 185 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE G 187 " --> pdb=" O VAL G 157 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N MET G 159 " --> pdb=" O ILE G 187 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N HIS G 156 " --> pdb=" O ILE G 224 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N TYR G 226 " --> pdb=" O HIS G 156 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ALA G 158 " --> pdb=" O TYR G 226 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU G 225 " --> pdb=" O LEU G 264 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 69 through 73 removed outlier: 3.687A pdb=" N ALA K 101 " --> pdb=" O VAL K 43 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG K 105 " --> pdb=" O CYS K 47 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE K 102 " --> pdb=" O LEU K 125 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 209 through 212 removed outlier: 6.902A pdb=" N VAL K 157 " --> pdb=" O TYR K 185 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE K 187 " --> pdb=" O VAL K 157 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N MET K 159 " --> pdb=" O ILE K 187 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N HIS K 156 " --> pdb=" O ILE K 224 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N TYR K 226 " --> pdb=" O HIS K 156 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ALA K 158 " --> pdb=" O TYR K 226 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU K 225 " --> pdb=" O LEU K 264 " (cutoff:3.500A) 870 hydrogen bonds defined for protein. 2367 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: 3.45 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7057 1.34 - 1.46: 3410 1.46 - 1.58: 11307 1.58 - 1.70: 66 1.70 - 1.82: 138 Bond restraints: 21978 Sorted by residual: bond pdb=" O4P CP G 401 " pdb=" P CP G 401 " ideal model delta sigma weight residual 1.810 1.627 0.183 2.00e-02 2.50e+03 8.35e+01 bond pdb=" O4P CP K 401 " pdb=" P CP K 401 " ideal model delta sigma weight residual 1.810 1.628 0.182 2.00e-02 2.50e+03 8.32e+01 bond pdb=" O4P CP B 401 " pdb=" P CP B 401 " ideal model delta sigma weight residual 1.810 1.628 0.182 2.00e-02 2.50e+03 8.31e+01 bond pdb=" O4P CP F 401 " pdb=" P CP F 401 " ideal model delta sigma weight residual 1.810 1.628 0.182 2.00e-02 2.50e+03 8.30e+01 bond pdb=" O4P CP A 401 " pdb=" P CP A 401 " ideal model delta sigma weight residual 1.810 1.628 0.182 2.00e-02 2.50e+03 8.29e+01 ... (remaining 21973 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 29622 3.01 - 6.01: 240 6.01 - 9.02: 6 9.02 - 12.03: 6 12.03 - 15.03: 12 Bond angle restraints: 29886 Sorted by residual: angle pdb=" PB CTP D 203 " pdb=" O3B CTP D 203 " pdb=" PG CTP D 203 " ideal model delta sigma weight residual 125.56 140.59 -15.03 3.00e+00 1.11e-01 2.51e+01 angle pdb=" PB CTP E 202 " pdb=" O3B CTP E 202 " pdb=" PG CTP E 202 " ideal model delta sigma weight residual 125.56 140.24 -14.68 3.00e+00 1.11e-01 2.40e+01 angle pdb=" PB CTP L 203 " pdb=" O3B CTP L 203 " pdb=" PG CTP L 203 " ideal model delta sigma weight residual 125.56 140.23 -14.67 3.00e+00 1.11e-01 2.39e+01 angle pdb=" PB CTP H 202 " pdb=" O3B CTP H 202 " pdb=" PG CTP H 202 " ideal model delta sigma weight residual 125.56 140.23 -14.67 3.00e+00 1.11e-01 2.39e+01 angle pdb=" PB CTP I 203 " pdb=" O3B CTP I 203 " pdb=" PG CTP I 203 " ideal model delta sigma weight residual 125.56 140.15 -14.59 3.00e+00 1.11e-01 2.37e+01 ... (remaining 29881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 11999 17.93 - 35.87: 1220 35.87 - 53.80: 383 53.80 - 71.73: 69 71.73 - 89.67: 15 Dihedral angle restraints: 13686 sinusoidal: 5730 harmonic: 7956 Sorted by residual: dihedral pdb=" CA LEU C 267 " pdb=" C LEU C 267 " pdb=" N PRO C 268 " pdb=" CA PRO C 268 " ideal model delta harmonic sigma weight residual 180.00 143.78 36.22 0 5.00e+00 4.00e-02 5.25e+01 dihedral pdb=" CA LEU G 267 " pdb=" C LEU G 267 " pdb=" N PRO G 268 " pdb=" CA PRO G 268 " ideal model delta harmonic sigma weight residual 180.00 143.80 36.20 0 5.00e+00 4.00e-02 5.24e+01 dihedral pdb=" CA LEU B 267 " pdb=" C LEU B 267 " pdb=" N PRO B 268 " pdb=" CA PRO B 268 " ideal model delta harmonic sigma weight residual 180.00 143.82 36.18 0 5.00e+00 4.00e-02 5.23e+01 ... (remaining 13683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2503 0.040 - 0.079: 625 0.079 - 0.119: 299 0.119 - 0.159: 15 0.159 - 0.198: 14 Chirality restraints: 3456 Sorted by residual: chirality pdb=" CA ILE J 21 " pdb=" N ILE J 21 " pdb=" C ILE J 21 " pdb=" CB ILE J 21 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.82e-01 chirality pdb=" CA LEU J 29 " pdb=" N LEU J 29 " pdb=" C LEU J 29 " pdb=" CB LEU J 29 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.73e-01 chirality pdb=" CA LEU E 29 " pdb=" N LEU E 29 " pdb=" C LEU E 29 " pdb=" CB LEU E 29 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.34e-01 ... (remaining 3453 not shown) Planarity restraints: 3828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F 267 " 0.050 5.00e-02 4.00e+02 7.68e-02 9.44e+00 pdb=" N PRO F 268 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO F 268 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO F 268 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 267 " -0.050 5.00e-02 4.00e+02 7.68e-02 9.43e+00 pdb=" N PRO A 268 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 268 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 268 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU K 267 " -0.050 5.00e-02 4.00e+02 7.68e-02 9.43e+00 pdb=" N PRO K 268 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO K 268 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO K 268 " -0.042 5.00e-02 4.00e+02 ... (remaining 3825 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 307 2.63 - 3.20: 20059 3.20 - 3.76: 33585 3.76 - 4.33: 45959 4.33 - 4.90: 74963 Nonbonded interactions: 174873 Sorted by model distance: nonbonded pdb=" O2B CTP I 202 " pdb="MG MG I 204 " model vdw 2.061 2.170 nonbonded pdb=" O2B CTP D 202 " pdb="MG MG D 204 " model vdw 2.062 2.170 nonbonded pdb=" O1G CTP E 203 " pdb="MG MG E 204 " model vdw 2.062 2.170 nonbonded pdb=" O2B CTP L 202 " pdb="MG MG L 204 " model vdw 2.065 2.170 nonbonded pdb=" O1G CTP E 202 " pdb="MG MG E 204 " model vdw 2.069 2.170 ... (remaining 174868 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'F' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 23.030 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.183 22002 Z= 0.311 Angle : 0.727 15.034 29922 Z= 0.347 Chirality : 0.043 0.198 3456 Planarity : 0.004 0.077 3828 Dihedral : 16.051 89.667 8502 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.16 % Favored : 96.70 % Rotamer: Outliers : 2.53 % Allowed : 17.57 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -0.21 (0.16), residues: 2694 helix: 0.80 (0.17), residues: 894 sheet: -0.18 (0.29), residues: 342 loop : -0.69 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 17 TYR 0.018 0.001 TYR B 197 PHE 0.013 0.001 PHE B 247 TRP 0.007 0.001 TRP B 209 HIS 0.003 0.001 HIS C 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.30 (21978) covalent geometry : angle 0.71439 / 0.35 (29886) hydrogen bonds : bond 0.18392 / 12.00 ( 868) hydrogen bonds : angle 8.44808 / 6.00 ( 2367) metal coordination : bond 0.06769 / 4.18 ( 24) metal coordination : angle 3.97108 / 2.41 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1550 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 1491 time to evaluate : 0.772 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: 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: 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: 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: 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: L 68 GLU cc_start: 0.8277 (tp30) cc_final: 0.7972 (tp30) REVERT: L 72 ASP cc_start: 0.7439 (m-30) cc_final: 0.6699 (m-30) REVERT: L 88 ASN cc_start: 0.7480 (m-40) cc_final: 0.6736 (m-40) REVERT: J 96 ARG cc_start: 0.7036 (mmm160) cc_final: 0.6493 (mmp80) REVERT: D 88 ASN cc_start: 0.8323 (m-40) cc_final: 0.7879 (m-40) REVERT: D 105 ASN cc_start: 0.7433 (OUTLIER) cc_final: 0.7192 (m-40) REVERT: D 122 SER cc_start: 0.7133 (m) cc_final: 0.6841 (m) REVERT: E 84 ASN cc_start: 0.7197 (m-40) cc_final: 0.6911 (m-40) REVERT: A 54 ARG cc_start: 0.8031 (mpp-170) cc_final: 0.7610 (mpp-170) REVERT: A 56 ARG cc_start: 0.8474 (ttp-110) cc_final: 0.8215 (ttt-90) REVERT: A 87 THR cc_start: 0.8443 (p) cc_final: 0.8217 (p) REVERT: A 160 VAL cc_start: 0.9209 (t) cc_final: 0.8208 (m) REVERT: A 198 ILE cc_start: 0.8931 (mm) cc_final: 0.8522 (mm) REVERT: A 227 MET cc_start: 0.7657 (mmm) cc_final: 0.7337 (mmm) REVERT: B 10 ILE cc_start: 0.8967 (mm) cc_final: 0.8699 (tt) REVERT: B 69 SER cc_start: 0.8916 (m) cc_final: 0.8580 (m) REVERT: B 160 VAL cc_start: 0.9054 (t) cc_final: 0.8030 (m) REVERT: B 187 ILE cc_start: 0.9251 (mp) cc_final: 0.8945 (tt) REVERT: B 227 MET cc_start: 0.7743 (mmm) cc_final: 0.7341 (mmm) REVERT: C 79 THR cc_start: 0.7987 (p) cc_final: 0.7720 (p) REVERT: C 134 HIS cc_start: 0.8225 (t-90) cc_final: 0.7801 (t-90) REVERT: C 212 HIS cc_start: 0.7639 (m-70) cc_final: 0.7412 (m90) REVERT: C 260 ASN cc_start: 0.7874 (p0) cc_final: 0.7534 (p0) REVERT: F 56 ARG cc_start: 0.8717 (ttp-110) cc_final: 0.8364 (tmm-80) REVERT: F 69 SER cc_start: 0.8905 (m) cc_final: 0.8681 (m) REVERT: F 134 HIS cc_start: 0.8215 (t-90) cc_final: 0.7154 (t-90) REVERT: F 160 VAL cc_start: 0.9309 (t) cc_final: 0.8479 (m) REVERT: F 187 ILE cc_start: 0.9330 (mp) cc_final: 0.8947 (tt) REVERT: F 202 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8285 (mt) REVERT: G 46 SER cc_start: 0.8096 (t) cc_final: 0.7756 (p) REVERT: G 79 THR cc_start: 0.8088 (p) cc_final: 0.7863 (p) REVERT: G 134 HIS cc_start: 0.8112 (t-90) cc_final: 0.7683 (t-90) REVERT: G 143 PHE cc_start: 0.7910 (t80) cc_final: 0.7620 (t80) REVERT: G 260 ASN cc_start: 0.7425 (p0) cc_final: 0.7088 (p0) REVERT: G 276 ASP cc_start: 0.8677 (p0) cc_final: 0.8468 (p0) REVERT: G 302 LEU cc_start: 0.8792 (tp) cc_final: 0.8506 (tp) REVERT: K 46 SER cc_start: 0.8059 (t) cc_final: 0.7639 (p) REVERT: K 48 PHE cc_start: 0.8045 (m-80) cc_final: 0.7659 (m-10) REVERT: K 79 THR cc_start: 0.7759 (p) cc_final: 0.7533 (p) REVERT: K 160 VAL cc_start: 0.9033 (t) cc_final: 0.8818 (t) REVERT: K 260 ASN cc_start: 0.7620 (p0) cc_final: 0.7338 (p0) REVERT: K 285 TYR cc_start: 0.7626 (p90) cc_final: 0.7245 (p90) REVERT: K 302 LEU cc_start: 0.8890 (tp) cc_final: 0.8595 (tp) outliers start: 59 outliers final: 20 residues processed: 1503 average time/residue: 0.1616 time to fit residues: 365.9159 Evaluate side-chains 1082 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 1060 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 96 ARG Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 125 PHE Chi-restraints excluded: chain L residue 140 TYR Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 28 LYS Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain F residue 202 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 84 ASN J 80 GLN ** J 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 HIS E 47 ASN ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 6 GLN A 170 HIS A 231 GLN B 6 GLN B 78 ASN ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 HIS ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 GLN C 6 GLN ** C 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN C 154 ASN C 182 ASN ** C 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN F 78 ASN ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 GLN G 6 GLN G 8 HIS G 41 HIS G 212 HIS ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN K 8 HIS K 41 HIS K 182 ASN ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.109574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.086795 restraints weight = 68998.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.089092 restraints weight = 50315.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.090855 restraints weight = 39569.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.092193 restraints weight = 32813.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.093234 restraints weight = 28338.382| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22002 Z= 0.165 Angle : 0.848 13.424 29922 Z= 0.404 Chirality : 0.052 0.272 3456 Planarity : 0.006 0.089 3828 Dihedral : 10.802 69.853 3452 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.71 % Favored : 95.17 % Rotamer: Outliers : 8.12 % Allowed : 25.90 % Favored : 65.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -0.44 (0.16), residues: 2694 helix: 0.39 (0.16), residues: 912 sheet: -0.33 (0.25), residues: 390 loop : -0.67 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 56 TYR 0.030 0.002 TYR A 98 PHE 0.020 0.002 PHE F 294 TRP 0.019 0.002 TRP K 209 HIS 0.014 0.002 HIS I 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (21978) covalent geometry : angle 0.82976 / 0.40 (29886) hydrogen bonds : bond 0.04748 / 3.11 ( 868) hydrogen bonds : angle 6.70834 / 4.74 ( 2367) metal coordination : bond 0.00733 / 0.53 ( 24) metal coordination : angle 5.08572 / 3.27 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1363 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 1174 time to evaluate : 0.843 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: 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: 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: 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: symmetry clash REVERT: L 27 PHE cc_start: 0.9084 (t80) cc_final: 0.8857 (t80) REVERT: L 28 LYS cc_start: 0.9705 (ttmm) cc_final: 0.9479 (ttmm) REVERT: L 41 ARG cc_start: 0.8852 (mmm-85) cc_final: 0.8430 (tpp80) REVERT: L 68 GLU cc_start: 0.9504 (tp30) cc_final: 0.9090 (tp30) REVERT: L 70 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8793 (mp10) REVERT: L 72 ASP cc_start: 0.8979 (m-30) cc_final: 0.8413 (m-30) REVERT: L 104 ASP cc_start: 0.8146 (t0) cc_final: 0.7868 (t0) REVERT: L 145 PHE cc_start: 0.5891 (m-10) cc_final: 0.4926 (m-10) REVERT: H 145 PHE cc_start: 0.7854 (m-80) cc_final: 0.7583 (m-80) REVERT: J 72 ASP cc_start: 0.9480 (m-30) cc_final: 0.8889 (m-30) REVERT: J 90 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8797 (mm-30) REVERT: J 101 GLU cc_start: 0.7328 (mp0) cc_final: 0.6733 (mp0) REVERT: J 145 PHE cc_start: 0.8290 (m-80) cc_final: 0.7787 (m-80) REVERT: D 68 GLU cc_start: 0.9157 (tp30) cc_final: 0.8843 (tp30) REVERT: D 72 ASP cc_start: 0.8838 (m-30) cc_final: 0.8518 (m-30) REVERT: D 94 LYS cc_start: 0.8488 (mttt) cc_final: 0.8119 (mmtt) REVERT: D 103 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.8088 (mp) REVERT: D 104 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.6844 (m-30) REVERT: D 122 SER cc_start: 0.8575 (m) cc_final: 0.7750 (t) REVERT: E 90 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8791 (mm-30) REVERT: I 28 LYS cc_start: 0.9616 (ptpp) cc_final: 0.9339 (ptpp) REVERT: I 56 LYS cc_start: 0.7134 (mttt) cc_final: 0.6638 (mttt) REVERT: I 90 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8898 (mm-30) REVERT: I 144 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8527 (tp30) REVERT: A 39 LEU cc_start: 0.9355 (mm) cc_final: 0.9133 (mm) REVERT: A 48 PHE cc_start: 0.9685 (m-80) cc_final: 0.9198 (m-80) REVERT: A 50 GLU cc_start: 0.8802 (tp30) cc_final: 0.8453 (tp30) REVERT: A 59 PHE cc_start: 0.9413 (m-80) cc_final: 0.9062 (m-80) REVERT: A 65 ARG cc_start: 0.7470 (mtp180) cc_final: 0.6663 (mtp180) REVERT: A 104 MET cc_start: 0.9192 (ppp) cc_final: 0.8980 (ppp) REVERT: A 105 ARG cc_start: 0.8325 (ptp-170) cc_final: 0.7600 (ptp-170) REVERT: A 113 ARG cc_start: 0.9341 (mmm-85) cc_final: 0.9027 (tpp80) REVERT: A 160 VAL cc_start: 0.9098 (t) cc_final: 0.8211 (m) REVERT: A 164 LYS cc_start: 0.9523 (ptmm) cc_final: 0.9251 (ptmm) REVERT: A 174 GLN cc_start: 0.9009 (tm-30) cc_final: 0.8637 (tm-30) REVERT: A 204 GLU cc_start: 0.8690 (pp20) cc_final: 0.8393 (pp20) REVERT: A 212 HIS cc_start: 0.8679 (m-70) cc_final: 0.8402 (m-70) REVERT: A 227 MET cc_start: 0.9238 (mmm) cc_final: 0.8727 (mmm) REVERT: A 269 ARG cc_start: 0.9091 (ttp-170) cc_final: 0.8806 (tmm-80) REVERT: A 297 GLN cc_start: 0.8866 (tt0) cc_final: 0.8382 (tp40) REVERT: B 12 ILE cc_start: 0.9186 (pt) cc_final: 0.8941 (pt) REVERT: B 37 GLU cc_start: 0.8898 (pm20) cc_final: 0.8684 (pm20) REVERT: B 39 LEU cc_start: 0.9342 (tp) cc_final: 0.9078 (tp) REVERT: B 59 PHE cc_start: 0.9798 (m-80) cc_final: 0.9432 (m-80) REVERT: B 69 SER cc_start: 0.8567 (m) cc_final: 0.7904 (p) REVERT: B 74 SER cc_start: 0.8935 (p) cc_final: 0.8175 (p) REVERT: B 117 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8369 (mp0) REVERT: B 137 GLN cc_start: 0.9147 (tp-100) cc_final: 0.8379 (tp-100) REVERT: B 147 GLU cc_start: 0.9115 (tt0) cc_final: 0.8849 (tt0) REVERT: B 160 VAL cc_start: 0.9542 (t) cc_final: 0.8448 (m) REVERT: B 164 LYS cc_start: 0.9589 (ttmm) cc_final: 0.9163 (ttpt) REVERT: B 165 TYR cc_start: 0.8608 (m-10) cc_final: 0.8398 (m-10) REVERT: B 174 GLN cc_start: 0.9083 (tm-30) cc_final: 0.8660 (tm-30) REVERT: B 227 MET cc_start: 0.9303 (mmm) cc_final: 0.8570 (mmm) REVERT: B 272 GLU cc_start: 0.8581 (mp0) cc_final: 0.8350 (mp0) REVERT: B 297 GLN cc_start: 0.8861 (tt0) cc_final: 0.8487 (tp40) REVERT: C 48 PHE cc_start: 0.8685 (m-10) cc_final: 0.8382 (m-10) REVERT: C 56 ARG cc_start: 0.9290 (ttp-110) cc_final: 0.8672 (mtp-110) REVERT: C 73 PHE cc_start: 0.8229 (p90) cc_final: 0.7892 (p90) REVERT: C 104 MET cc_start: 0.9456 (tmm) cc_final: 0.9237 (tmm) REVERT: C 106 HIS cc_start: 0.9032 (t-90) cc_final: 0.8509 (t-90) REVERT: C 117 GLU cc_start: 0.8547 (tt0) cc_final: 0.8204 (tt0) REVERT: C 118 PHE cc_start: 0.9249 (m-10) cc_final: 0.8338 (m-80) REVERT: C 134 HIS cc_start: 0.8649 (t-90) cc_final: 0.8322 (t-90) REVERT: C 153 ASP cc_start: 0.9189 (OUTLIER) cc_final: 0.8541 (t0) REVERT: C 154 ASN cc_start: 0.9667 (m-40) cc_final: 0.9304 (p0) REVERT: C 167 ARG cc_start: 0.8738 (ptm-80) cc_final: 0.8450 (ptm-80) REVERT: C 201 MET cc_start: 0.9521 (tmm) cc_final: 0.9088 (tmm) REVERT: C 205 LYS cc_start: 0.9312 (mmmt) cc_final: 0.9039 (mmtm) REVERT: C 211 LEU cc_start: 0.9419 (tp) cc_final: 0.9096 (tt) REVERT: C 214 SER cc_start: 0.7016 (OUTLIER) cc_final: 0.6798 (t) REVERT: C 260 ASN cc_start: 0.8841 (p0) cc_final: 0.8317 (p0) REVERT: C 267 LEU cc_start: 0.9774 (mt) cc_final: 0.9496 (mt) REVERT: F 39 LEU cc_start: 0.9343 (mm) cc_final: 0.9094 (mm) REVERT: F 50 GLU cc_start: 0.8609 (tp30) cc_final: 0.8192 (tp30) REVERT: F 59 PHE cc_start: 0.9510 (m-80) cc_final: 0.9195 (m-80) REVERT: F 69 SER cc_start: 0.8309 (m) cc_final: 0.7776 (p) REVERT: F 106 HIS cc_start: 0.9146 (t-90) cc_final: 0.8944 (t-90) REVERT: F 147 GLU cc_start: 0.9151 (tt0) cc_final: 0.8760 (mt-10) REVERT: F 160 VAL cc_start: 0.9444 (t) cc_final: 0.8737 (m) REVERT: F 227 MET cc_start: 0.8773 (mmm) cc_final: 0.8286 (mmm) REVERT: F 297 GLN cc_start: 0.8712 (tt0) cc_final: 0.8369 (tp40) REVERT: G 48 PHE cc_start: 0.8977 (m-10) cc_final: 0.8673 (m-10) REVERT: G 49 PHE cc_start: 0.9623 (m-80) cc_final: 0.9216 (m-80) REVERT: G 59 PHE cc_start: 0.9834 (OUTLIER) cc_final: 0.9630 (m-80) REVERT: G 73 PHE cc_start: 0.8818 (p90) cc_final: 0.8433 (p90) REVERT: G 104 MET cc_start: 0.9488 (ppp) cc_final: 0.9283 (tmm) REVERT: G 118 PHE cc_start: 0.9266 (m-10) cc_final: 0.9000 (m-10) REVERT: G 134 HIS cc_start: 0.8539 (t-90) cc_final: 0.8242 (t-90) REVERT: G 142 LEU cc_start: 0.9241 (mm) cc_final: 0.8830 (mm) REVERT: G 143 PHE cc_start: 0.8527 (t80) cc_final: 0.8151 (t80) REVERT: G 152 LEU cc_start: 0.9494 (mt) cc_final: 0.9147 (mt) REVERT: G 153 ASP cc_start: 0.9317 (OUTLIER) cc_final: 0.8804 (t0) REVERT: G 154 ASN cc_start: 0.9626 (m-40) cc_final: 0.9325 (p0) REVERT: G 167 ARG cc_start: 0.8609 (ptm-80) cc_final: 0.8301 (ptm-80) REVERT: G 179 PHE cc_start: 0.9343 (m-80) cc_final: 0.8936 (t80) REVERT: G 204 GLU cc_start: 0.9444 (pt0) cc_final: 0.9020 (pt0) REVERT: G 260 ASN cc_start: 0.8716 (p0) cc_final: 0.8155 (p0) REVERT: G 267 LEU cc_start: 0.9769 (mt) cc_final: 0.9500 (mt) REVERT: G 273 ILE cc_start: 0.9445 (mm) cc_final: 0.9172 (mm) REVERT: G 296 ARG cc_start: 0.9015 (mtt90) cc_final: 0.8467 (mtt90) REVERT: G 302 LEU cc_start: 0.9673 (tp) cc_final: 0.9464 (tp) REVERT: K 59 PHE cc_start: 0.9747 (OUTLIER) cc_final: 0.9538 (m-10) REVERT: K 118 PHE cc_start: 0.9067 (m-10) cc_final: 0.8741 (m-10) REVERT: K 142 LEU cc_start: 0.9363 (mm) cc_final: 0.9087 (mm) REVERT: K 152 LEU cc_start: 0.9386 (mt) cc_final: 0.8913 (mt) REVERT: K 153 ASP cc_start: 0.9330 (OUTLIER) cc_final: 0.8850 (t0) REVERT: K 154 ASN cc_start: 0.9658 (m-40) cc_final: 0.9233 (p0) REVERT: K 167 ARG cc_start: 0.8642 (ptm-80) cc_final: 0.8360 (ptm-80) REVERT: K 179 PHE cc_start: 0.9293 (m-80) cc_final: 0.8788 (t80) REVERT: K 186 PHE cc_start: 0.9033 (m-80) cc_final: 0.8808 (m-80) REVERT: K 204 GLU cc_start: 0.9440 (pt0) cc_final: 0.9055 (pt0) REVERT: K 267 LEU cc_start: 0.9772 (mt) cc_final: 0.9482 (mt) REVERT: K 285 TYR cc_start: 0.8897 (p90) cc_final: 0.7524 (p90) REVERT: K 296 ARG cc_start: 0.9577 (mtt-85) cc_final: 0.9250 (mtt90) outliers start: 189 outliers final: 127 residues processed: 1231 average time/residue: 0.1491 time to fit residues: 281.7651 Evaluate side-chains 1180 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 1044 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 70 GLN Chi-restraints excluded: chain L residue 77 TYR Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 96 ARG Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 125 PHE Chi-restraints excluded: chain L residue 140 TYR Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 57 ASP Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 80 GLN Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 28 LYS Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 PHE Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 69 ASP Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 146 SER Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 170 HIS Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 250 ARG Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 174 GLN Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 231 GLN Chi-restraints excluded: chain F residue 250 ARG Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 40 LYS Chi-restraints excluded: chain G residue 59 PHE Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 207 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 228 THR Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 288 GLN Chi-restraints excluded: chain K residue 9 ILE Chi-restraints excluded: chain K residue 10 ILE Chi-restraints excluded: chain K residue 40 LYS Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 153 ASP Chi-restraints excluded: chain K residue 168 THR Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 174 GLN Chi-restraints excluded: chain K residue 228 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 100 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 85 optimal weight: 0.2980 chunk 25 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 249 optimal weight: 0.7980 chunk 156 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 143 optimal weight: 0.2980 chunk 204 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 73 GLN L 84 ASN H 70 GLN J 80 GLN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 ASN ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN A 78 ASN ** B 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN B 212 HIS B 231 GLN C 41 HIS ** C 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN ** F 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 ASN ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** G 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 8 HIS K 182 ASN ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.107897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.085100 restraints weight = 69093.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.087394 restraints weight = 50393.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.089163 restraints weight = 39626.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.090527 restraints weight = 32880.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.091576 restraints weight = 28342.063| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22002 Z= 0.154 Angle : 0.821 13.647 29922 Z= 0.387 Chirality : 0.050 0.287 3456 Planarity : 0.005 0.088 3828 Dihedral : 10.188 67.447 3440 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.12 % Favored : 95.77 % Rotamer: Outliers : 8.12 % Allowed : 29.21 % Favored : 62.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -0.60 (0.16), residues: 2694 helix: 0.32 (0.16), residues: 912 sheet: -0.47 (0.25), residues: 390 loop : -0.80 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 128 TYR 0.019 0.002 TYR F 98 PHE 0.028 0.002 PHE K 73 TRP 0.020 0.001 TRP C 284 HIS 0.012 0.002 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (21978) covalent geometry : angle 0.80050 / 0.39 (29886) hydrogen bonds : bond 0.04033 / 2.67 ( 868) hydrogen bonds : angle 6.34180 / 4.51 ( 2367) metal coordination : bond 0.00752 / 0.51 ( 24) metal coordination : angle 5.33625 / 3.41 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1310 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 1121 time to evaluate : 0.889 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: 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: 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: 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: L 28 LYS cc_start: 0.9725 (ttmm) cc_final: 0.9516 (ttmm) REVERT: L 41 ARG cc_start: 0.8809 (mmm-85) cc_final: 0.8395 (tpp80) REVERT: L 56 LYS cc_start: 0.6911 (mttt) cc_final: 0.4953 (mttt) REVERT: L 70 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8811 (mp10) REVERT: L 72 ASP cc_start: 0.8962 (m-30) cc_final: 0.8719 (m-30) REVERT: L 88 ASN cc_start: 0.8711 (m-40) cc_final: 0.8452 (m-40) REVERT: L 102 ARG cc_start: 0.8755 (tpp-160) cc_final: 0.8476 (tpp-160) REVERT: L 103 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8237 (mp) REVERT: L 145 PHE cc_start: 0.6518 (m-10) cc_final: 0.6155 (m-10) REVERT: H 24 GLN cc_start: 0.9442 (mm-40) cc_final: 0.9093 (mm-40) REVERT: H 40 GLN cc_start: 0.9236 (mp10) cc_final: 0.8951 (mp10) REVERT: H 41 ARG cc_start: 0.7187 (mmt180) cc_final: 0.6916 (mmt180) REVERT: H 90 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8802 (mm-30) REVERT: H 104 ASP cc_start: 0.8615 (m-30) cc_final: 0.8401 (m-30) REVERT: J 40 GLN cc_start: 0.9470 (mp10) cc_final: 0.9264 (mp10) REVERT: J 90 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8785 (mm-30) REVERT: D 25 ILE cc_start: 0.9480 (pt) cc_final: 0.9066 (pp) REVERT: D 28 LYS cc_start: 0.9546 (mtmm) cc_final: 0.9203 (mtmm) REVERT: D 41 ARG cc_start: 0.8714 (mmm160) cc_final: 0.8121 (mmm-85) REVERT: D 47 ASN cc_start: 0.8497 (t0) cc_final: 0.8089 (t0) REVERT: D 56 LYS cc_start: 0.6035 (mttt) cc_final: 0.5169 (mtpt) REVERT: D 68 GLU cc_start: 0.9197 (tp30) cc_final: 0.8864 (tp30) REVERT: D 72 ASP cc_start: 0.8893 (m-30) cc_final: 0.8522 (m-30) REVERT: D 94 LYS cc_start: 0.8524 (mttt) cc_final: 0.8151 (mmtt) REVERT: E 66 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8986 (tp) REVERT: E 72 ASP cc_start: 0.9460 (OUTLIER) cc_final: 0.9080 (t0) REVERT: E 90 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8847 (mm-30) REVERT: E 128 ARG cc_start: 0.8875 (mtm110) cc_final: 0.8673 (ttp80) REVERT: I 28 LYS cc_start: 0.9632 (ptpp) cc_final: 0.9336 (ptpp) REVERT: I 56 LYS cc_start: 0.7560 (mttt) cc_final: 0.6741 (mttt) REVERT: I 68 GLU cc_start: 0.9668 (tp30) cc_final: 0.9352 (tp30) REVERT: I 90 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8897 (mm-30) REVERT: I 144 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8445 (tp30) REVERT: A 31 LYS cc_start: 0.9291 (mmmm) cc_final: 0.9010 (mmmm) REVERT: A 39 LEU cc_start: 0.9380 (mm) cc_final: 0.9176 (mm) REVERT: A 59 PHE cc_start: 0.9513 (m-80) cc_final: 0.9074 (m-80) REVERT: A 66 LEU cc_start: 0.9337 (mt) cc_final: 0.8948 (mt) REVERT: A 74 SER cc_start: 0.8500 (p) cc_final: 0.8185 (p) REVERT: A 78 ASN cc_start: 0.8953 (OUTLIER) cc_final: 0.8497 (t0) REVERT: A 104 MET cc_start: 0.9360 (ppp) cc_final: 0.8931 (ppp) REVERT: A 113 ARG cc_start: 0.9357 (mmm-85) cc_final: 0.9150 (tpp80) REVERT: A 147 GLU cc_start: 0.9106 (tt0) cc_final: 0.8817 (pt0) REVERT: A 160 VAL cc_start: 0.9216 (t) cc_final: 0.8109 (p) REVERT: A 164 LYS cc_start: 0.9488 (ptmm) cc_final: 0.9071 (ptpt) REVERT: A 167 ARG cc_start: 0.9144 (ttp80) cc_final: 0.8864 (ttp-110) REVERT: A 174 GLN cc_start: 0.9253 (tm-30) cc_final: 0.8969 (tm-30) REVERT: A 198 ILE cc_start: 0.9595 (mm) cc_final: 0.9355 (mp) REVERT: A 212 HIS cc_start: 0.8729 (m-70) cc_final: 0.8517 (m-70) REVERT: A 227 MET cc_start: 0.9249 (mmm) cc_final: 0.8759 (mmm) REVERT: A 297 GLN cc_start: 0.8754 (tt0) cc_final: 0.8249 (tp40) REVERT: B 39 LEU cc_start: 0.9327 (tp) cc_final: 0.9000 (tp) REVERT: B 59 PHE cc_start: 0.9785 (m-80) cc_final: 0.9377 (m-80) REVERT: B 74 SER cc_start: 0.8631 (p) cc_final: 0.8233 (p) REVERT: B 137 GLN cc_start: 0.9180 (tp-100) cc_final: 0.8618 (tp-100) REVERT: B 141 ASP cc_start: 0.9426 (m-30) cc_final: 0.9139 (m-30) REVERT: B 147 GLU cc_start: 0.9193 (tt0) cc_final: 0.8955 (tt0) REVERT: B 157 VAL cc_start: 0.9644 (t) cc_final: 0.9350 (p) REVERT: B 160 VAL cc_start: 0.9350 (t) cc_final: 0.8110 (m) REVERT: B 174 GLN cc_start: 0.9165 (tm-30) cc_final: 0.8707 (tm-30) REVERT: B 196 GLN cc_start: 0.9556 (tp-100) cc_final: 0.9210 (tp-100) REVERT: B 200 ASP cc_start: 0.9520 (m-30) cc_final: 0.9234 (m-30) REVERT: B 227 MET cc_start: 0.9247 (mmm) cc_final: 0.8577 (mmm) REVERT: B 272 GLU cc_start: 0.8545 (mp0) cc_final: 0.8330 (mp0) REVERT: C 48 PHE cc_start: 0.8439 (m-10) cc_final: 0.7946 (m-10) REVERT: C 56 ARG cc_start: 0.9264 (ttp-110) cc_final: 0.8846 (mtp-110) REVERT: C 59 PHE cc_start: 0.9680 (OUTLIER) cc_final: 0.9346 (m-10) REVERT: C 73 PHE cc_start: 0.8381 (p90) cc_final: 0.7969 (p90) REVERT: C 104 MET cc_start: 0.9498 (tmm) cc_final: 0.9036 (tmm) REVERT: C 117 GLU cc_start: 0.8508 (tt0) cc_final: 0.7969 (tt0) REVERT: C 118 PHE cc_start: 0.9251 (m-10) cc_final: 0.8235 (m-10) REVERT: C 134 HIS cc_start: 0.8582 (t-90) cc_final: 0.8254 (t-90) REVERT: C 167 ARG cc_start: 0.8754 (ptm-80) cc_final: 0.8405 (ptm-80) REVERT: C 214 SER cc_start: 0.6886 (OUTLIER) cc_final: 0.6364 (t) REVERT: C 260 ASN cc_start: 0.9007 (p0) cc_final: 0.8374 (t0) REVERT: C 267 LEU cc_start: 0.9816 (mt) cc_final: 0.9572 (mt) REVERT: C 279 LYS cc_start: 0.8626 (mppt) cc_final: 0.8414 (mppt) REVERT: C 282 HIS cc_start: 0.8516 (m-70) cc_final: 0.8058 (m-70) REVERT: C 297 GLN cc_start: 0.9533 (tt0) cc_final: 0.9098 (tp40) REVERT: C 308 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.5936 (pp) REVERT: F 50 GLU cc_start: 0.8612 (tp30) cc_final: 0.8210 (tp30) REVERT: F 59 PHE cc_start: 0.9609 (m-80) cc_final: 0.9155 (m-80) REVERT: F 66 LEU cc_start: 0.9272 (mt) cc_final: 0.9033 (mt) REVERT: F 106 HIS cc_start: 0.9113 (t-90) cc_final: 0.8889 (t-90) REVERT: F 117 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8656 (mt-10) REVERT: F 131 SER cc_start: 0.9796 (t) cc_final: 0.9556 (p) REVERT: F 134 HIS cc_start: 0.9348 (t-90) cc_final: 0.8567 (t-90) REVERT: F 147 GLU cc_start: 0.9159 (tt0) cc_final: 0.8617 (pt0) REVERT: F 160 VAL cc_start: 0.9310 (t) cc_final: 0.8512 (m) REVERT: F 196 GLN cc_start: 0.9471 (tp-100) cc_final: 0.9051 (tp-100) REVERT: F 200 ASP cc_start: 0.9490 (m-30) cc_final: 0.9031 (m-30) REVERT: F 227 MET cc_start: 0.8805 (mmm) cc_final: 0.8299 (mmm) REVERT: F 240 TYR cc_start: 0.9434 (t80) cc_final: 0.9171 (t80) REVERT: F 297 GLN cc_start: 0.8825 (tt0) cc_final: 0.8436 (mt0) REVERT: G 48 PHE cc_start: 0.8871 (m-10) cc_final: 0.8475 (m-10) REVERT: G 49 PHE cc_start: 0.9670 (m-80) cc_final: 0.8958 (m-80) REVERT: G 50 GLU cc_start: 0.9314 (tp30) cc_final: 0.9098 (mt-10) REVERT: G 73 PHE cc_start: 0.8887 (p90) cc_final: 0.8455 (p90) REVERT: G 104 MET cc_start: 0.9493 (ppp) cc_final: 0.9264 (ppp) REVERT: G 117 GLU cc_start: 0.8449 (tt0) cc_final: 0.8186 (tt0) REVERT: G 134 HIS cc_start: 0.8449 (t-90) cc_final: 0.7996 (t-90) REVERT: G 142 LEU cc_start: 0.9298 (mm) cc_final: 0.9028 (mm) REVERT: G 146 GLN cc_start: 0.9290 (tp40) cc_final: 0.9019 (mm110) REVERT: G 154 ASN cc_start: 0.9592 (m-40) cc_final: 0.9263 (p0) REVERT: G 167 ARG cc_start: 0.8586 (ptm-80) cc_final: 0.8263 (ptm-80) REVERT: G 199 LEU cc_start: 0.9727 (OUTLIER) cc_final: 0.9300 (mt) REVERT: G 260 ASN cc_start: 0.8779 (p0) cc_final: 0.8290 (p0) REVERT: G 267 LEU cc_start: 0.9803 (mt) cc_final: 0.9562 (mt) REVERT: G 296 ARG cc_start: 0.8969 (mtt90) cc_final: 0.8307 (mtt90) REVERT: G 297 GLN cc_start: 0.9588 (tt0) cc_final: 0.9220 (tp40) REVERT: K 56 ARG cc_start: 0.9355 (ttp-110) cc_final: 0.8627 (mtp-110) REVERT: K 118 PHE cc_start: 0.9135 (m-10) cc_final: 0.8912 (m-10) REVERT: K 133 GLN cc_start: 0.8942 (pt0) cc_final: 0.8700 (pt0) REVERT: K 142 LEU cc_start: 0.9337 (mm) cc_final: 0.8983 (mm) REVERT: K 154 ASN cc_start: 0.9632 (m-40) cc_final: 0.9281 (p0) REVERT: K 167 ARG cc_start: 0.8513 (ptm-80) cc_final: 0.8134 (ptm-80) REVERT: K 187 ILE cc_start: 0.9440 (mp) cc_final: 0.9153 (mp) REVERT: K 199 LEU cc_start: 0.9728 (OUTLIER) cc_final: 0.9329 (mt) REVERT: K 249 LEU cc_start: 0.9333 (tp) cc_final: 0.9032 (mm) REVERT: K 250 ARG cc_start: 0.9481 (ptm-80) cc_final: 0.9263 (mtm110) REVERT: K 267 LEU cc_start: 0.9786 (mt) cc_final: 0.9568 (mt) REVERT: K 296 ARG cc_start: 0.9573 (mtt-85) cc_final: 0.9049 (mtt90) REVERT: K 297 GLN cc_start: 0.9590 (tp40) cc_final: 0.9011 (tp40) outliers start: 189 outliers final: 129 residues processed: 1180 average time/residue: 0.1454 time to fit residues: 265.0000 Evaluate side-chains 1195 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 1056 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 70 GLN Chi-restraints excluded: chain L residue 77 TYR Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 125 PHE Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 57 ASP Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 80 GLN Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 125 PHE Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 PHE Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 69 ASP Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 146 SER Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 250 ARG Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 174 GLN Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 288 GLN Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 250 ARG Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 40 LYS Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 207 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 288 GLN Chi-restraints excluded: chain K residue 9 ILE Chi-restraints excluded: chain K residue 10 ILE Chi-restraints excluded: chain K residue 40 LYS Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 168 THR Chi-restraints excluded: chain K residue 174 GLN Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain K residue 288 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 215 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 123 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 143 optimal weight: 0.7980 chunk 147 optimal weight: 0.0370 chunk 9 optimal weight: 8.9990 overall best weight: 1.1260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 47 ASN ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 ASN ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN B 231 GLN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 GLN ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 297 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.106116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.084729 restraints weight = 72215.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.086999 restraints weight = 51936.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.088741 restraints weight = 40408.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.090050 restraints weight = 33201.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.091091 restraints weight = 28430.086| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22002 Z= 0.159 Angle : 0.813 14.862 29922 Z= 0.383 Chirality : 0.050 0.284 3456 Planarity : 0.006 0.085 3828 Dihedral : 9.652 63.365 3430 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 20.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.49 % Favored : 95.43 % Rotamer: Outliers : 8.20 % Allowed : 31.06 % Favored : 60.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -0.76 (0.15), residues: 2694 helix: 0.14 (0.16), residues: 948 sheet: -0.38 (0.25), residues: 378 loop : -0.94 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 128 TYR 0.018 0.001 TYR F 197 PHE 0.032 0.002 PHE L 27 TRP 0.015 0.001 TRP C 284 HIS 0.007 0.001 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (21978) covalent geometry : angle 0.79403 / 0.38 (29886) hydrogen bonds : bond 0.03851 / 2.51 ( 868) hydrogen bonds : angle 6.12852 / 4.35 ( 2367) metal coordination : bond 0.00810 / 0.53 ( 24) metal coordination : angle 5.08186 / 3.26 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1291 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 1100 time to evaluate : 0.653 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: 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: 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: 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: symmetry clash REVERT: L 28 LYS cc_start: 0.9710 (ttmm) cc_final: 0.9499 (ttmm) REVERT: L 41 ARG cc_start: 0.8809 (mmm-85) cc_final: 0.8405 (tpp80) REVERT: L 88 ASN cc_start: 0.8841 (m-40) cc_final: 0.8611 (m-40) REVERT: L 99 LEU cc_start: 0.8853 (tp) cc_final: 0.8608 (tt) REVERT: L 128 ARG cc_start: 0.9259 (mmm160) cc_final: 0.8752 (mmm160) REVERT: L 145 PHE cc_start: 0.7219 (m-10) cc_final: 0.6771 (m-10) REVERT: H 24 GLN cc_start: 0.9415 (mm-40) cc_final: 0.9050 (mm-40) REVERT: H 40 GLN cc_start: 0.9231 (mp10) cc_final: 0.8998 (mp10) REVERT: H 44 ILE cc_start: 0.9729 (pp) cc_final: 0.9335 (mm) REVERT: H 55 ARG cc_start: 0.9347 (tpp-160) cc_final: 0.9092 (tpp80) REVERT: H 90 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8806 (mm-30) REVERT: H 102 ARG cc_start: 0.8995 (tpp80) cc_final: 0.8678 (tpp80) REVERT: J 40 GLN cc_start: 0.9468 (mp10) cc_final: 0.9247 (mp10) REVERT: J 72 ASP cc_start: 0.9450 (m-30) cc_final: 0.8869 (m-30) REVERT: J 90 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8703 (mm-30) REVERT: J 94 LYS cc_start: 0.8285 (mmtt) cc_final: 0.7433 (mptt) REVERT: J 122 SER cc_start: 0.9181 (m) cc_final: 0.8874 (p) REVERT: D 41 ARG cc_start: 0.8673 (mmm160) cc_final: 0.8017 (mmm-85) REVERT: D 47 ASN cc_start: 0.8521 (t0) cc_final: 0.8266 (t0) REVERT: D 56 LYS cc_start: 0.6564 (mttt) cc_final: 0.5544 (mtpt) REVERT: D 68 GLU cc_start: 0.9178 (tp30) cc_final: 0.8752 (tp30) REVERT: D 72 ASP cc_start: 0.8928 (m-30) cc_final: 0.8528 (m-30) REVERT: D 80 GLN cc_start: 0.8614 (tp40) cc_final: 0.8201 (tp40) REVERT: D 94 LYS cc_start: 0.8709 (mttt) cc_final: 0.8484 (mmtt) REVERT: D 121 VAL cc_start: 0.8904 (OUTLIER) cc_final: 0.8060 (m) REVERT: D 128 ARG cc_start: 0.9267 (mmm160) cc_final: 0.8693 (mmm160) REVERT: D 139 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8220 (pptt) REVERT: E 36 THR cc_start: 0.8989 (p) cc_final: 0.8734 (p) REVERT: E 66 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8887 (tp) REVERT: E 90 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8862 (mm-30) REVERT: E 116 SER cc_start: 0.9414 (m) cc_final: 0.9185 (p) REVERT: I 25 ILE cc_start: 0.9473 (pt) cc_final: 0.9250 (pp) REVERT: I 28 LYS cc_start: 0.9640 (ptpp) cc_final: 0.9382 (ptpp) REVERT: I 40 GLN cc_start: 0.9469 (mp10) cc_final: 0.9261 (mp10) REVERT: I 56 LYS cc_start: 0.7826 (mttt) cc_final: 0.6678 (mttt) REVERT: I 68 GLU cc_start: 0.9641 (tp30) cc_final: 0.9316 (tp30) REVERT: I 90 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8803 (mm-30) REVERT: I 144 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8498 (mm-30) REVERT: A 31 LYS cc_start: 0.9315 (mmmm) cc_final: 0.9086 (mmmm) REVERT: A 38 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9125 (tt) REVERT: A 39 LEU cc_start: 0.9433 (mm) cc_final: 0.9010 (mm) REVERT: A 59 PHE cc_start: 0.9598 (m-80) cc_final: 0.9048 (m-80) REVERT: A 104 MET cc_start: 0.9320 (ppp) cc_final: 0.8940 (ppp) REVERT: A 113 ARG cc_start: 0.9454 (mmm-85) cc_final: 0.9056 (tpp80) REVERT: A 114 LEU cc_start: 0.9785 (mt) cc_final: 0.9436 (mp) REVERT: A 117 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8783 (mp0) REVERT: A 147 GLU cc_start: 0.9114 (tt0) cc_final: 0.8775 (pt0) REVERT: A 157 VAL cc_start: 0.9557 (t) cc_final: 0.9238 (p) REVERT: A 160 VAL cc_start: 0.9156 (t) cc_final: 0.7906 (p) REVERT: A 164 LYS cc_start: 0.9515 (ptmm) cc_final: 0.9275 (ptmm) REVERT: A 174 GLN cc_start: 0.9351 (tm-30) cc_final: 0.9006 (tm-30) REVERT: A 197 TYR cc_start: 0.9399 (p90) cc_final: 0.9123 (p90) REVERT: A 198 ILE cc_start: 0.9450 (mm) cc_final: 0.9218 (mm) REVERT: A 200 ASP cc_start: 0.9129 (m-30) cc_final: 0.8883 (m-30) REVERT: A 227 MET cc_start: 0.9314 (mmm) cc_final: 0.8782 (mmm) REVERT: A 240 TYR cc_start: 0.9262 (t80) cc_final: 0.8686 (t80) REVERT: B 31 LYS cc_start: 0.9528 (mmmm) cc_final: 0.9159 (mmmm) REVERT: B 39 LEU cc_start: 0.9264 (tp) cc_final: 0.8899 (tp) REVERT: B 59 PHE cc_start: 0.9787 (m-80) cc_final: 0.9360 (m-80) REVERT: B 74 SER cc_start: 0.8724 (p) cc_final: 0.8444 (p) REVERT: B 117 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8391 (mt-10) REVERT: B 137 GLN cc_start: 0.9258 (tp-100) cc_final: 0.8610 (tp-100) REVERT: B 141 ASP cc_start: 0.9449 (m-30) cc_final: 0.9181 (m-30) REVERT: B 147 GLU cc_start: 0.9124 (tt0) cc_final: 0.8772 (pt0) REVERT: B 157 VAL cc_start: 0.9635 (t) cc_final: 0.9320 (p) REVERT: B 160 VAL cc_start: 0.9284 (t) cc_final: 0.8098 (m) REVERT: B 227 MET cc_start: 0.9303 (mmm) cc_final: 0.8752 (mmm) REVERT: B 240 TYR cc_start: 0.9491 (t80) cc_final: 0.9139 (t80) REVERT: B 272 GLU cc_start: 0.8528 (mp0) cc_final: 0.8245 (mp0) REVERT: B 297 GLN cc_start: 0.8735 (tt0) cc_final: 0.7861 (mt0) REVERT: C 48 PHE cc_start: 0.8444 (m-10) cc_final: 0.7979 (m-10) REVERT: C 56 ARG cc_start: 0.9313 (ttp-110) cc_final: 0.8890 (mtp-110) REVERT: C 59 PHE cc_start: 0.9671 (m-10) cc_final: 0.9318 (m-10) REVERT: C 73 PHE cc_start: 0.8516 (p90) cc_final: 0.7426 (p90) REVERT: C 104 MET cc_start: 0.9498 (tmm) cc_final: 0.9290 (tmm) REVERT: C 117 GLU cc_start: 0.8437 (tt0) cc_final: 0.7877 (tt0) REVERT: C 118 PHE cc_start: 0.9251 (m-10) cc_final: 0.8765 (m-10) REVERT: C 134 HIS cc_start: 0.8606 (t-90) cc_final: 0.8336 (t-90) REVERT: C 153 ASP cc_start: 0.9382 (p0) cc_final: 0.8946 (t0) REVERT: C 167 ARG cc_start: 0.8701 (ptm-80) cc_final: 0.8305 (ptm-80) REVERT: C 201 MET cc_start: 0.9476 (tmm) cc_final: 0.9269 (ppp) REVERT: C 260 ASN cc_start: 0.8902 (p0) cc_final: 0.8305 (t0) REVERT: C 267 LEU cc_start: 0.9792 (mt) cc_final: 0.9546 (mt) REVERT: C 296 ARG cc_start: 0.9480 (mtt90) cc_final: 0.8888 (mtt180) REVERT: C 297 GLN cc_start: 0.9524 (tt0) cc_final: 0.9166 (tp40) REVERT: F 31 LYS cc_start: 0.9477 (mmmm) cc_final: 0.9215 (mmmm) REVERT: F 59 PHE cc_start: 0.9683 (m-80) cc_final: 0.9128 (m-80) REVERT: F 66 LEU cc_start: 0.9215 (mt) cc_final: 0.8953 (mt) REVERT: F 106 HIS cc_start: 0.9068 (t-90) cc_final: 0.8675 (t-90) REVERT: F 117 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8554 (mt-10) REVERT: F 147 GLU cc_start: 0.9187 (tt0) cc_final: 0.8777 (pt0) REVERT: F 164 LYS cc_start: 0.9307 (ptpp) cc_final: 0.8800 (ptpt) REVERT: F 240 TYR cc_start: 0.9410 (t80) cc_final: 0.9190 (t80) REVERT: F 286 PHE cc_start: 0.8978 (m-80) cc_final: 0.8602 (m-80) REVERT: G 49 PHE cc_start: 0.9688 (m-80) cc_final: 0.9039 (m-80) REVERT: G 73 PHE cc_start: 0.8970 (p90) cc_final: 0.8457 (p90) REVERT: G 118 PHE cc_start: 0.9359 (m-10) cc_final: 0.9137 (m-10) REVERT: G 133 GLN cc_start: 0.8997 (pt0) cc_final: 0.8679 (pt0) REVERT: G 134 HIS cc_start: 0.8559 (t-90) cc_final: 0.8136 (t-90) REVERT: G 142 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9145 (mm) REVERT: G 167 ARG cc_start: 0.8526 (ptm-80) cc_final: 0.8107 (ptm-80) REVERT: G 183 ARG cc_start: 0.8550 (mmm-85) cc_final: 0.8245 (mmm-85) REVERT: G 199 LEU cc_start: 0.9765 (OUTLIER) cc_final: 0.9364 (mt) REVERT: G 247 PHE cc_start: 0.8671 (m-10) cc_final: 0.8432 (m-10) REVERT: G 296 ARG cc_start: 0.8970 (mtt90) cc_final: 0.8738 (mtt90) REVERT: G 297 GLN cc_start: 0.9568 (tt0) cc_final: 0.9174 (tp40) REVERT: K 56 ARG cc_start: 0.9373 (ttp-110) cc_final: 0.8868 (mtp-110) REVERT: K 69 SER cc_start: 0.8909 (m) cc_final: 0.8554 (t) REVERT: K 73 PHE cc_start: 0.8379 (p90) cc_final: 0.7745 (p90) REVERT: K 90 ASP cc_start: 0.9246 (m-30) cc_final: 0.8935 (m-30) REVERT: K 104 MET cc_start: 0.9411 (tmm) cc_final: 0.9089 (tmm) REVERT: K 133 GLN cc_start: 0.8887 (pt0) cc_final: 0.8587 (pt0) REVERT: K 142 LEU cc_start: 0.9320 (mm) cc_final: 0.8980 (mm) REVERT: K 152 LEU cc_start: 0.9554 (mt) cc_final: 0.9220 (mt) REVERT: K 153 ASP cc_start: 0.9127 (t0) cc_final: 0.8103 (t0) REVERT: K 167 ARG cc_start: 0.8490 (ptm-80) cc_final: 0.8052 (ptm-80) REVERT: K 179 PHE cc_start: 0.9061 (m-80) cc_final: 0.8827 (t80) REVERT: K 199 LEU cc_start: 0.9731 (OUTLIER) cc_final: 0.9362 (mt) REVERT: K 250 ARG cc_start: 0.9538 (ptm-80) cc_final: 0.9277 (mtm110) REVERT: K 267 LEU cc_start: 0.9783 (mt) cc_final: 0.9564 (mt) REVERT: K 297 GLN cc_start: 0.9634 (OUTLIER) cc_final: 0.9035 (tp40) outliers start: 191 outliers final: 139 residues processed: 1164 average time/residue: 0.1477 time to fit residues: 263.9009 Evaluate side-chains 1160 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 1013 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 125 PHE Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 80 GLN Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 69 ASP Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 105 ASN Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 146 SER Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 250 ARG Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 174 GLN Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 118 PHE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 231 GLN Chi-restraints excluded: chain F residue 250 ARG Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 40 LYS Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 207 ILE Chi-restraints excluded: chain G residue 228 THR Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 288 GLN Chi-restraints excluded: chain K residue 9 ILE Chi-restraints excluded: chain K residue 40 LYS Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 117 GLU Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 168 THR Chi-restraints excluded: chain K residue 174 GLN Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 207 ILE Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain K residue 288 GLN Chi-restraints excluded: chain K residue 297 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 142 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 182 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 193 optimal weight: 10.0000 chunk 171 optimal weight: 8.9990 chunk 255 optimal weight: 1.9990 chunk 220 optimal weight: 9.9990 chunk 77 optimal weight: 0.0070 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 GLN ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 ASN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 ASN ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 212 HIS ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 297 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.105363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.083998 restraints weight = 71069.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.086203 restraints weight = 51009.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.087929 restraints weight = 39798.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.089229 restraints weight = 32794.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.090238 restraints weight = 28127.400| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.5885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 22002 Z= 0.150 Angle : 0.825 13.987 29922 Z= 0.390 Chirality : 0.050 0.217 3456 Planarity : 0.006 0.088 3828 Dihedral : 9.423 59.259 3430 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.01 % Favored : 94.91 % Rotamer: Outliers : 8.33 % Allowed : 34.49 % Favored : 57.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -0.82 (0.15), residues: 2694 helix: 0.09 (0.16), residues: 948 sheet: -0.36 (0.25), residues: 378 loop : -1.00 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 128 TYR 0.021 0.001 TYR F 197 PHE 0.028 0.002 PHE L 27 TRP 0.021 0.001 TRP C 284 HIS 0.006 0.001 HIS C 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (21978) covalent geometry : angle 0.81040 / 0.39 (29886) hydrogen bonds : bond 0.03757 / 2.45 ( 868) hydrogen bonds : angle 6.09836 / 4.32 ( 2367) metal coordination : bond 0.00720 / 0.46 ( 24) metal coordination : angle 4.59742 / 3.04 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1291 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 1097 time to evaluate : 0.833 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: 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: 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: 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: L 28 LYS cc_start: 0.9677 (ttmm) cc_final: 0.9452 (ttmm) REVERT: L 41 ARG cc_start: 0.8817 (mmm-85) cc_final: 0.8393 (tpp80) REVERT: L 60 LYS cc_start: 0.8982 (mttm) cc_final: 0.8715 (mttt) REVERT: L 69 ASP cc_start: 0.9458 (m-30) cc_final: 0.8827 (p0) REVERT: L 73 GLN cc_start: 0.9251 (mm110) cc_final: 0.8743 (mm110) REVERT: L 88 ASN cc_start: 0.8974 (m-40) cc_final: 0.8768 (m-40) REVERT: L 96 ARG cc_start: 0.8685 (mmm-85) cc_final: 0.8192 (mmp80) REVERT: L 104 ASP cc_start: 0.8131 (t0) cc_final: 0.7749 (t0) REVERT: L 128 ARG cc_start: 0.9252 (mmm160) cc_final: 0.8747 (mmm160) REVERT: H 24 GLN cc_start: 0.9404 (mm-40) cc_final: 0.9064 (mm-40) REVERT: H 41 ARG cc_start: 0.7235 (mmt180) cc_final: 0.7035 (mpt180) REVERT: H 44 ILE cc_start: 0.9724 (pp) cc_final: 0.9313 (mm) REVERT: H 90 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8819 (mm-30) REVERT: J 40 GLN cc_start: 0.9507 (mp10) cc_final: 0.9207 (mp10) REVERT: J 66 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8456 (tp) REVERT: J 72 ASP cc_start: 0.9461 (m-30) cc_final: 0.8961 (m-30) REVERT: J 90 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8649 (mm-30) REVERT: J 94 LYS cc_start: 0.8317 (mmtt) cc_final: 0.7643 (mptt) REVERT: J 122 SER cc_start: 0.9247 (m) cc_final: 0.8973 (p) REVERT: D 25 ILE cc_start: 0.9675 (pp) cc_final: 0.9085 (pp) REVERT: D 28 LYS cc_start: 0.9487 (mppt) cc_final: 0.9277 (mtmm) REVERT: D 41 ARG cc_start: 0.8646 (mmm160) cc_final: 0.7976 (mmm-85) REVERT: D 56 LYS cc_start: 0.6868 (mttt) cc_final: 0.4259 (mttt) REVERT: D 60 LYS cc_start: 0.8661 (mmtp) cc_final: 0.8323 (mmtt) REVERT: D 68 GLU cc_start: 0.9158 (tp30) cc_final: 0.8700 (tp30) REVERT: D 72 ASP cc_start: 0.8945 (m-30) cc_final: 0.8531 (m-30) REVERT: D 94 LYS cc_start: 0.8849 (mttt) cc_final: 0.8566 (mmtt) REVERT: D 121 VAL cc_start: 0.8917 (OUTLIER) cc_final: 0.7936 (m) REVERT: D 128 ARG cc_start: 0.9322 (mmm160) cc_final: 0.8868 (mmm160) REVERT: D 139 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8220 (pptt) REVERT: E 36 THR cc_start: 0.8970 (p) cc_final: 0.8737 (p) REVERT: E 66 LEU cc_start: 0.9121 (tp) cc_final: 0.8886 (tp) REVERT: E 72 ASP cc_start: 0.9361 (t0) cc_final: 0.8924 (t70) REVERT: E 87 ASP cc_start: 0.8392 (m-30) cc_final: 0.8011 (m-30) REVERT: E 90 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8670 (mm-30) REVERT: I 25 ILE cc_start: 0.9500 (OUTLIER) cc_final: 0.9287 (pp) REVERT: I 28 LYS cc_start: 0.9644 (ptpp) cc_final: 0.9380 (ptpp) REVERT: I 40 GLN cc_start: 0.9451 (mp10) cc_final: 0.9187 (mp10) REVERT: I 56 LYS cc_start: 0.7923 (mttt) cc_final: 0.6572 (mmtt) REVERT: I 68 GLU cc_start: 0.9623 (tp30) cc_final: 0.9311 (tp30) REVERT: I 90 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8823 (mm-30) REVERT: A 31 LYS cc_start: 0.9280 (mmmm) cc_final: 0.9068 (mmmm) REVERT: A 38 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9091 (tt) REVERT: A 39 LEU cc_start: 0.9499 (mm) cc_final: 0.8977 (mm) REVERT: A 59 PHE cc_start: 0.9619 (m-80) cc_final: 0.9099 (m-80) REVERT: A 60 GLU cc_start: 0.9490 (mt-10) cc_final: 0.9164 (mt-10) REVERT: A 78 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8691 (t0) REVERT: A 104 MET cc_start: 0.9352 (ppp) cc_final: 0.8922 (ppp) REVERT: A 113 ARG cc_start: 0.9442 (mmm-85) cc_final: 0.9043 (tpp80) REVERT: A 114 LEU cc_start: 0.9769 (mt) cc_final: 0.9436 (mt) REVERT: A 134 HIS cc_start: 0.9394 (t-90) cc_final: 0.8560 (t-90) REVERT: A 147 GLU cc_start: 0.9149 (tt0) cc_final: 0.8823 (pt0) REVERT: A 157 VAL cc_start: 0.9568 (t) cc_final: 0.9252 (p) REVERT: A 160 VAL cc_start: 0.9115 (t) cc_final: 0.7890 (p) REVERT: A 198 ILE cc_start: 0.9411 (mm) cc_final: 0.9177 (mm) REVERT: A 200 ASP cc_start: 0.9180 (m-30) cc_final: 0.8898 (m-30) REVERT: A 227 MET cc_start: 0.9326 (mmm) cc_final: 0.8822 (mmm) REVERT: A 240 TYR cc_start: 0.9211 (t80) cc_final: 0.8544 (t80) REVERT: A 272 GLU cc_start: 0.7894 (mp0) cc_final: 0.7683 (mp0) REVERT: A 297 GLN cc_start: 0.8527 (tt0) cc_final: 0.7893 (tp40) REVERT: B 31 LYS cc_start: 0.9559 (mmmm) cc_final: 0.9165 (mmmm) REVERT: B 39 LEU cc_start: 0.9317 (tp) cc_final: 0.8959 (tp) REVERT: B 59 PHE cc_start: 0.9798 (m-80) cc_final: 0.9259 (m-80) REVERT: B 60 GLU cc_start: 0.9423 (mt-10) cc_final: 0.9134 (mt-10) REVERT: B 74 SER cc_start: 0.8624 (p) cc_final: 0.8245 (p) REVERT: B 117 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8337 (mt-10) REVERT: B 137 GLN cc_start: 0.9371 (tp-100) cc_final: 0.8852 (tp-100) REVERT: B 147 GLU cc_start: 0.9141 (tt0) cc_final: 0.8764 (pt0) REVERT: B 157 VAL cc_start: 0.9619 (t) cc_final: 0.9318 (p) REVERT: B 160 VAL cc_start: 0.9206 (t) cc_final: 0.8058 (m) REVERT: B 174 GLN cc_start: 0.9219 (tm-30) cc_final: 0.8761 (tm-30) REVERT: B 196 GLN cc_start: 0.9573 (tp-100) cc_final: 0.9208 (tp-100) REVERT: B 200 ASP cc_start: 0.9489 (m-30) cc_final: 0.9055 (m-30) REVERT: B 227 MET cc_start: 0.9297 (mmm) cc_final: 0.8810 (mmm) REVERT: B 240 TYR cc_start: 0.9482 (t80) cc_final: 0.9137 (t80) REVERT: B 272 GLU cc_start: 0.8585 (mp0) cc_final: 0.8331 (mp0) REVERT: B 297 GLN cc_start: 0.8634 (tt0) cc_final: 0.7797 (mt0) REVERT: C 48 PHE cc_start: 0.8058 (m-10) cc_final: 0.7606 (m-10) REVERT: C 56 ARG cc_start: 0.9329 (ttp-110) cc_final: 0.8814 (mtp-110) REVERT: C 59 PHE cc_start: 0.9668 (m-10) cc_final: 0.9422 (m-10) REVERT: C 64 HIS cc_start: 0.8916 (m-70) cc_final: 0.8643 (m-70) REVERT: C 73 PHE cc_start: 0.8112 (p90) cc_final: 0.7707 (p90) REVERT: C 104 MET cc_start: 0.9624 (tmm) cc_final: 0.9197 (tmm) REVERT: C 117 GLU cc_start: 0.8401 (tt0) cc_final: 0.7636 (tt0) REVERT: C 118 PHE cc_start: 0.9243 (m-10) cc_final: 0.8888 (m-10) REVERT: C 133 GLN cc_start: 0.9406 (pt0) cc_final: 0.9122 (pt0) REVERT: C 134 HIS cc_start: 0.8655 (t-90) cc_final: 0.8312 (t-90) REVERT: C 144 THR cc_start: 0.9512 (t) cc_final: 0.8848 (t) REVERT: C 147 GLU cc_start: 0.8688 (pp20) cc_final: 0.8441 (pt0) REVERT: C 153 ASP cc_start: 0.9394 (p0) cc_final: 0.8929 (t0) REVERT: C 164 LYS cc_start: 0.9066 (ptmm) cc_final: 0.8648 (ptpp) REVERT: C 167 ARG cc_start: 0.8684 (ptm-80) cc_final: 0.8270 (ptm-80) REVERT: C 234 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6337 (ttt180) REVERT: C 260 ASN cc_start: 0.8499 (p0) cc_final: 0.8028 (p0) REVERT: C 267 LEU cc_start: 0.9784 (mt) cc_final: 0.9543 (mt) REVERT: C 297 GLN cc_start: 0.9533 (tt0) cc_final: 0.9160 (tp40) REVERT: F 31 LYS cc_start: 0.9506 (mmmm) cc_final: 0.9227 (mmmm) REVERT: F 59 PHE cc_start: 0.9711 (m-80) cc_final: 0.9112 (m-80) REVERT: F 106 HIS cc_start: 0.9078 (t-90) cc_final: 0.8582 (t-90) REVERT: F 117 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8583 (mt-10) REVERT: F 147 GLU cc_start: 0.9226 (tt0) cc_final: 0.8801 (pt0) REVERT: F 297 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8255 (tt0) REVERT: G 54 ARG cc_start: 0.8437 (mtt180) cc_final: 0.8209 (mtt180) REVERT: G 73 PHE cc_start: 0.9048 (p90) cc_final: 0.8252 (p90) REVERT: G 133 GLN cc_start: 0.9078 (pt0) cc_final: 0.8778 (pt0) REVERT: G 134 HIS cc_start: 0.8645 (t-90) cc_final: 0.8222 (t-90) REVERT: G 142 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9176 (mm) REVERT: G 164 LYS cc_start: 0.9092 (ptmm) cc_final: 0.8874 (ttpp) REVERT: G 167 ARG cc_start: 0.8565 (ptm-80) cc_final: 0.8136 (ptm-80) REVERT: G 199 LEU cc_start: 0.9770 (OUTLIER) cc_final: 0.9384 (mt) REVERT: G 236 ASP cc_start: 0.8589 (p0) cc_final: 0.8075 (p0) REVERT: G 239 GLU cc_start: 0.9563 (OUTLIER) cc_final: 0.9252 (mp0) REVERT: G 282 HIS cc_start: 0.8756 (m-70) cc_final: 0.8440 (m-70) REVERT: G 297 GLN cc_start: 0.9565 (tt0) cc_final: 0.9139 (tp40) REVERT: K 54 ARG cc_start: 0.9236 (mpp-170) cc_final: 0.8995 (mtt180) REVERT: K 56 ARG cc_start: 0.9366 (ttp-110) cc_final: 0.8968 (mtp-110) REVERT: K 69 SER cc_start: 0.8894 (m) cc_final: 0.8359 (t) REVERT: K 73 PHE cc_start: 0.8431 (p90) cc_final: 0.7766 (p90) REVERT: K 90 ASP cc_start: 0.9273 (m-30) cc_final: 0.8291 (p0) REVERT: K 104 MET cc_start: 0.9411 (tmm) cc_final: 0.9130 (tmm) REVERT: K 142 LEU cc_start: 0.9337 (mm) cc_final: 0.9038 (mm) REVERT: K 152 LEU cc_start: 0.9552 (mt) cc_final: 0.9225 (mt) REVERT: K 153 ASP cc_start: 0.9260 (t0) cc_final: 0.8155 (t0) REVERT: K 167 ARG cc_start: 0.8424 (ptm-80) cc_final: 0.7931 (ptm-80) REVERT: K 179 PHE cc_start: 0.9070 (m-80) cc_final: 0.8797 (t80) REVERT: K 187 ILE cc_start: 0.9437 (mp) cc_final: 0.8957 (mp) REVERT: K 199 LEU cc_start: 0.9741 (OUTLIER) cc_final: 0.9351 (mt) REVERT: K 234 ARG cc_start: 0.6881 (OUTLIER) cc_final: 0.6643 (ttt-90) REVERT: K 236 ASP cc_start: 0.9040 (p0) cc_final: 0.8743 (p0) REVERT: K 249 LEU cc_start: 0.8862 (mm) cc_final: 0.8372 (mm) REVERT: K 261 MET cc_start: 0.8798 (tpp) cc_final: 0.7761 (tpp) REVERT: K 282 HIS cc_start: 0.8796 (m-70) cc_final: 0.8312 (m-70) REVERT: K 297 GLN cc_start: 0.9712 (OUTLIER) cc_final: 0.9502 (tp40) outliers start: 194 outliers final: 143 residues processed: 1159 average time/residue: 0.1420 time to fit residues: 253.2416 Evaluate side-chains 1159 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 1002 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 125 PHE Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 80 GLN Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 57 ASP Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 69 ASP Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 146 SER Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 250 ARG Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 234 ARG Chi-restraints excluded: chain C residue 242 ASN Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 118 PHE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 196 GLN Chi-restraints excluded: chain F residue 250 ARG Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 207 ILE Chi-restraints excluded: chain G residue 239 GLU Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain K residue 10 ILE Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 117 GLU Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 207 ILE Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain K residue 234 ARG Chi-restraints excluded: chain K residue 288 GLN Chi-restraints excluded: chain K residue 297 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 69 optimal weight: 0.0270 chunk 171 optimal weight: 0.2980 chunk 135 optimal weight: 4.9990 chunk 203 optimal weight: 0.7980 chunk 213 optimal weight: 0.0870 chunk 158 optimal weight: 10.0000 chunk 173 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 200 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 73 GLN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 ASN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 GLN ** B 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 GLN F 78 ASN ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 287 GLN ** K 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 297 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.105860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.083759 restraints weight = 69993.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.086038 restraints weight = 50528.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.087795 restraints weight = 39524.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.089116 restraints weight = 32690.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.090148 restraints weight = 28168.078| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.6112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22002 Z= 0.143 Angle : 0.873 14.707 29922 Z= 0.407 Chirality : 0.051 0.213 3456 Planarity : 0.005 0.088 3828 Dihedral : 9.157 59.726 3430 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.94 % Favored : 94.99 % Rotamer: Outliers : 6.83 % Allowed : 38.45 % Favored : 54.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.16), residues: 2694 helix: 0.09 (0.16), residues: 912 sheet: -0.28 (0.26), residues: 372 loop : -0.86 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 128 TYR 0.018 0.001 TYR F 197 PHE 0.029 0.002 PHE J 145 TRP 0.012 0.001 TRP C 284 HIS 0.005 0.001 HIS G 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (21978) covalent geometry : angle 0.86067 / 0.41 (29886) hydrogen bonds : bond 0.03687 / 2.42 ( 868) hydrogen bonds : angle 6.03257 / 4.27 ( 2367) metal coordination : bond 0.00624 / 0.42 ( 24) metal coordination : angle 4.35789 / 2.90 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1236 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 1077 time to evaluate : 0.778 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: 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: 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: 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: L 41 ARG cc_start: 0.8811 (mmm-85) cc_final: 0.8385 (tpp80) REVERT: L 69 ASP cc_start: 0.9460 (m-30) cc_final: 0.9228 (p0) REVERT: L 96 ARG cc_start: 0.8748 (mmm-85) cc_final: 0.8401 (mmp80) REVERT: L 128 ARG cc_start: 0.9168 (mmm160) cc_final: 0.8654 (mmm160) REVERT: H 24 GLN cc_start: 0.9301 (mm-40) cc_final: 0.9039 (mm-40) REVERT: H 90 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8833 (mm-30) REVERT: J 40 GLN cc_start: 0.9539 (mp10) cc_final: 0.9247 (mp10) REVERT: J 72 ASP cc_start: 0.9451 (m-30) cc_final: 0.9026 (m-30) REVERT: J 90 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8657 (mm-30) REVERT: J 94 LYS cc_start: 0.8346 (mmtt) cc_final: 0.7553 (mptt) REVERT: J 122 SER cc_start: 0.9270 (m) cc_final: 0.9016 (p) REVERT: D 25 ILE cc_start: 0.9682 (pp) cc_final: 0.9210 (pp) REVERT: D 41 ARG cc_start: 0.8660 (mmm160) cc_final: 0.8000 (mmm-85) REVERT: D 47 ASN cc_start: 0.8528 (t0) cc_final: 0.8272 (t0) REVERT: D 56 LYS cc_start: 0.6908 (mttt) cc_final: 0.4270 (mttt) REVERT: D 68 GLU cc_start: 0.9190 (tp30) cc_final: 0.8743 (tp30) REVERT: D 72 ASP cc_start: 0.8966 (m-30) cc_final: 0.8566 (m-30) REVERT: D 90 GLU cc_start: 0.9188 (mm-30) cc_final: 0.8986 (mm-30) REVERT: D 94 LYS cc_start: 0.8898 (mttt) cc_final: 0.8633 (mmtt) REVERT: D 102 ARG cc_start: 0.8697 (tpp-160) cc_final: 0.8415 (tpp-160) REVERT: D 121 VAL cc_start: 0.8920 (OUTLIER) cc_final: 0.7890 (m) REVERT: D 125 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.8014 (p90) REVERT: D 128 ARG cc_start: 0.9334 (mmm160) cc_final: 0.8878 (mmm160) REVERT: E 36 THR cc_start: 0.8984 (p) cc_final: 0.8761 (p) REVERT: E 40 GLN cc_start: 0.9367 (mp10) cc_final: 0.9165 (pm20) REVERT: E 66 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8913 (tp) REVERT: E 87 ASP cc_start: 0.8502 (m-30) cc_final: 0.8119 (m-30) REVERT: E 90 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8691 (mm-30) REVERT: I 25 ILE cc_start: 0.9485 (pt) cc_final: 0.9281 (pp) REVERT: I 28 LYS cc_start: 0.9595 (ptpp) cc_final: 0.9340 (ptpp) REVERT: I 40 GLN cc_start: 0.9531 (mp10) cc_final: 0.9242 (mp10) REVERT: I 56 LYS cc_start: 0.8058 (mttt) cc_final: 0.6704 (mmtt) REVERT: I 68 GLU cc_start: 0.9638 (tp30) cc_final: 0.9348 (tp30) REVERT: I 90 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8840 (mm-30) REVERT: A 50 GLU cc_start: 0.8838 (tp30) cc_final: 0.8585 (tp30) REVERT: A 59 PHE cc_start: 0.9662 (m-80) cc_final: 0.9050 (m-80) REVERT: A 60 GLU cc_start: 0.9472 (mt-10) cc_final: 0.9130 (mt-10) REVERT: A 78 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8770 (t0) REVERT: A 104 MET cc_start: 0.9387 (ppp) cc_final: 0.8934 (ppp) REVERT: A 105 ARG cc_start: 0.9101 (ptp-170) cc_final: 0.7761 (ptp-170) REVERT: A 113 ARG cc_start: 0.9405 (mmm-85) cc_final: 0.9128 (mmm-85) REVERT: A 147 GLU cc_start: 0.9168 (tt0) cc_final: 0.8833 (pt0) REVERT: A 157 VAL cc_start: 0.9545 (t) cc_final: 0.9312 (p) REVERT: A 160 VAL cc_start: 0.9047 (t) cc_final: 0.7833 (p) REVERT: A 164 LYS cc_start: 0.9433 (ptmm) cc_final: 0.9208 (ptpt) REVERT: A 227 MET cc_start: 0.9263 (mmm) cc_final: 0.8745 (mmm) REVERT: A 272 GLU cc_start: 0.7946 (mp0) cc_final: 0.7713 (mp0) REVERT: A 276 ASP cc_start: 0.9439 (p0) cc_final: 0.9219 (p0) REVERT: A 297 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7779 (tp40) REVERT: B 31 LYS cc_start: 0.9559 (mmmm) cc_final: 0.9309 (mmmm) REVERT: B 59 PHE cc_start: 0.9777 (m-80) cc_final: 0.9236 (m-80) REVERT: B 60 GLU cc_start: 0.9397 (mt-10) cc_final: 0.9094 (mt-10) REVERT: B 66 LEU cc_start: 0.9268 (mt) cc_final: 0.8912 (mt) REVERT: B 73 PHE cc_start: 0.9075 (p90) cc_final: 0.8697 (p90) REVERT: B 117 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8350 (mt-10) REVERT: B 137 GLN cc_start: 0.9433 (tp-100) cc_final: 0.8962 (tp-100) REVERT: B 157 VAL cc_start: 0.9623 (t) cc_final: 0.9321 (p) REVERT: B 160 VAL cc_start: 0.9200 (t) cc_final: 0.7995 (m) REVERT: B 167 ARG cc_start: 0.9155 (ttp80) cc_final: 0.8901 (ttp80) REVERT: B 194 MET cc_start: 0.8296 (tpp) cc_final: 0.8073 (tmm) REVERT: B 227 MET cc_start: 0.9294 (mmm) cc_final: 0.8783 (mmm) REVERT: C 48 PHE cc_start: 0.7964 (m-10) cc_final: 0.7607 (m-10) REVERT: C 56 ARG cc_start: 0.9324 (ttp-110) cc_final: 0.8794 (mtp-110) REVERT: C 59 PHE cc_start: 0.9670 (m-10) cc_final: 0.9391 (m-10) REVERT: C 73 PHE cc_start: 0.8198 (p90) cc_final: 0.7755 (p90) REVERT: C 104 MET cc_start: 0.9618 (tmm) cc_final: 0.9253 (tmm) REVERT: C 117 GLU cc_start: 0.8416 (tt0) cc_final: 0.7615 (tt0) REVERT: C 118 PHE cc_start: 0.9185 (m-10) cc_final: 0.8854 (m-10) REVERT: C 133 GLN cc_start: 0.9435 (pt0) cc_final: 0.9185 (pt0) REVERT: C 137 GLN cc_start: 0.9484 (tp40) cc_final: 0.9230 (tp-100) REVERT: C 142 LEU cc_start: 0.9390 (mm) cc_final: 0.9105 (mm) REVERT: C 147 GLU cc_start: 0.8658 (pp20) cc_final: 0.8457 (pp20) REVERT: C 153 ASP cc_start: 0.9397 (p0) cc_final: 0.9015 (t0) REVERT: C 167 ARG cc_start: 0.8698 (ptm-80) cc_final: 0.8232 (ptm-80) REVERT: C 234 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.6134 (ttt180) REVERT: C 239 GLU cc_start: 0.9577 (mp0) cc_final: 0.9332 (mp0) REVERT: C 260 ASN cc_start: 0.8451 (p0) cc_final: 0.7967 (p0) REVERT: C 296 ARG cc_start: 0.9445 (mtt90) cc_final: 0.9162 (mtt90) REVERT: C 297 GLN cc_start: 0.9548 (tt0) cc_final: 0.9223 (tp40) REVERT: F 31 LYS cc_start: 0.9469 (mmmm) cc_final: 0.9169 (mmmm) REVERT: F 49 PHE cc_start: 0.9552 (m-80) cc_final: 0.9220 (m-10) REVERT: F 50 GLU cc_start: 0.8694 (tp30) cc_final: 0.8252 (tp30) REVERT: F 59 PHE cc_start: 0.9724 (m-80) cc_final: 0.9078 (m-80) REVERT: F 106 HIS cc_start: 0.9068 (t-90) cc_final: 0.8652 (t-90) REVERT: F 117 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8542 (mt-10) REVERT: F 147 GLU cc_start: 0.9296 (tt0) cc_final: 0.8870 (pt0) REVERT: F 194 MET cc_start: 0.8494 (tpp) cc_final: 0.8105 (tpp) REVERT: F 199 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9193 (mm) REVERT: F 244 LYS cc_start: 0.9260 (ptmt) cc_final: 0.9018 (ptmt) REVERT: F 297 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8193 (tt0) REVERT: G 22 LEU cc_start: 0.9352 (tt) cc_final: 0.9065 (pp) REVERT: G 73 PHE cc_start: 0.9072 (p90) cc_final: 0.8147 (p90) REVERT: G 104 MET cc_start: 0.9606 (tmm) cc_final: 0.9066 (tmm) REVERT: G 117 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8217 (pp20) REVERT: G 118 PHE cc_start: 0.9196 (m-10) cc_final: 0.8970 (m-10) REVERT: G 142 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9079 (mm) REVERT: G 164 LYS cc_start: 0.9054 (ptmm) cc_final: 0.8805 (ttpp) REVERT: G 167 ARG cc_start: 0.8524 (ptm-80) cc_final: 0.8090 (ptm-80) REVERT: G 194 MET cc_start: 0.9070 (tpp) cc_final: 0.8843 (tpp) REVERT: G 199 LEU cc_start: 0.9736 (OUTLIER) cc_final: 0.9390 (mt) REVERT: G 236 ASP cc_start: 0.8616 (p0) cc_final: 0.8050 (p0) REVERT: G 239 GLU cc_start: 0.9552 (mp0) cc_final: 0.9237 (mp0) REVERT: G 282 HIS cc_start: 0.8815 (m-70) cc_final: 0.8550 (m-70) REVERT: G 297 GLN cc_start: 0.9575 (tt0) cc_final: 0.9129 (tp40) REVERT: K 50 GLU cc_start: 0.9243 (mm-30) cc_final: 0.8834 (mp0) REVERT: K 56 ARG cc_start: 0.9313 (ttp-110) cc_final: 0.8915 (mtp-110) REVERT: K 73 PHE cc_start: 0.8656 (p90) cc_final: 0.7956 (p90) REVERT: K 90 ASP cc_start: 0.9305 (m-30) cc_final: 0.8339 (p0) REVERT: K 104 MET cc_start: 0.9478 (tmm) cc_final: 0.9153 (tmm) REVERT: K 118 PHE cc_start: 0.9207 (m-10) cc_final: 0.8934 (m-10) REVERT: K 137 GLN cc_start: 0.9139 (tp-100) cc_final: 0.8911 (tp-100) REVERT: K 142 LEU cc_start: 0.9373 (mm) cc_final: 0.9016 (mm) REVERT: K 183 ARG cc_start: 0.8656 (mmm-85) cc_final: 0.8421 (mmm-85) REVERT: K 187 ILE cc_start: 0.9387 (mp) cc_final: 0.8980 (mp) REVERT: K 194 MET cc_start: 0.8929 (tpp) cc_final: 0.8480 (tpp) REVERT: K 199 LEU cc_start: 0.9722 (OUTLIER) cc_final: 0.9371 (mt) REVERT: K 234 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.6556 (ttt-90) REVERT: K 236 ASP cc_start: 0.8786 (p0) cc_final: 0.8236 (p0) REVERT: K 239 GLU cc_start: 0.9616 (mp0) cc_final: 0.9265 (mp0) REVERT: K 261 MET cc_start: 0.8893 (tpp) cc_final: 0.7583 (tpp) REVERT: K 282 HIS cc_start: 0.8852 (m-70) cc_final: 0.8311 (m-70) REVERT: K 297 GLN cc_start: 0.9670 (OUTLIER) cc_final: 0.9404 (tp40) outliers start: 159 outliers final: 120 residues processed: 1129 average time/residue: 0.1436 time to fit residues: 247.6884 Evaluate side-chains 1160 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 1027 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 73 GLN Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 125 PHE Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 80 GLN Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 117 HIS Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 125 PHE Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 PHE Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 146 SER Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 250 ARG Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 234 ARG Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 118 PHE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 146 GLN Chi-restraints excluded: chain F residue 196 GLN Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 250 ARG Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 207 ILE Chi-restraints excluded: chain G residue 228 THR Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 207 ILE Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain K residue 234 ARG Chi-restraints excluded: chain K residue 288 GLN Chi-restraints excluded: chain K residue 297 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 57 optimal weight: 0.9990 chunk 231 optimal weight: 6.9990 chunk 245 optimal weight: 5.9990 chunk 239 optimal weight: 5.9990 chunk 236 optimal weight: 2.9990 chunk 242 optimal weight: 5.9990 chunk 119 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 HIS H 63 ASN D 20 HIS D 111 ASN ** I 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 ASN ** I 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 ASN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN B 108 GLN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 HIS ** C 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 ASN ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 291 ASN K 297 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.102291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.081475 restraints weight = 73328.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.083689 restraints weight = 52080.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.085373 restraints weight = 40329.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.086641 restraints weight = 33082.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.087634 restraints weight = 28347.827| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.6388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22002 Z= 0.179 Angle : 0.870 13.268 29922 Z= 0.412 Chirality : 0.052 0.221 3456 Planarity : 0.006 0.094 3828 Dihedral : 9.305 56.757 3430 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 23.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.57 % Favored : 94.36 % Rotamer: Outliers : 8.81 % Allowed : 37.76 % Favored : 53.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -0.82 (0.16), residues: 2694 helix: 0.06 (0.16), residues: 912 sheet: -0.29 (0.24), residues: 450 loop : -1.00 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 128 TYR 0.020 0.002 TYR F 197 PHE 0.026 0.002 PHE J 145 TRP 0.012 0.002 TRP C 284 HIS 0.006 0.001 HIS C 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (21978) covalent geometry : angle 0.85209 / 0.41 (29886) hydrogen bonds : bond 0.03747 / 2.45 ( 868) hydrogen bonds : angle 6.14975 / 4.37 ( 2367) metal coordination : bond 0.00878 / 0.53 ( 24) metal coordination : angle 5.10424 / 3.33 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1235 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 1030 time to evaluate : 0.827 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 64 THR cc_start: 0.8945 (m) cc_final: 0.8691 (p) REVERT: L 69 ASP cc_start: 0.9523 (m-30) cc_final: 0.8934 (p0) REVERT: L 72 ASP cc_start: 0.9043 (m-30) cc_final: 0.8763 (m-30) REVERT: L 73 GLN cc_start: 0.9319 (mm110) cc_final: 0.8807 (mm110) REVERT: L 104 ASP cc_start: 0.7922 (t0) cc_final: 0.7448 (t0) REVERT: H 24 GLN cc_start: 0.9340 (mm-40) cc_final: 0.9097 (mm-40) REVERT: H 40 GLN cc_start: 0.9226 (mp10) cc_final: 0.8910 (mp10) REVERT: H 90 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8820 (mm-30) REVERT: H 96 ARG cc_start: 0.8664 (mmp80) cc_final: 0.7910 (mmm160) REVERT: H 105 ASN cc_start: 0.9116 (m-40) cc_final: 0.8796 (m-40) REVERT: J 40 GLN cc_start: 0.9506 (mp10) cc_final: 0.9171 (mp10) REVERT: J 66 LEU cc_start: 0.8460 (tp) cc_final: 0.8175 (tp) REVERT: J 72 ASP cc_start: 0.9444 (m-30) cc_final: 0.9033 (m-30) REVERT: J 90 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8654 (mm-30) REVERT: J 94 LYS cc_start: 0.8436 (mmtt) cc_final: 0.7750 (mptt) REVERT: J 122 SER cc_start: 0.9258 (m) cc_final: 0.9058 (p) REVERT: D 41 ARG cc_start: 0.8722 (mmm160) cc_final: 0.8190 (mtt180) REVERT: D 47 ASN cc_start: 0.8602 (t0) cc_final: 0.8314 (t0) REVERT: D 56 LYS cc_start: 0.7134 (mttt) cc_final: 0.4407 (mttt) REVERT: D 68 GLU cc_start: 0.9150 (tp30) cc_final: 0.8691 (tp30) REVERT: D 72 ASP cc_start: 0.8986 (m-30) cc_final: 0.8546 (m-30) REVERT: D 90 GLU cc_start: 0.9223 (mm-30) cc_final: 0.9018 (mm-30) REVERT: D 94 LYS cc_start: 0.8989 (mttt) cc_final: 0.8739 (mmtt) REVERT: D 102 ARG cc_start: 0.8806 (tpp-160) cc_final: 0.8531 (tpp-160) REVERT: D 121 VAL cc_start: 0.8918 (OUTLIER) cc_final: 0.7813 (m) REVERT: D 125 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7939 (p90) REVERT: D 128 ARG cc_start: 0.9352 (mmm160) cc_final: 0.8907 (mmm160) REVERT: D 143 LYS cc_start: 0.9329 (OUTLIER) cc_final: 0.9121 (pttp) REVERT: D 145 PHE cc_start: 0.8613 (m-10) cc_final: 0.8248 (m-10) REVERT: E 66 LEU cc_start: 0.9056 (tp) cc_final: 0.8844 (tp) REVERT: E 90 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8690 (mm-30) REVERT: I 25 ILE cc_start: 0.9497 (OUTLIER) cc_final: 0.9294 (pp) REVERT: I 28 LYS cc_start: 0.9618 (ptpp) cc_final: 0.9385 (ptpp) REVERT: I 40 GLN cc_start: 0.9558 (mp10) cc_final: 0.9252 (mp10) REVERT: I 52 GLU cc_start: 0.8678 (mp0) cc_final: 0.8415 (mp0) REVERT: I 56 LYS cc_start: 0.8451 (mttt) cc_final: 0.6640 (mmtt) REVERT: I 90 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8769 (mm-30) REVERT: A 37 GLU cc_start: 0.8923 (pm20) cc_final: 0.8712 (pm20) REVERT: A 38 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9118 (tt) REVERT: A 40 LYS cc_start: 0.9485 (mtpp) cc_final: 0.9250 (ttmm) REVERT: A 50 GLU cc_start: 0.8824 (tp30) cc_final: 0.8560 (tp30) REVERT: A 59 PHE cc_start: 0.9645 (m-80) cc_final: 0.9018 (m-80) REVERT: A 60 GLU cc_start: 0.9451 (mt-10) cc_final: 0.9134 (mt-10) REVERT: A 104 MET cc_start: 0.9405 (ppp) cc_final: 0.8917 (ppp) REVERT: A 105 ARG cc_start: 0.9014 (ptp-170) cc_final: 0.7710 (ptp-170) REVERT: A 147 GLU cc_start: 0.9216 (tt0) cc_final: 0.8887 (pt0) REVERT: A 160 VAL cc_start: 0.9112 (t) cc_final: 0.7890 (p) REVERT: A 164 LYS cc_start: 0.9440 (ptmm) cc_final: 0.9219 (ptpt) REVERT: A 196 GLN cc_start: 0.9180 (tp40) cc_final: 0.8906 (tp-100) REVERT: A 227 MET cc_start: 0.9311 (mmm) cc_final: 0.8877 (mmm) REVERT: A 234 ARG cc_start: 0.8904 (ttp80) cc_final: 0.8529 (ttp80) REVERT: A 272 GLU cc_start: 0.7982 (mp0) cc_final: 0.7758 (mp0) REVERT: A 297 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8008 (tp40) REVERT: B 31 LYS cc_start: 0.9552 (mmmm) cc_final: 0.9275 (mmmm) REVERT: B 39 LEU cc_start: 0.9440 (tp) cc_final: 0.9108 (tp) REVERT: B 59 PHE cc_start: 0.9793 (m-80) cc_final: 0.9252 (m-80) REVERT: B 60 GLU cc_start: 0.9452 (mt-10) cc_final: 0.9147 (mt-10) REVERT: B 66 LEU cc_start: 0.9245 (mt) cc_final: 0.8968 (mt) REVERT: B 117 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8368 (mt-10) REVERT: B 137 GLN cc_start: 0.9490 (tp-100) cc_final: 0.8996 (tp-100) REVERT: B 147 GLU cc_start: 0.9183 (tt0) cc_final: 0.8797 (pt0) REVERT: B 157 VAL cc_start: 0.9645 (t) cc_final: 0.9370 (p) REVERT: B 160 VAL cc_start: 0.9264 (t) cc_final: 0.8124 (m) REVERT: B 164 LYS cc_start: 0.9430 (ptmm) cc_final: 0.8950 (ptpt) REVERT: B 167 ARG cc_start: 0.9210 (ttp80) cc_final: 0.8931 (ttp80) REVERT: B 227 MET cc_start: 0.9315 (mmm) cc_final: 0.8815 (mmm) REVERT: B 297 GLN cc_start: 0.8716 (tt0) cc_final: 0.8398 (mt0) REVERT: C 50 GLU cc_start: 0.9282 (mm-30) cc_final: 0.9070 (mp0) REVERT: C 56 ARG cc_start: 0.9376 (ttp-110) cc_final: 0.8801 (mtp-110) REVERT: C 59 PHE cc_start: 0.9687 (m-10) cc_final: 0.9374 (m-10) REVERT: C 73 PHE cc_start: 0.8276 (p90) cc_final: 0.7807 (p90) REVERT: C 104 MET cc_start: 0.9552 (tmm) cc_final: 0.9141 (tmm) REVERT: C 117 GLU cc_start: 0.8421 (tt0) cc_final: 0.7702 (tt0) REVERT: C 118 PHE cc_start: 0.9209 (m-10) cc_final: 0.8862 (m-10) REVERT: C 133 GLN cc_start: 0.9383 (pt0) cc_final: 0.9122 (pt0) REVERT: C 137 GLN cc_start: 0.9549 (tp40) cc_final: 0.9163 (tp-100) REVERT: C 142 LEU cc_start: 0.9462 (mm) cc_final: 0.9187 (mm) REVERT: C 167 ARG cc_start: 0.8686 (ptm-80) cc_final: 0.8196 (ptm-80) REVERT: C 194 MET cc_start: 0.9112 (tpp) cc_final: 0.8816 (tpp) REVERT: C 201 MET cc_start: 0.9469 (ppp) cc_final: 0.9260 (ppp) REVERT: C 221 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8729 (pm20) REVERT: C 234 ARG cc_start: 0.6996 (OUTLIER) cc_final: 0.6220 (ttt180) REVERT: C 239 GLU cc_start: 0.9589 (mp0) cc_final: 0.9357 (mp0) REVERT: C 260 ASN cc_start: 0.8358 (p0) cc_final: 0.7922 (p0) REVERT: C 296 ARG cc_start: 0.9446 (mtt90) cc_final: 0.8807 (mtt180) REVERT: C 297 GLN cc_start: 0.9487 (tt0) cc_final: 0.9162 (tp40) REVERT: F 31 LYS cc_start: 0.9457 (mmmm) cc_final: 0.9244 (mmmm) REVERT: F 49 PHE cc_start: 0.9558 (m-80) cc_final: 0.9243 (m-10) REVERT: F 50 GLU cc_start: 0.8620 (tp30) cc_final: 0.8209 (tp30) REVERT: F 59 PHE cc_start: 0.9735 (m-80) cc_final: 0.9089 (m-80) REVERT: F 66 LEU cc_start: 0.9101 (mt) cc_final: 0.8775 (mt) REVERT: F 147 GLU cc_start: 0.9275 (tt0) cc_final: 0.8881 (pt0) REVERT: F 194 MET cc_start: 0.8561 (tpp) cc_final: 0.8262 (tpp) REVERT: F 199 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9258 (mm) REVERT: F 244 LYS cc_start: 0.9238 (ptmt) cc_final: 0.9028 (ptmt) REVERT: F 285 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.8018 (p90) REVERT: F 286 PHE cc_start: 0.9058 (m-80) cc_final: 0.8832 (m-80) REVERT: G 22 LEU cc_start: 0.9385 (tt) cc_final: 0.9102 (pp) REVERT: G 73 PHE cc_start: 0.9037 (p90) cc_final: 0.8057 (p90) REVERT: G 104 MET cc_start: 0.9578 (tmm) cc_final: 0.9287 (tmm) REVERT: G 117 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8233 (pp20) REVERT: G 118 PHE cc_start: 0.9200 (OUTLIER) cc_final: 0.8934 (m-80) REVERT: G 164 LYS cc_start: 0.9097 (ptmm) cc_final: 0.8781 (ttpp) REVERT: G 187 ILE cc_start: 0.9406 (mp) cc_final: 0.9131 (mp) REVERT: G 194 MET cc_start: 0.9149 (tpp) cc_final: 0.8851 (tpp) REVERT: G 199 LEU cc_start: 0.9739 (OUTLIER) cc_final: 0.9343 (mt) REVERT: G 214 SER cc_start: 0.7009 (OUTLIER) cc_final: 0.6709 (t) REVERT: G 226 TYR cc_start: 0.9170 (t80) cc_final: 0.8548 (t80) REVERT: G 236 ASP cc_start: 0.8589 (p0) cc_final: 0.7990 (p0) REVERT: G 239 GLU cc_start: 0.9557 (mp0) cc_final: 0.9256 (mp0) REVERT: G 282 HIS cc_start: 0.8886 (m-70) cc_final: 0.8601 (m-70) REVERT: G 296 ARG cc_start: 0.8950 (mtt90) cc_final: 0.8299 (mtt90) REVERT: G 297 GLN cc_start: 0.9558 (tt0) cc_final: 0.9068 (tp40) REVERT: K 50 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8860 (mp0) REVERT: K 56 ARG cc_start: 0.9396 (ttp-110) cc_final: 0.8902 (mtp-110) REVERT: K 73 PHE cc_start: 0.8702 (p90) cc_final: 0.7988 (p90) REVERT: K 90 ASP cc_start: 0.9376 (m-30) cc_final: 0.9152 (m-30) REVERT: K 104 MET cc_start: 0.9480 (tmm) cc_final: 0.9141 (tmm) REVERT: K 117 GLU cc_start: 0.8299 (tt0) cc_final: 0.8067 (tt0) REVERT: K 118 PHE cc_start: 0.9262 (m-10) cc_final: 0.8792 (m-10) REVERT: K 137 GLN cc_start: 0.9203 (tp-100) cc_final: 0.8972 (tp-100) REVERT: K 142 LEU cc_start: 0.9394 (mm) cc_final: 0.9034 (mm) REVERT: K 147 GLU cc_start: 0.8691 (pp20) cc_final: 0.8480 (pp20) REVERT: K 164 LYS cc_start: 0.9106 (ptmm) cc_final: 0.8745 (ptpp) REVERT: K 186 PHE cc_start: 0.8970 (m-80) cc_final: 0.8650 (m-80) REVERT: K 187 ILE cc_start: 0.9402 (mp) cc_final: 0.9043 (mp) REVERT: K 194 MET cc_start: 0.9113 (tpp) cc_final: 0.8667 (tpp) REVERT: K 199 LEU cc_start: 0.9743 (OUTLIER) cc_final: 0.9281 (mt) REVERT: K 209 TRP cc_start: 0.9062 (p-90) cc_final: 0.8317 (p-90) REVERT: K 234 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6899 (ttt-90) REVERT: K 236 ASP cc_start: 0.8724 (p0) cc_final: 0.8168 (p0) REVERT: K 239 GLU cc_start: 0.9635 (OUTLIER) cc_final: 0.9295 (mp0) REVERT: K 261 MET cc_start: 0.8870 (tpp) cc_final: 0.7869 (tpp) REVERT: K 282 HIS cc_start: 0.8937 (m-70) cc_final: 0.8569 (m-70) REVERT: K 297 GLN cc_start: 0.9667 (OUTLIER) cc_final: 0.9368 (tp40) outliers start: 205 outliers final: 150 residues processed: 1103 average time/residue: 0.1442 time to fit residues: 243.7355 Evaluate side-chains 1166 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 1000 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 125 PHE Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 80 GLN Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 125 PHE Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 PHE Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 57 ASP Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 69 ASP Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 105 ASN Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 146 SER Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 250 ARG Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 234 ARG Chi-restraints excluded: chain C residue 242 ASN Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 118 PHE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 146 GLN Chi-restraints excluded: chain F residue 196 GLN Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 240 TYR Chi-restraints excluded: chain F residue 250 ARG Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 40 LYS Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 207 ILE Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 228 THR Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 279 LYS Chi-restraints excluded: chain K residue 9 ILE Chi-restraints excluded: chain K residue 10 ILE Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 168 THR Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 207 ILE Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain K residue 234 ARG Chi-restraints excluded: chain K residue 239 GLU Chi-restraints excluded: chain K residue 288 GLN Chi-restraints excluded: chain K residue 297 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 16 optimal weight: 0.0980 chunk 151 optimal weight: 2.9990 chunk 217 optimal weight: 0.7980 chunk 179 optimal weight: 1.9990 chunk 93 optimal weight: 0.1980 chunk 150 optimal weight: 5.9990 chunk 249 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 ASN ** I 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 ASN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN B 108 GLN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 ASN ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 78 ASN ** G 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 78 ASN ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 297 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.101743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.081188 restraints weight = 73343.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.083357 restraints weight = 51984.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.085023 restraints weight = 40390.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.086286 restraints weight = 33103.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.087275 restraints weight = 28360.676| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.6600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22002 Z= 0.166 Angle : 0.914 17.555 29922 Z= 0.426 Chirality : 0.052 0.253 3456 Planarity : 0.006 0.096 3828 Dihedral : 9.255 59.586 3430 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 23.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.42 % Favored : 94.51 % Rotamer: Outliers : 8.03 % Allowed : 38.83 % Favored : 53.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -0.94 (0.16), residues: 2694 helix: -0.13 (0.16), residues: 936 sheet: -0.54 (0.25), residues: 414 loop : -0.93 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 250 TYR 0.024 0.002 TYR A 185 PHE 0.023 0.002 PHE D 125 TRP 0.023 0.002 TRP C 284 HIS 0.010 0.001 HIS I 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (21978) covalent geometry : angle 0.88932 / 0.42 (29886) hydrogen bonds : bond 0.03741 / 2.45 ( 868) hydrogen bonds : angle 6.15853 / 4.39 ( 2367) metal coordination : bond 0.01043 / 0.60 ( 24) metal coordination : angle 6.15939 / 3.74 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1217 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 1030 time to evaluate : 0.806 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: 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: 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: 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: L 64 THR cc_start: 0.8977 (m) cc_final: 0.8729 (p) REVERT: L 69 ASP cc_start: 0.9524 (m-30) cc_final: 0.9161 (p0) REVERT: L 85 ARG cc_start: 0.9388 (mtm110) cc_final: 0.9145 (mtm110) REVERT: L 102 ARG cc_start: 0.8896 (tpp-160) cc_final: 0.8412 (tpp-160) REVERT: L 128 ARG cc_start: 0.9187 (mmm160) cc_final: 0.8907 (mmm-85) REVERT: H 24 GLN cc_start: 0.9337 (mm-40) cc_final: 0.9069 (mm-40) REVERT: H 40 GLN cc_start: 0.9228 (mp10) cc_final: 0.8851 (mp10) REVERT: H 90 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8821 (mm-30) REVERT: H 96 ARG cc_start: 0.8728 (mmp80) cc_final: 0.8046 (mmm160) REVERT: H 105 ASN cc_start: 0.9103 (m-40) cc_final: 0.8787 (m-40) REVERT: J 40 GLN cc_start: 0.9505 (mp10) cc_final: 0.9262 (mp10) REVERT: J 66 LEU cc_start: 0.8494 (tp) cc_final: 0.8290 (tp) REVERT: J 72 ASP cc_start: 0.9453 (m-30) cc_final: 0.9061 (m-30) REVERT: J 90 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8714 (mm-30) REVERT: J 94 LYS cc_start: 0.8453 (mmtt) cc_final: 0.7766 (mptt) REVERT: J 122 SER cc_start: 0.9398 (m) cc_final: 0.9132 (p) REVERT: D 41 ARG cc_start: 0.8742 (mmm160) cc_final: 0.8173 (mtt180) REVERT: D 47 ASN cc_start: 0.8592 (t0) cc_final: 0.8286 (t0) REVERT: D 90 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8998 (mm-30) REVERT: D 94 LYS cc_start: 0.8959 (mttt) cc_final: 0.8718 (mmtt) REVERT: D 121 VAL cc_start: 0.9017 (OUTLIER) cc_final: 0.7861 (m) REVERT: D 125 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7690 (p90) REVERT: D 128 ARG cc_start: 0.9411 (mmm160) cc_final: 0.8943 (mmm160) REVERT: D 139 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8284 (pptt) REVERT: D 143 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.9040 (pttp) REVERT: D 145 PHE cc_start: 0.8499 (m-10) cc_final: 0.8095 (m-10) REVERT: E 66 LEU cc_start: 0.9032 (tp) cc_final: 0.8820 (tp) REVERT: E 88 ASN cc_start: 0.8545 (m-40) cc_final: 0.8110 (m-40) REVERT: E 90 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8623 (mm-30) REVERT: I 25 ILE cc_start: 0.9500 (OUTLIER) cc_final: 0.9299 (pp) REVERT: I 28 LYS cc_start: 0.9624 (ptpp) cc_final: 0.9379 (ptpp) REVERT: I 40 GLN cc_start: 0.9546 (mp10) cc_final: 0.9228 (mp10) REVERT: I 105 ASN cc_start: 0.8818 (OUTLIER) cc_final: 0.8454 (m-40) REVERT: A 38 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9149 (tt) REVERT: A 50 GLU cc_start: 0.8854 (tp30) cc_final: 0.8489 (tp30) REVERT: A 59 PHE cc_start: 0.9669 (m-80) cc_final: 0.9048 (m-80) REVERT: A 60 GLU cc_start: 0.9449 (mt-10) cc_final: 0.9124 (mt-10) REVERT: A 104 MET cc_start: 0.9423 (ppp) cc_final: 0.8927 (ppp) REVERT: A 147 GLU cc_start: 0.9195 (tt0) cc_final: 0.8877 (pt0) REVERT: A 160 VAL cc_start: 0.9066 (t) cc_final: 0.7746 (p) REVERT: A 164 LYS cc_start: 0.9404 (ptmm) cc_final: 0.9115 (ptpt) REVERT: A 227 MET cc_start: 0.9287 (mmm) cc_final: 0.8864 (mmm) REVERT: A 233 GLU cc_start: 0.9660 (pm20) cc_final: 0.9397 (pm20) REVERT: A 244 LYS cc_start: 0.9316 (ptmt) cc_final: 0.9109 (ptmt) REVERT: A 297 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8000 (tp40) REVERT: B 31 LYS cc_start: 0.9550 (mmmm) cc_final: 0.9256 (mmmm) REVERT: B 39 LEU cc_start: 0.9435 (tp) cc_final: 0.9133 (tp) REVERT: B 59 PHE cc_start: 0.9778 (m-80) cc_final: 0.9234 (m-80) REVERT: B 60 GLU cc_start: 0.9467 (mt-10) cc_final: 0.9133 (mt-10) REVERT: B 64 HIS cc_start: 0.9485 (m-70) cc_final: 0.9222 (t-90) REVERT: B 66 LEU cc_start: 0.9290 (mt) cc_final: 0.9013 (mt) REVERT: B 117 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8429 (mt-10) REVERT: B 137 GLN cc_start: 0.9487 (tp-100) cc_final: 0.9046 (tp-100) REVERT: B 147 GLU cc_start: 0.9208 (tt0) cc_final: 0.8832 (pt0) REVERT: B 157 VAL cc_start: 0.9651 (t) cc_final: 0.9385 (p) REVERT: B 160 VAL cc_start: 0.9266 (t) cc_final: 0.8144 (m) REVERT: B 167 ARG cc_start: 0.9175 (ttp80) cc_final: 0.8911 (ttp-110) REVERT: B 200 ASP cc_start: 0.9434 (m-30) cc_final: 0.9222 (p0) REVERT: B 201 MET cc_start: 0.8909 (mmt) cc_final: 0.8634 (mpp) REVERT: B 227 MET cc_start: 0.9305 (mmm) cc_final: 0.8837 (mmm) REVERT: C 56 ARG cc_start: 0.9388 (ttp-110) cc_final: 0.8759 (mtp-110) REVERT: C 59 PHE cc_start: 0.9682 (OUTLIER) cc_final: 0.9357 (m-10) REVERT: C 73 PHE cc_start: 0.8248 (p90) cc_final: 0.7801 (p90) REVERT: C 104 MET cc_start: 0.9573 (tmm) cc_final: 0.9215 (tmm) REVERT: C 117 GLU cc_start: 0.8387 (tt0) cc_final: 0.7678 (tt0) REVERT: C 118 PHE cc_start: 0.9209 (m-10) cc_final: 0.8846 (m-10) REVERT: C 137 GLN cc_start: 0.9507 (tp40) cc_final: 0.9158 (tp-100) REVERT: C 142 LEU cc_start: 0.9400 (mm) cc_final: 0.9099 (mm) REVERT: C 194 MET cc_start: 0.9178 (tpp) cc_final: 0.8841 (tpp) REVERT: C 201 MET cc_start: 0.9489 (ppp) cc_final: 0.9260 (ppp) REVERT: C 221 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8715 (pm20) REVERT: C 234 ARG cc_start: 0.6940 (OUTLIER) cc_final: 0.6170 (ttt180) REVERT: C 239 GLU cc_start: 0.9590 (mp0) cc_final: 0.9358 (mp0) REVERT: C 296 ARG cc_start: 0.9452 (mtt90) cc_final: 0.8889 (mtt90) REVERT: C 297 GLN cc_start: 0.9477 (tt0) cc_final: 0.9144 (tp40) REVERT: F 49 PHE cc_start: 0.9562 (m-80) cc_final: 0.9293 (m-10) REVERT: F 59 PHE cc_start: 0.9737 (m-80) cc_final: 0.9115 (m-80) REVERT: F 60 GLU cc_start: 0.9502 (mt-10) cc_final: 0.9168 (mt-10) REVERT: F 147 GLU cc_start: 0.9279 (tt0) cc_final: 0.8945 (pt0) REVERT: F 194 MET cc_start: 0.8575 (tpp) cc_final: 0.8338 (tpp) REVERT: F 199 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9224 (mm) REVERT: F 244 LYS cc_start: 0.9233 (ptmt) cc_final: 0.9008 (ptmt) REVERT: F 249 LEU cc_start: 0.9438 (mm) cc_final: 0.9172 (mm) REVERT: F 269 ARG cc_start: 0.9303 (tmm-80) cc_final: 0.8414 (ttt90) REVERT: F 285 TYR cc_start: 0.8748 (OUTLIER) cc_final: 0.8031 (p90) REVERT: F 286 PHE cc_start: 0.9043 (m-80) cc_final: 0.8817 (m-80) REVERT: F 297 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8126 (tt0) REVERT: G 22 LEU cc_start: 0.9405 (tt) cc_final: 0.9128 (pp) REVERT: G 48 PHE cc_start: 0.8536 (m-10) cc_final: 0.8212 (m-10) REVERT: G 73 PHE cc_start: 0.9037 (p90) cc_final: 0.8030 (p90) REVERT: G 104 MET cc_start: 0.9650 (tmm) cc_final: 0.9370 (tmm) REVERT: G 117 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8197 (pp20) REVERT: G 118 PHE cc_start: 0.9172 (OUTLIER) cc_final: 0.8890 (m-10) REVERT: G 164 LYS cc_start: 0.9134 (ptmm) cc_final: 0.8920 (ttpp) REVERT: G 187 ILE cc_start: 0.9475 (mp) cc_final: 0.9224 (mp) REVERT: G 194 MET cc_start: 0.9192 (tpp) cc_final: 0.8917 (tpp) REVERT: G 199 LEU cc_start: 0.9713 (OUTLIER) cc_final: 0.9307 (mt) REVERT: G 214 SER cc_start: 0.7008 (OUTLIER) cc_final: 0.6628 (t) REVERT: G 221 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8899 (pm20) REVERT: G 226 TYR cc_start: 0.9180 (t80) cc_final: 0.8531 (t80) REVERT: G 239 GLU cc_start: 0.9553 (mp0) cc_final: 0.9252 (mp0) REVERT: G 282 HIS cc_start: 0.8909 (m-70) cc_final: 0.8647 (m-70) REVERT: G 297 GLN cc_start: 0.9548 (tt0) cc_final: 0.9061 (tp40) REVERT: K 56 ARG cc_start: 0.9377 (ttp-110) cc_final: 0.8648 (mtp-110) REVERT: K 73 PHE cc_start: 0.8771 (p90) cc_final: 0.8031 (p90) REVERT: K 90 ASP cc_start: 0.9363 (m-30) cc_final: 0.9093 (m-30) REVERT: K 104 MET cc_start: 0.9444 (tmm) cc_final: 0.9104 (tmm) REVERT: K 117 GLU cc_start: 0.8354 (tt0) cc_final: 0.8115 (tt0) REVERT: K 118 PHE cc_start: 0.9269 (m-10) cc_final: 0.8804 (m-10) REVERT: K 137 GLN cc_start: 0.9218 (tp-100) cc_final: 0.8968 (tp-100) REVERT: K 142 LEU cc_start: 0.9404 (mm) cc_final: 0.9020 (mm) REVERT: K 186 PHE cc_start: 0.9116 (m-80) cc_final: 0.8789 (m-80) REVERT: K 187 ILE cc_start: 0.9372 (mp) cc_final: 0.9166 (mp) REVERT: K 194 MET cc_start: 0.9166 (tpp) cc_final: 0.8700 (tpp) REVERT: K 199 LEU cc_start: 0.9733 (OUTLIER) cc_final: 0.9257 (mt) REVERT: K 209 TRP cc_start: 0.9060 (p-90) cc_final: 0.8309 (p-90) REVERT: K 221 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8764 (pm20) REVERT: K 234 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6960 (ttt-90) REVERT: K 236 ASP cc_start: 0.8708 (p0) cc_final: 0.8111 (p0) REVERT: K 239 GLU cc_start: 0.9639 (OUTLIER) cc_final: 0.9300 (mp0) REVERT: K 261 MET cc_start: 0.8881 (tpp) cc_final: 0.7909 (tpp) REVERT: K 282 HIS cc_start: 0.8897 (m-70) cc_final: 0.8528 (m-70) REVERT: K 297 GLN cc_start: 0.9709 (OUTLIER) cc_final: 0.9425 (tp40) outliers start: 187 outliers final: 142 residues processed: 1095 average time/residue: 0.1433 time to fit residues: 240.2014 Evaluate side-chains 1162 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 1000 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 125 PHE Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 80 GLN Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 125 PHE Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 57 ASP Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 105 ASN Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 146 SER Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 185 TYR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 234 ARG Chi-restraints excluded: chain C residue 242 ASN Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 146 GLN Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 196 GLN Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 240 TYR Chi-restraints excluded: chain F residue 250 ARG Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 40 LYS Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 207 ILE Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 228 THR Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 275 THR Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 279 LYS Chi-restraints excluded: chain G residue 288 GLN Chi-restraints excluded: chain K residue 9 ILE Chi-restraints excluded: chain K residue 10 ILE Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 207 ILE Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain K residue 234 ARG Chi-restraints excluded: chain K residue 239 GLU Chi-restraints excluded: chain K residue 288 GLN Chi-restraints excluded: chain K residue 297 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 185 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 259 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 240 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 196 optimal weight: 0.1980 chunk 236 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 73 GLN ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 HIS ** C 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 ASN ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 78 ASN ** G 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 78 ASN ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.098982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.078341 restraints weight = 74385.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.080512 restraints weight = 52651.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.082175 restraints weight = 40686.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.083445 restraints weight = 33381.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.084416 restraints weight = 28579.074| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.6862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22002 Z= 0.192 Angle : 0.952 18.586 29922 Z= 0.447 Chirality : 0.054 0.305 3456 Planarity : 0.006 0.104 3828 Dihedral : 9.311 59.556 3428 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 26.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.20 % Favored : 93.76 % Rotamer: Outliers : 7.86 % Allowed : 39.69 % Favored : 52.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -0.98 (0.16), residues: 2694 helix: -0.09 (0.16), residues: 918 sheet: -0.40 (0.24), residues: 450 loop : -1.08 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 14 TYR 0.020 0.002 TYR F 197 PHE 0.022 0.002 PHE D 125 TRP 0.029 0.003 TRP K 284 HIS 0.010 0.002 HIS I 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (21978) covalent geometry : angle 0.92427 / 0.45 (29886) hydrogen bonds : bond 0.03885 / 2.55 ( 868) hydrogen bonds : angle 6.30770 / 4.50 ( 2367) metal coordination : bond 0.01121 / 0.66 ( 24) metal coordination : angle 6.60281 / 4.08 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1200 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 1017 time to evaluate : 0.785 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: 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: 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: 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: L 27 PHE cc_start: 0.9214 (t80) cc_final: 0.9002 (t80) REVERT: L 28 LYS cc_start: 0.9684 (ttmm) cc_final: 0.9429 (ttpp) REVERT: L 69 ASP cc_start: 0.9504 (m-30) cc_final: 0.9163 (p0) REVERT: L 85 ARG cc_start: 0.9422 (mtm110) cc_final: 0.9172 (mtm110) REVERT: L 102 ARG cc_start: 0.8914 (tpp-160) cc_final: 0.8355 (tpp-160) REVERT: L 145 PHE cc_start: 0.7901 (m-10) cc_final: 0.7479 (m-10) REVERT: H 24 GLN cc_start: 0.9418 (mm-40) cc_final: 0.9109 (mm-40) REVERT: H 40 GLN cc_start: 0.9146 (mp10) cc_final: 0.8745 (mp10) REVERT: H 94 LYS cc_start: 0.8996 (mmtt) cc_final: 0.8410 (mptt) REVERT: J 40 GLN cc_start: 0.9580 (mp10) cc_final: 0.9329 (mp10) REVERT: J 66 LEU cc_start: 0.8669 (tp) cc_final: 0.8446 (tp) REVERT: J 72 ASP cc_start: 0.9466 (m-30) cc_final: 0.9053 (m-30) REVERT: J 90 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8722 (mm-30) REVERT: J 94 LYS cc_start: 0.8474 (mmtt) cc_final: 0.7831 (mptt) REVERT: J 122 SER cc_start: 0.9425 (m) cc_final: 0.9167 (p) REVERT: J 143 LYS cc_start: 0.9602 (ptpp) cc_final: 0.9379 (ptpp) REVERT: D 41 ARG cc_start: 0.8779 (mmm160) cc_final: 0.8175 (mtt180) REVERT: D 47 ASN cc_start: 0.8616 (t0) cc_final: 0.8309 (t0) REVERT: D 73 GLN cc_start: 0.9296 (mm110) cc_final: 0.8841 (mm110) REVERT: D 94 LYS cc_start: 0.8964 (mttt) cc_final: 0.8757 (mmtt) REVERT: D 104 ASP cc_start: 0.8610 (t0) cc_final: 0.8055 (t0) REVERT: D 121 VAL cc_start: 0.9033 (OUTLIER) cc_final: 0.7811 (m) REVERT: D 125 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7908 (p90) REVERT: D 128 ARG cc_start: 0.9355 (mmm160) cc_final: 0.8903 (mmm160) REVERT: D 143 LYS cc_start: 0.9473 (OUTLIER) cc_final: 0.9087 (pttp) REVERT: D 145 PHE cc_start: 0.8436 (m-10) cc_final: 0.8045 (m-10) REVERT: E 66 LEU cc_start: 0.9106 (tp) cc_final: 0.8802 (tp) REVERT: E 84 ASN cc_start: 0.8534 (m-40) cc_final: 0.8109 (t0) REVERT: E 88 ASN cc_start: 0.8802 (m-40) cc_final: 0.8425 (m-40) REVERT: E 90 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8707 (mm-30) REVERT: I 40 GLN cc_start: 0.9558 (mp10) cc_final: 0.9239 (mp10) REVERT: I 53 MET cc_start: 0.9075 (pmm) cc_final: 0.8831 (pmm) REVERT: I 68 GLU cc_start: 0.9644 (tp30) cc_final: 0.9169 (tp30) REVERT: A 59 PHE cc_start: 0.9680 (m-80) cc_final: 0.9053 (m-80) REVERT: A 60 GLU cc_start: 0.9475 (mt-10) cc_final: 0.9144 (mt-10) REVERT: A 104 MET cc_start: 0.9412 (ppp) cc_final: 0.8907 (ppp) REVERT: A 147 GLU cc_start: 0.9202 (tt0) cc_final: 0.8875 (pt0) REVERT: A 160 VAL cc_start: 0.9053 (t) cc_final: 0.7769 (p) REVERT: A 164 LYS cc_start: 0.9387 (ptmm) cc_final: 0.9093 (ptpt) REVERT: A 227 MET cc_start: 0.9317 (mmm) cc_final: 0.8928 (mmm) REVERT: A 232 LYS cc_start: 0.9743 (pptt) cc_final: 0.9525 (tptp) REVERT: A 297 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7997 (tp40) REVERT: B 31 LYS cc_start: 0.9575 (mmmm) cc_final: 0.9266 (mmmm) REVERT: B 59 PHE cc_start: 0.9791 (m-80) cc_final: 0.9252 (m-80) REVERT: B 60 GLU cc_start: 0.9479 (mt-10) cc_final: 0.9121 (mt-10) REVERT: B 64 HIS cc_start: 0.9484 (m-70) cc_final: 0.9265 (t-90) REVERT: B 66 LEU cc_start: 0.9287 (mt) cc_final: 0.8976 (mt) REVERT: B 117 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8517 (mt-10) REVERT: B 134 HIS cc_start: 0.9205 (t-90) cc_final: 0.8694 (t-90) REVERT: B 137 GLN cc_start: 0.9516 (tp-100) cc_final: 0.9211 (tp-100) REVERT: B 147 GLU cc_start: 0.9255 (tt0) cc_final: 0.8881 (pt0) REVERT: B 157 VAL cc_start: 0.9639 (t) cc_final: 0.9380 (p) REVERT: B 160 VAL cc_start: 0.9317 (t) cc_final: 0.8256 (m) REVERT: B 164 LYS cc_start: 0.9396 (ptmm) cc_final: 0.8843 (ptpt) REVERT: B 167 ARG cc_start: 0.9194 (ttp80) cc_final: 0.8922 (ttp-110) REVERT: B 168 THR cc_start: 0.9633 (p) cc_final: 0.9411 (p) REVERT: B 227 MET cc_start: 0.9306 (mmm) cc_final: 0.8950 (mmm) REVERT: B 297 GLN cc_start: 0.8947 (mt0) cc_final: 0.8370 (mm-40) REVERT: C 56 ARG cc_start: 0.9380 (ttp-110) cc_final: 0.8839 (ttp-110) REVERT: C 59 PHE cc_start: 0.9683 (OUTLIER) cc_final: 0.9456 (m-10) REVERT: C 73 PHE cc_start: 0.8321 (p90) cc_final: 0.7850 (p90) REVERT: C 117 GLU cc_start: 0.8351 (tt0) cc_final: 0.7664 (tt0) REVERT: C 118 PHE cc_start: 0.9204 (m-10) cc_final: 0.8827 (m-10) REVERT: C 137 GLN cc_start: 0.9525 (tp40) cc_final: 0.9147 (tp-100) REVERT: C 142 LEU cc_start: 0.9434 (mm) cc_final: 0.9141 (mm) REVERT: C 164 LYS cc_start: 0.9120 (ptmm) cc_final: 0.8873 (ptpp) REVERT: C 186 PHE cc_start: 0.9204 (m-80) cc_final: 0.8919 (m-80) REVERT: C 194 MET cc_start: 0.9298 (tpp) cc_final: 0.8950 (tpp) REVERT: C 201 MET cc_start: 0.9499 (ppp) cc_final: 0.9185 (ppp) REVERT: C 209 TRP cc_start: 0.8893 (p-90) cc_final: 0.8143 (p-90) REVERT: C 221 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8766 (pm20) REVERT: C 234 ARG cc_start: 0.7106 (OUTLIER) cc_final: 0.6388 (ttt180) REVERT: C 239 GLU cc_start: 0.9602 (mp0) cc_final: 0.9378 (mp0) REVERT: C 296 ARG cc_start: 0.9445 (mtt90) cc_final: 0.8965 (mtt180) REVERT: C 297 GLN cc_start: 0.9458 (tt0) cc_final: 0.9116 (tp40) REVERT: F 49 PHE cc_start: 0.9554 (m-80) cc_final: 0.9273 (m-10) REVERT: F 59 PHE cc_start: 0.9730 (m-80) cc_final: 0.9148 (m-80) REVERT: F 60 GLU cc_start: 0.9501 (mt-10) cc_final: 0.9139 (mt-10) REVERT: F 90 ASP cc_start: 0.9417 (OUTLIER) cc_final: 0.8992 (p0) REVERT: F 147 GLU cc_start: 0.9298 (tt0) cc_final: 0.8992 (pt0) REVERT: F 160 VAL cc_start: 0.9156 (t) cc_final: 0.8910 (m) REVERT: F 174 GLN cc_start: 0.9296 (tm-30) cc_final: 0.9086 (pt0) REVERT: F 194 MET cc_start: 0.8540 (tpp) cc_final: 0.8284 (tpp) REVERT: F 199 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9204 (mm) REVERT: F 244 LYS cc_start: 0.9258 (ptmt) cc_final: 0.9019 (ptmt) REVERT: F 297 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8198 (tt0) REVERT: G 73 PHE cc_start: 0.9021 (p90) cc_final: 0.8314 (p90) REVERT: G 104 MET cc_start: 0.9623 (tmm) cc_final: 0.9327 (tmm) REVERT: G 117 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8170 (pp20) REVERT: G 118 PHE cc_start: 0.9191 (OUTLIER) cc_final: 0.8918 (m-80) REVERT: G 187 ILE cc_start: 0.9484 (mp) cc_final: 0.9181 (mp) REVERT: G 194 MET cc_start: 0.9253 (tpp) cc_final: 0.8944 (tpp) REVERT: G 199 LEU cc_start: 0.9732 (OUTLIER) cc_final: 0.9239 (mt) REVERT: G 201 MET cc_start: 0.9516 (ppp) cc_final: 0.9272 (ppp) REVERT: G 209 TRP cc_start: 0.8854 (p-90) cc_final: 0.8423 (p-90) REVERT: G 214 SER cc_start: 0.7063 (OUTLIER) cc_final: 0.6675 (t) REVERT: G 221 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8961 (pm20) REVERT: G 239 GLU cc_start: 0.9579 (OUTLIER) cc_final: 0.9287 (mp0) REVERT: G 282 HIS cc_start: 0.8879 (m-70) cc_final: 0.8630 (m-70) REVERT: G 297 GLN cc_start: 0.9553 (tt0) cc_final: 0.9038 (tp40) REVERT: K 37 GLU cc_start: 0.9222 (tm-30) cc_final: 0.8986 (pm20) REVERT: K 56 ARG cc_start: 0.9426 (ttp-110) cc_final: 0.8721 (mtp-110) REVERT: K 73 PHE cc_start: 0.8786 (p90) cc_final: 0.8550 (p90) REVERT: K 78 ASN cc_start: 0.8311 (OUTLIER) cc_final: 0.8018 (t160) REVERT: K 90 ASP cc_start: 0.9360 (m-30) cc_final: 0.8642 (p0) REVERT: K 104 MET cc_start: 0.9456 (tmm) cc_final: 0.9106 (tmm) REVERT: K 117 GLU cc_start: 0.8478 (tt0) cc_final: 0.8228 (tt0) REVERT: K 118 PHE cc_start: 0.9354 (m-10) cc_final: 0.8892 (m-10) REVERT: K 137 GLN cc_start: 0.9186 (tp-100) cc_final: 0.8948 (tp-100) REVERT: K 142 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9041 (mm) REVERT: K 186 PHE cc_start: 0.9173 (m-80) cc_final: 0.8814 (m-80) REVERT: K 187 ILE cc_start: 0.9431 (mp) cc_final: 0.9135 (mp) REVERT: K 194 MET cc_start: 0.9247 (tpp) cc_final: 0.8829 (tpp) REVERT: K 199 LEU cc_start: 0.9751 (OUTLIER) cc_final: 0.9250 (mt) REVERT: K 209 TRP cc_start: 0.9131 (p-90) cc_final: 0.8366 (p-90) REVERT: K 221 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8802 (pm20) REVERT: K 234 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.7124 (ttt180) REVERT: K 236 ASP cc_start: 0.8692 (p0) cc_final: 0.8120 (p0) REVERT: K 239 GLU cc_start: 0.9652 (OUTLIER) cc_final: 0.9317 (mp0) REVERT: K 297 GLN cc_start: 0.9644 (tp40) cc_final: 0.9289 (tp40) outliers start: 183 outliers final: 144 residues processed: 1084 average time/residue: 0.1468 time to fit residues: 243.4378 Evaluate side-chains 1163 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 1001 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 125 PHE Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 80 GLN Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 125 PHE Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 57 ASP Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 69 ASP Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 146 SER Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 250 ARG Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 185 TYR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 234 ARG Chi-restraints excluded: chain C residue 242 ASN Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 146 GLN Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 196 GLN Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 250 ARG Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 40 LYS Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 207 ILE Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 228 THR Chi-restraints excluded: chain G residue 239 GLU Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 279 LYS Chi-restraints excluded: chain G residue 288 GLN Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain K residue 9 ILE Chi-restraints excluded: chain K residue 10 ILE Chi-restraints excluded: chain K residue 78 ASN Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 168 THR Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 207 ILE Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain K residue 234 ARG Chi-restraints excluded: chain K residue 239 GLU Chi-restraints excluded: chain K residue 288 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 167 optimal weight: 2.9990 chunk 234 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 0.0010 chunk 255 optimal weight: 0.9980 chunk 254 optimal weight: 0.9980 chunk 176 optimal weight: 0.5980 chunk 50 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 253 optimal weight: 3.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 63 ASN ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 ASN ** I 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 HIS ** C 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 ASN ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 78 ASN ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.101566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.079962 restraints weight = 72612.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.082236 restraints weight = 51953.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.083978 restraints weight = 40424.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.085271 restraints weight = 33252.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.086290 restraints weight = 28579.466| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.6997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22002 Z= 0.161 Angle : 1.013 15.972 29922 Z= 0.468 Chirality : 0.055 0.365 3456 Planarity : 0.006 0.102 3828 Dihedral : 9.066 58.905 3428 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 22.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.94 % Favored : 94.02 % Rotamer: Outliers : 6.49 % Allowed : 42.01 % Favored : 51.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.16), residues: 2694 helix: -0.18 (0.16), residues: 918 sheet: -0.35 (0.25), residues: 438 loop : -1.11 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 234 TYR 0.019 0.002 TYR A 197 PHE 0.022 0.002 PHE D 125 TRP 0.041 0.002 TRP K 284 HIS 0.008 0.001 HIS I 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (21978) covalent geometry : angle 0.99180 / 0.47 (29886) hydrogen bonds : bond 0.03842 / 2.53 ( 868) hydrogen bonds : angle 6.26726 / 4.45 ( 2367) metal coordination : bond 0.00869 / 0.55 ( 24) metal coordination : angle 6.02842 / 3.84 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1189 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 1038 time to evaluate : 0.782 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: 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: 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: 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: L 60 LYS cc_start: 0.8902 (mttt) cc_final: 0.8174 (mttt) REVERT: L 69 ASP cc_start: 0.9501 (m-30) cc_final: 0.8904 (p0) REVERT: L 73 GLN cc_start: 0.9167 (mm-40) cc_final: 0.8660 (mm110) REVERT: H 24 GLN cc_start: 0.9408 (mm-40) cc_final: 0.9090 (mm-40) REVERT: H 40 GLN cc_start: 0.9169 (mp10) cc_final: 0.8912 (mp10) REVERT: H 72 ASP cc_start: 0.9578 (OUTLIER) cc_final: 0.8736 (t0) REVERT: H 88 ASN cc_start: 0.9173 (m-40) cc_final: 0.8789 (m-40) REVERT: H 90 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8906 (mm-30) REVERT: H 94 LYS cc_start: 0.8963 (mmtt) cc_final: 0.8161 (mptt) REVERT: J 60 LYS cc_start: 0.7722 (mttt) cc_final: 0.7264 (mmtt) REVERT: J 66 LEU cc_start: 0.8655 (tp) cc_final: 0.8422 (tp) REVERT: J 72 ASP cc_start: 0.9454 (m-30) cc_final: 0.9143 (m-30) REVERT: J 90 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8776 (mm-30) REVERT: J 94 LYS cc_start: 0.8477 (mmtt) cc_final: 0.7784 (mptt) REVERT: J 143 LYS cc_start: 0.9564 (ptpp) cc_final: 0.9316 (ptpp) REVERT: D 41 ARG cc_start: 0.8665 (mmm160) cc_final: 0.8145 (mtt180) REVERT: D 68 GLU cc_start: 0.9531 (tp30) cc_final: 0.8840 (tp30) REVERT: D 72 ASP cc_start: 0.9223 (m-30) cc_final: 0.8905 (m-30) REVERT: D 104 ASP cc_start: 0.8533 (t0) cc_final: 0.8302 (t0) REVERT: D 121 VAL cc_start: 0.9018 (OUTLIER) cc_final: 0.7725 (m) REVERT: D 125 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7974 (p90) REVERT: D 128 ARG cc_start: 0.9392 (mmm160) cc_final: 0.8994 (mmm160) REVERT: D 143 LYS cc_start: 0.9431 (OUTLIER) cc_final: 0.9100 (pttp) REVERT: D 145 PHE cc_start: 0.8356 (m-10) cc_final: 0.7856 (m-10) REVERT: E 12 ILE cc_start: 0.8740 (pt) cc_final: 0.8251 (tp) REVERT: E 84 ASN cc_start: 0.8458 (m-40) cc_final: 0.8219 (t0) REVERT: E 88 ASN cc_start: 0.8930 (m-40) cc_final: 0.8523 (m-40) REVERT: E 90 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8671 (mm-30) REVERT: E 128 ARG cc_start: 0.9026 (mtm110) cc_final: 0.8608 (ttp80) REVERT: I 53 MET cc_start: 0.9093 (pmm) cc_final: 0.8863 (pmm) REVERT: I 68 GLU cc_start: 0.9669 (tp30) cc_final: 0.9068 (tp30) REVERT: I 72 ASP cc_start: 0.9183 (m-30) cc_final: 0.8591 (m-30) REVERT: I 73 GLN cc_start: 0.9227 (mm110) cc_final: 0.8793 (mm110) REVERT: I 104 ASP cc_start: 0.8333 (t0) cc_final: 0.7976 (t0) REVERT: I 105 ASN cc_start: 0.8551 (m-40) cc_final: 0.8318 (m-40) REVERT: A 7 LYS cc_start: 0.9448 (tttt) cc_final: 0.9159 (ttmt) REVERT: A 50 GLU cc_start: 0.8898 (tp30) cc_final: 0.8536 (tp30) REVERT: A 59 PHE cc_start: 0.9695 (m-80) cc_final: 0.9090 (m-80) REVERT: A 60 GLU cc_start: 0.9492 (mt-10) cc_final: 0.9161 (mt-10) REVERT: A 90 ASP cc_start: 0.9239 (m-30) cc_final: 0.8922 (p0) REVERT: A 104 MET cc_start: 0.9404 (ppp) cc_final: 0.8940 (ppp) REVERT: A 147 GLU cc_start: 0.9240 (tt0) cc_final: 0.8883 (pt0) REVERT: A 160 VAL cc_start: 0.8989 (t) cc_final: 0.7646 (p) REVERT: A 164 LYS cc_start: 0.9345 (ptmm) cc_final: 0.9052 (ptpt) REVERT: A 194 MET cc_start: 0.8262 (tpp) cc_final: 0.8027 (tpp) REVERT: A 196 GLN cc_start: 0.9300 (tp40) cc_final: 0.9053 (tp-100) REVERT: A 211 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9127 (tt) REVERT: A 227 MET cc_start: 0.9180 (mmm) cc_final: 0.8801 (mmm) REVERT: A 232 LYS cc_start: 0.9732 (pptt) cc_final: 0.9516 (tptp) REVERT: A 297 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7902 (tp40) REVERT: B 31 LYS cc_start: 0.9539 (mmmm) cc_final: 0.9142 (mmmm) REVERT: B 42 LYS cc_start: 0.8871 (mptt) cc_final: 0.8669 (mmtm) REVERT: B 59 PHE cc_start: 0.9773 (m-80) cc_final: 0.9207 (m-80) REVERT: B 60 GLU cc_start: 0.9477 (mt-10) cc_final: 0.9104 (mt-10) REVERT: B 64 HIS cc_start: 0.9447 (m-70) cc_final: 0.9223 (t-90) REVERT: B 66 LEU cc_start: 0.9279 (mt) cc_final: 0.8998 (mt) REVERT: B 117 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8459 (mt-10) REVERT: B 133 GLN cc_start: 0.8728 (pt0) cc_final: 0.8305 (pm20) REVERT: B 137 GLN cc_start: 0.9488 (tp-100) cc_final: 0.8987 (tp-100) REVERT: B 147 GLU cc_start: 0.9275 (tt0) cc_final: 0.8838 (pt0) REVERT: B 160 VAL cc_start: 0.9288 (t) cc_final: 0.8209 (m) REVERT: B 164 LYS cc_start: 0.9347 (ptmm) cc_final: 0.8869 (ptpt) REVERT: B 167 ARG cc_start: 0.9146 (ttp80) cc_final: 0.8886 (ttp-110) REVERT: B 168 THR cc_start: 0.9638 (p) cc_final: 0.9417 (p) REVERT: B 201 MET cc_start: 0.9270 (ptp) cc_final: 0.9063 (mpp) REVERT: B 223 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8543 (p0) REVERT: B 227 MET cc_start: 0.9351 (mmm) cc_final: 0.8893 (mmm) REVERT: B 297 GLN cc_start: 0.8820 (mt0) cc_final: 0.8434 (mt0) REVERT: C 22 LEU cc_start: 0.9436 (tt) cc_final: 0.9164 (pp) REVERT: C 56 ARG cc_start: 0.9360 (ttp-110) cc_final: 0.8795 (ttp-110) REVERT: C 73 PHE cc_start: 0.8279 (p90) cc_final: 0.7835 (p90) REVERT: C 91 THR cc_start: 0.9302 (OUTLIER) cc_final: 0.9093 (p) REVERT: C 104 MET cc_start: 0.9482 (tmm) cc_final: 0.8944 (tmm) REVERT: C 117 GLU cc_start: 0.8279 (tt0) cc_final: 0.7596 (tt0) REVERT: C 118 PHE cc_start: 0.9170 (m-10) cc_final: 0.8777 (m-10) REVERT: C 137 GLN cc_start: 0.9479 (tp40) cc_final: 0.9093 (tp-100) REVERT: C 142 LEU cc_start: 0.9408 (mm) cc_final: 0.9112 (mm) REVERT: C 152 LEU cc_start: 0.9218 (tp) cc_final: 0.8864 (tp) REVERT: C 153 ASP cc_start: 0.9453 (p0) cc_final: 0.9068 (t0) REVERT: C 164 LYS cc_start: 0.9119 (ptmm) cc_final: 0.8897 (ptpp) REVERT: C 186 PHE cc_start: 0.9191 (m-80) cc_final: 0.8911 (m-80) REVERT: C 194 MET cc_start: 0.9318 (tpp) cc_final: 0.9029 (tpp) REVERT: C 209 TRP cc_start: 0.8894 (p-90) cc_final: 0.8208 (p-90) REVERT: C 221 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8723 (pm20) REVERT: C 234 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.6262 (ttt180) REVERT: C 239 GLU cc_start: 0.9606 (mp0) cc_final: 0.9386 (mp0) REVERT: C 261 MET cc_start: 0.8781 (tpp) cc_final: 0.8501 (tpp) REVERT: C 296 ARG cc_start: 0.9448 (mtt90) cc_final: 0.9198 (mtt180) REVERT: C 297 GLN cc_start: 0.9519 (tt0) cc_final: 0.9178 (tp40) REVERT: F 49 PHE cc_start: 0.9581 (m-80) cc_final: 0.9307 (m-10) REVERT: F 59 PHE cc_start: 0.9740 (m-80) cc_final: 0.9152 (m-80) REVERT: F 60 GLU cc_start: 0.9510 (mt-10) cc_final: 0.9143 (mt-10) REVERT: F 147 GLU cc_start: 0.9327 (tt0) cc_final: 0.9012 (pt0) REVERT: F 160 VAL cc_start: 0.9115 (t) cc_final: 0.8827 (m) REVERT: F 194 MET cc_start: 0.8567 (tpp) cc_final: 0.8184 (tpp) REVERT: F 196 GLN cc_start: 0.9532 (OUTLIER) cc_final: 0.9083 (tp-100) REVERT: F 199 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9134 (mm) REVERT: F 200 ASP cc_start: 0.9412 (p0) cc_final: 0.9135 (p0) REVERT: F 244 LYS cc_start: 0.9231 (ptmt) cc_final: 0.8970 (ptmt) REVERT: F 249 LEU cc_start: 0.9456 (mm) cc_final: 0.9176 (mm) REVERT: F 269 ARG cc_start: 0.9224 (tmm-80) cc_final: 0.8014 (ttt90) REVERT: F 285 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.8004 (p90) REVERT: F 297 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8260 (tt0) REVERT: G 37 GLU cc_start: 0.9104 (tm-30) cc_final: 0.8866 (pm20) REVERT: G 48 PHE cc_start: 0.8831 (m-10) cc_final: 0.8330 (m-10) REVERT: G 73 PHE cc_start: 0.9008 (p90) cc_final: 0.8006 (p90) REVERT: G 104 MET cc_start: 0.9628 (tmm) cc_final: 0.9341 (tmm) REVERT: G 117 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8227 (pp20) REVERT: G 118 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8902 (m-80) REVERT: G 187 ILE cc_start: 0.9452 (mp) cc_final: 0.9128 (mp) REVERT: G 194 MET cc_start: 0.9226 (tpp) cc_final: 0.8824 (tpp) REVERT: G 199 LEU cc_start: 0.9743 (OUTLIER) cc_final: 0.9377 (mt) REVERT: G 201 MET cc_start: 0.9521 (ppp) cc_final: 0.9086 (ppp) REVERT: G 214 SER cc_start: 0.6937 (OUTLIER) cc_final: 0.6481 (t) REVERT: G 221 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8922 (pm20) REVERT: G 226 TYR cc_start: 0.9168 (t80) cc_final: 0.8554 (t80) REVERT: G 239 GLU cc_start: 0.9585 (OUTLIER) cc_final: 0.9291 (mp0) REVERT: G 282 HIS cc_start: 0.8943 (m-70) cc_final: 0.8670 (m-70) REVERT: G 297 GLN cc_start: 0.9573 (tt0) cc_final: 0.9067 (tp40) REVERT: K 56 ARG cc_start: 0.9373 (ttp-110) cc_final: 0.8631 (mtp-110) REVERT: K 73 PHE cc_start: 0.8836 (p90) cc_final: 0.8103 (p90) REVERT: K 104 MET cc_start: 0.9408 (tmm) cc_final: 0.9062 (tmm) REVERT: K 117 GLU cc_start: 0.8519 (tt0) cc_final: 0.8278 (tt0) REVERT: K 118 PHE cc_start: 0.9389 (m-10) cc_final: 0.9008 (m-10) REVERT: K 142 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9066 (mm) REVERT: K 186 PHE cc_start: 0.9166 (m-80) cc_final: 0.8869 (m-80) REVERT: K 187 ILE cc_start: 0.9424 (mp) cc_final: 0.9128 (mp) REVERT: K 194 MET cc_start: 0.9264 (tpp) cc_final: 0.8825 (tpp) REVERT: K 199 LEU cc_start: 0.9726 (OUTLIER) cc_final: 0.9235 (mt) REVERT: K 209 TRP cc_start: 0.8981 (p-90) cc_final: 0.8252 (p-90) REVERT: K 221 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8778 (pm20) REVERT: K 234 ARG cc_start: 0.7213 (OUTLIER) cc_final: 0.6957 (ttt180) REVERT: K 236 ASP cc_start: 0.8742 (p0) cc_final: 0.8190 (p0) REVERT: K 239 GLU cc_start: 0.9642 (OUTLIER) cc_final: 0.9320 (mp0) REVERT: K 250 ARG cc_start: 0.9660 (ptm160) cc_final: 0.9335 (ttp80) REVERT: K 297 GLN cc_start: 0.9514 (tp40) cc_final: 0.9263 (tp40) outliers start: 151 outliers final: 119 residues processed: 1090 average time/residue: 0.1416 time to fit residues: 237.6964 Evaluate side-chains 1157 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 1017 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 125 PHE Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 80 GLN Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 125 PHE Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 125 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 125 PHE Chi-restraints excluded: chain I residue 146 SER Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 185 TYR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 234 ARG Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 196 GLN Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 40 LYS Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 207 ILE Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 239 GLU Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 279 LYS Chi-restraints excluded: chain K residue 9 ILE Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 168 THR Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 207 ILE Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain K residue 234 ARG Chi-restraints excluded: chain K residue 239 GLU Chi-restraints excluded: chain K residue 288 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 119 optimal weight: 0.6980 chunk 262 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 179 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 259 optimal weight: 0.0040 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 ASN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 ASN ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 149 GLN ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.102457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.081372 restraints weight = 74437.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.083620 restraints weight = 52951.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.085339 restraints weight = 40991.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.086655 restraints weight = 33615.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.087670 restraints weight = 28767.820| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.7116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22002 Z= 0.168 Angle : 1.024 15.930 29922 Z= 0.479 Chirality : 0.055 0.374 3456 Planarity : 0.006 0.098 3828 Dihedral : 8.916 59.980 3428 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 23.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.01 % Favored : 93.95 % Rotamer: Outliers : 6.23 % Allowed : 43.08 % Favored : 50.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.09 (0.15), residues: 2694 helix: -0.23 (0.16), residues: 912 sheet: -0.50 (0.28), residues: 342 loop : -1.05 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 128 TYR 0.027 0.002 TYR F 197 PHE 0.021 0.002 PHE D 125 TRP 0.047 0.003 TRP K 284 HIS 0.009 0.001 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (21978) covalent geometry : angle 1.00305 / 0.48 (29886) hydrogen bonds : bond 0.03902 / 2.58 ( 868) hydrogen bonds : angle 6.28227 / 4.47 ( 2367) metal coordination : bond 0.00876 / 0.54 ( 24) metal coordination : angle 6.04897 / 3.83 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5239.94 seconds wall clock time: 91 minutes 0.20 seconds (5460.20 seconds total)