Starting phenix.real_space_refine on Thu Oct 29 21:46:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lf0_23296/10_2026/7lf0_23296.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lf0_23296/10_2026/7lf0_23296.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lf0_23296/10_2026/7lf0_23296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lf0_23296/10_2026/7lf0_23296.map" model { file = "/net/cci-nas-00/data/ceres_data/7lf0_23296/10_2026/7lf0_23296.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lf0_23296/10_2026/7lf0_23296.cif" } resolution = 3.68 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= 0.005 sd= 0.082 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: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 21804 2.51 5 N 5850 2.21 5 O 6768 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34548 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "D" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1709 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 207} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Restraints were copied for chains: B, C, M, N, J, F, G, K, Q, R, H, I, L, O, P Time building chain proxies: 5.18, per 1000 atoms: 0.15 Number of scatterers: 34548 At special positions: 0 Unit cell: (117.52, 119.6, 239.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 6768 8.00 N 5850 7.00 C 21804 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 152 " - pdb=" SG CYS D 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.02 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.02 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 194 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.02 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 134 " - pdb=" SG CYS O 194 " distance=2.02 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 134 " - pdb=" SG CYS P 194 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 152 " - pdb=" SG CYS F 207 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 152 " - pdb=" SG CYS G 207 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.04 Simple disulfide: pdb=" SG CYS K 152 " - pdb=" SG CYS K 207 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 152 " - pdb=" SG CYS Q 207 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.04 Simple disulfide: pdb=" SG CYS R 152 " - pdb=" SG CYS R 207 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 1.7 seconds 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8280 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 72 sheets defined 20.2% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 23 through 25 No H-bonds generated for 'chain 'A' and resid 23 through 25' Processing helix chain 'A' and resid 26 through 34 removed outlier: 3.776A pdb=" N VAL A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 41 Processing helix chain 'A' and resid 69 through 90 removed outlier: 4.070A pdb=" N VAL A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 102 No H-bonds generated for 'chain 'A' and resid 100 through 102' Processing helix chain 'A' and resid 103 through 113 removed outlier: 3.974A pdb=" N HIS A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 149 removed outlier: 4.362A pdb=" N PHE A 147 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 148 " --> pdb=" O PRO A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 153 Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 183 through 193 Processing helix chain 'A' and resid 199 through 221 removed outlier: 7.078A pdb=" N ILE A 208 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N GLY A 209 " --> pdb=" O ARG A 205 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 Processing helix chain 'A' and resid 285 through 304 removed outlier: 3.582A pdb=" N VAL A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.920A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 126 Processing helix chain 'E' and resid 183 through 187 Processing helix chain 'B' and resid 23 through 25 No H-bonds generated for 'chain 'B' and resid 23 through 25' Processing helix chain 'B' and resid 26 through 34 removed outlier: 3.776A pdb=" N VAL B 30 " --> pdb=" O GLU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 41 Processing helix chain 'B' and resid 69 through 90 removed outlier: 4.068A pdb=" N VAL B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 102 No H-bonds generated for 'chain 'B' and resid 100 through 102' Processing helix chain 'B' and resid 103 through 113 removed outlier: 3.974A pdb=" N HIS B 111 " --> pdb=" O SER B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 149 removed outlier: 4.361A pdb=" N PHE B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 153 Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 183 through 193 Processing helix chain 'B' and resid 199 through 221 removed outlier: 7.078A pdb=" N ILE B 208 " --> pdb=" O ASP B 204 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N GLY B 209 " --> pdb=" O ARG B 205 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 266 Processing helix chain 'B' and resid 285 through 304 removed outlier: 3.582A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 25 No H-bonds generated for 'chain 'C' and resid 23 through 25' Processing helix chain 'C' and resid 26 through 34 removed outlier: 3.775A pdb=" N VAL C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 41 Processing helix chain 'C' and resid 69 through 90 removed outlier: 4.069A pdb=" N VAL C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 102 No H-bonds generated for 'chain 'C' and resid 100 through 102' Processing helix chain 'C' and resid 103 through 113 removed outlier: 3.974A pdb=" N HIS C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 149 removed outlier: 4.362A pdb=" N PHE C 147 " --> pdb=" O GLN C 143 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 148 " --> pdb=" O PRO C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 153 Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 183 through 193 Processing helix chain 'C' and resid 199 through 221 removed outlier: 7.078A pdb=" N ILE C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N GLY C 209 " --> pdb=" O ARG C 205 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS C 210 " --> pdb=" O LEU C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 266 Processing helix chain 'C' and resid 285 through 304 removed outlier: 3.582A pdb=" N VAL C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.920A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 126 Processing helix chain 'H' and resid 183 through 187 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.921A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 126 Processing helix chain 'I' and resid 183 through 187 Processing helix chain 'M' and resid 23 through 25 No H-bonds generated for 'chain 'M' and resid 23 through 25' Processing helix chain 'M' and resid 26 through 34 removed outlier: 3.776A pdb=" N VAL M 30 " --> pdb=" O GLU M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 41 Processing helix chain 'M' and resid 69 through 90 removed outlier: 4.068A pdb=" N VAL M 73 " --> pdb=" O ASN M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 102 No H-bonds generated for 'chain 'M' and resid 100 through 102' Processing helix chain 'M' and resid 103 through 113 removed outlier: 3.974A pdb=" N HIS M 111 " --> pdb=" O SER M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 149 removed outlier: 4.362A pdb=" N PHE M 147 " --> pdb=" O GLN M 143 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU M 148 " --> pdb=" O PRO M 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 150 through 153 Processing helix chain 'M' and resid 170 through 172 No H-bonds generated for 'chain 'M' and resid 170 through 172' Processing helix chain 'M' and resid 183 through 193 Processing helix chain 'M' and resid 199 through 221 removed outlier: 7.078A pdb=" N ILE M 208 " --> pdb=" O ASP M 204 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N GLY M 209 " --> pdb=" O ARG M 205 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS M 210 " --> pdb=" O LEU M 206 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 266 Processing helix chain 'M' and resid 285 through 304 removed outlier: 3.582A pdb=" N VAL M 289 " --> pdb=" O THR M 285 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.920A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 183 through 187 Processing helix chain 'N' and resid 23 through 25 No H-bonds generated for 'chain 'N' and resid 23 through 25' Processing helix chain 'N' and resid 26 through 34 removed outlier: 3.776A pdb=" N VAL N 30 " --> pdb=" O GLU N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 35 through 41 Processing helix chain 'N' and resid 69 through 90 removed outlier: 4.069A pdb=" N VAL N 73 " --> pdb=" O ASN N 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 102 No H-bonds generated for 'chain 'N' and resid 100 through 102' Processing helix chain 'N' and resid 103 through 113 removed outlier: 3.974A pdb=" N HIS N 111 " --> pdb=" O SER N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 143 through 149 removed outlier: 4.362A pdb=" N PHE N 147 " --> pdb=" O GLN N 143 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU N 148 " --> pdb=" O PRO N 144 " (cutoff:3.500A) Processing helix chain 'N' and resid 150 through 153 Processing helix chain 'N' and resid 170 through 172 No H-bonds generated for 'chain 'N' and resid 170 through 172' Processing helix chain 'N' and resid 183 through 193 Processing helix chain 'N' and resid 199 through 221 removed outlier: 7.078A pdb=" N ILE N 208 " --> pdb=" O ASP N 204 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N GLY N 209 " --> pdb=" O ARG N 205 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS N 210 " --> pdb=" O LEU N 206 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 266 Processing helix chain 'N' and resid 285 through 304 removed outlier: 3.582A pdb=" N VAL N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 25 No H-bonds generated for 'chain 'J' and resid 23 through 25' Processing helix chain 'J' and resid 26 through 34 removed outlier: 3.775A pdb=" N VAL J 30 " --> pdb=" O GLU J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 41 Processing helix chain 'J' and resid 69 through 90 removed outlier: 4.069A pdb=" N VAL J 73 " --> pdb=" O ASN J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 102 No H-bonds generated for 'chain 'J' and resid 100 through 102' Processing helix chain 'J' and resid 103 through 113 removed outlier: 3.974A pdb=" N HIS J 111 " --> pdb=" O SER J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 149 removed outlier: 4.362A pdb=" N PHE J 147 " --> pdb=" O GLN J 143 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU J 148 " --> pdb=" O PRO J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 153 Processing helix chain 'J' and resid 170 through 172 No H-bonds generated for 'chain 'J' and resid 170 through 172' Processing helix chain 'J' and resid 183 through 193 Processing helix chain 'J' and resid 199 through 221 removed outlier: 7.078A pdb=" N ILE J 208 " --> pdb=" O ASP J 204 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N GLY J 209 " --> pdb=" O ARG J 205 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS J 210 " --> pdb=" O LEU J 206 " (cutoff:3.500A) Processing helix chain 'J' and resid 253 through 266 Processing helix chain 'J' and resid 285 through 304 removed outlier: 3.582A pdb=" N VAL J 289 " --> pdb=" O THR J 285 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 83 removed outlier: 3.920A pdb=" N PHE O 83 " --> pdb=" O PRO O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 121 through 126 Processing helix chain 'O' and resid 183 through 187 Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.920A pdb=" N PHE P 83 " --> pdb=" O PRO P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 126 Processing helix chain 'P' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 49 removed outlier: 6.900A pdb=" N ILE A 8 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N SER A 94 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE A 275 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL A 96 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE A 227 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU A 273 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU A 229 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE A 275 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N PHE A 231 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY A 119 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N SER A 230 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE A 121 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASP A 232 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL A 123 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE A 198 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR A 176 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.554A pdb=" N SER D 25 " --> pdb=" O GLN D 3 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER D 7 " --> pdb=" O SER D 21 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.973A pdb=" N THR D 122 " --> pdb=" O GLU D 10 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS D 12 " --> pdb=" O THR D 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 46 through 50 removed outlier: 5.443A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 69 through 72 Processing sheet with id=AA6, first strand: chain 'D' and resid 132 through 133 removed outlier: 3.525A pdb=" N LEU D 150 " --> pdb=" O THR D 194 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N THR D 188 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU D 189 " --> pdb=" O ALA D 180 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA D 180 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER D 191 " --> pdb=" O PHE D 178 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 163 through 166 Processing sheet with id=AA8, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12 removed outlier: 7.239A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR E 86 " --> pdb=" O THR E 102 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG E 45 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 114 through 118 removed outlier: 3.996A pdb=" N VAL E 133 " --> pdb=" O PHE E 118 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS E 134 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER E 176 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER E 162 " --> pdb=" O SER E 176 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 129 through 131 Processing sheet with id=AB3, first strand: chain 'E' and resid 153 through 154 removed outlier: 4.094A pdb=" N LYS E 149 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR E 193 " --> pdb=" O LYS E 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 48 through 49 removed outlier: 6.900A pdb=" N ILE B 8 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N SER B 94 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE B 275 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL B 96 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE B 227 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU B 273 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU B 229 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE B 275 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N PHE B 231 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY B 119 " --> pdb=" O HIS B 228 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER B 230 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE B 121 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASP B 232 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL B 123 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE B 198 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR B 176 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 48 through 49 removed outlier: 6.900A pdb=" N ILE C 8 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N SER C 94 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE C 275 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL C 96 " --> pdb=" O ILE C 275 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE C 227 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU C 273 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU C 229 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE C 275 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N PHE C 231 " --> pdb=" O ILE C 275 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLY C 119 " --> pdb=" O HIS C 228 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N SER C 230 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE C 121 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASP C 232 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL C 123 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N PHE C 198 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TYR C 176 " --> pdb=" O PHE C 198 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.239A pdb=" N LEU H 11 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR H 86 " --> pdb=" O THR H 102 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG H 45 " --> pdb=" O GLN H 37 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 114 through 118 removed outlier: 3.997A pdb=" N VAL H 133 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS H 134 " --> pdb=" O SER H 177 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER H 176 " --> pdb=" O SER H 162 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER H 162 " --> pdb=" O SER H 176 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 129 through 131 Processing sheet with id=AC1, first strand: chain 'H' and resid 153 through 154 removed outlier: 4.094A pdb=" N LYS H 149 " --> pdb=" O THR H 193 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR H 193 " --> pdb=" O LYS H 149 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 5 through 6 Processing sheet with id=AC3, first strand: chain 'I' and resid 10 through 12 removed outlier: 7.248A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR I 86 " --> pdb=" O THR I 102 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG I 45 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 114 through 118 removed outlier: 3.997A pdb=" N VAL I 133 " --> pdb=" O PHE I 118 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS I 134 " --> pdb=" O SER I 177 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N TYR I 173 " --> pdb=" O ASN I 138 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER I 176 " --> pdb=" O SER I 162 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER I 162 " --> pdb=" O SER I 176 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 129 through 131 Processing sheet with id=AC6, first strand: chain 'I' and resid 153 through 154 removed outlier: 4.095A pdb=" N LYS I 149 " --> pdb=" O THR I 193 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR I 193 " --> pdb=" O LYS I 149 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 48 through 49 removed outlier: 6.900A pdb=" N ILE M 8 " --> pdb=" O LYS M 48 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N SER M 94 " --> pdb=" O LEU M 273 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE M 275 " --> pdb=" O SER M 94 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL M 96 " --> pdb=" O ILE M 275 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE M 227 " --> pdb=" O SER M 271 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU M 273 " --> pdb=" O ILE M 227 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU M 229 " --> pdb=" O LEU M 273 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE M 275 " --> pdb=" O LEU M 229 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N PHE M 231 " --> pdb=" O ILE M 275 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY M 119 " --> pdb=" O HIS M 228 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N SER M 230 " --> pdb=" O GLY M 119 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE M 121 " --> pdb=" O SER M 230 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASP M 232 " --> pdb=" O ILE M 121 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL M 123 " --> pdb=" O ASP M 232 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE M 198 " --> pdb=" O ILE M 174 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TYR M 176 " --> pdb=" O PHE M 198 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AC9, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.239A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR L 86 " --> pdb=" O THR L 102 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG L 45 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.997A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS L 134 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER L 176 " --> pdb=" O SER L 162 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER L 162 " --> pdb=" O SER L 176 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 129 through 131 Processing sheet with id=AD3, first strand: chain 'L' and resid 153 through 154 removed outlier: 4.094A pdb=" N LYS L 149 " --> pdb=" O THR L 193 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR L 193 " --> pdb=" O LYS L 149 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 48 through 49 removed outlier: 6.900A pdb=" N ILE N 8 " --> pdb=" O LYS N 48 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N SER N 94 " --> pdb=" O LEU N 273 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE N 275 " --> pdb=" O SER N 94 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL N 96 " --> pdb=" O ILE N 275 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE N 227 " --> pdb=" O SER N 271 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU N 273 " --> pdb=" O ILE N 227 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU N 229 " --> pdb=" O LEU N 273 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE N 275 " --> pdb=" O LEU N 229 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N PHE N 231 " --> pdb=" O ILE N 275 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY N 119 " --> pdb=" O HIS N 228 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER N 230 " --> pdb=" O GLY N 119 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE N 121 " --> pdb=" O SER N 230 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASP N 232 " --> pdb=" O ILE N 121 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL N 123 " --> pdb=" O ASP N 232 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE N 198 " --> pdb=" O ILE N 174 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TYR N 176 " --> pdb=" O PHE N 198 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 48 through 49 removed outlier: 6.900A pdb=" N ILE J 8 " --> pdb=" O LYS J 48 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N SER J 94 " --> pdb=" O LEU J 273 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE J 275 " --> pdb=" O SER J 94 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL J 96 " --> pdb=" O ILE J 275 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE J 227 " --> pdb=" O SER J 271 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU J 273 " --> pdb=" O ILE J 227 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU J 229 " --> pdb=" O LEU J 273 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE J 275 " --> pdb=" O LEU J 229 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N PHE J 231 " --> pdb=" O ILE J 275 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLY J 119 " --> pdb=" O HIS J 228 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER J 230 " --> pdb=" O GLY J 119 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE J 121 " --> pdb=" O SER J 230 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASP J 232 " --> pdb=" O ILE J 121 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL J 123 " --> pdb=" O ASP J 232 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE J 198 " --> pdb=" O ILE J 174 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR J 176 " --> pdb=" O PHE J 198 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 5 through 6 Processing sheet with id=AD7, first strand: chain 'O' and resid 10 through 12 removed outlier: 7.239A pdb=" N LEU O 11 " --> pdb=" O GLU O 105 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR O 86 " --> pdb=" O THR O 102 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG O 45 " --> pdb=" O GLN O 37 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 114 through 118 removed outlier: 3.997A pdb=" N VAL O 133 " --> pdb=" O PHE O 118 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS O 134 " --> pdb=" O SER O 177 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N TYR O 173 " --> pdb=" O ASN O 138 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER O 176 " --> pdb=" O SER O 162 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER O 162 " --> pdb=" O SER O 176 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 129 through 131 Processing sheet with id=AE1, first strand: chain 'O' and resid 153 through 154 removed outlier: 4.094A pdb=" N LYS O 149 " --> pdb=" O THR O 193 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR O 193 " --> pdb=" O LYS O 149 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 5 through 6 Processing sheet with id=AE3, first strand: chain 'P' and resid 10 through 12 removed outlier: 7.239A pdb=" N LEU P 11 " --> pdb=" O GLU P 105 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR P 86 " --> pdb=" O THR P 102 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG P 45 " --> pdb=" O GLN P 37 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 114 through 118 removed outlier: 3.997A pdb=" N VAL P 133 " --> pdb=" O PHE P 118 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS P 134 " --> pdb=" O SER P 177 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N TYR P 173 " --> pdb=" O ASN P 138 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER P 176 " --> pdb=" O SER P 162 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER P 162 " --> pdb=" O SER P 176 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 129 through 131 Processing sheet with id=AE6, first strand: chain 'P' and resid 153 through 154 removed outlier: 4.094A pdb=" N LYS P 149 " --> pdb=" O THR P 193 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR P 193 " --> pdb=" O LYS P 149 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.554A pdb=" N SER F 25 " --> pdb=" O GLN F 3 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER F 7 " --> pdb=" O SER F 21 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER F 21 " --> pdb=" O SER F 7 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.972A pdb=" N THR F 122 " --> pdb=" O GLU F 10 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS F 12 " --> pdb=" O THR F 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'F' and resid 46 through 50 removed outlier: 5.442A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 69 through 72 Processing sheet with id=AF2, first strand: chain 'F' and resid 132 through 133 removed outlier: 3.525A pdb=" N LEU F 150 " --> pdb=" O THR F 194 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N THR F 188 " --> pdb=" O GLY F 156 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU F 189 " --> pdb=" O ALA F 180 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ALA F 180 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER F 191 " --> pdb=" O PHE F 178 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 163 through 166 Processing sheet with id=AF4, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.554A pdb=" N SER G 25 " --> pdb=" O GLN G 3 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER G 7 " --> pdb=" O SER G 21 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.973A pdb=" N THR G 122 " --> pdb=" O GLU G 10 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS G 12 " --> pdb=" O THR G 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'G' and resid 46 through 50 removed outlier: 5.443A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 69 through 72 Processing sheet with id=AF8, first strand: chain 'G' and resid 132 through 133 removed outlier: 3.526A pdb=" N LEU G 150 " --> pdb=" O THR G 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR G 188 " --> pdb=" O GLY G 156 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU G 189 " --> pdb=" O ALA G 180 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA G 180 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER G 191 " --> pdb=" O PHE G 178 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 163 through 166 Processing sheet with id=AG1, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.554A pdb=" N SER K 25 " --> pdb=" O GLN K 3 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER K 7 " --> pdb=" O SER K 21 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER K 21 " --> pdb=" O SER K 7 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.972A pdb=" N THR K 122 " --> pdb=" O GLU K 10 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS K 12 " --> pdb=" O THR K 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'K' and resid 46 through 50 removed outlier: 5.443A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 69 through 72 Processing sheet with id=AG5, first strand: chain 'K' and resid 132 through 133 removed outlier: 3.525A pdb=" N LEU K 150 " --> pdb=" O THR K 194 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N THR K 188 " --> pdb=" O GLY K 156 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU K 189 " --> pdb=" O ALA K 180 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA K 180 " --> pdb=" O LEU K 189 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER K 191 " --> pdb=" O PHE K 178 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 163 through 166 Processing sheet with id=AG7, first strand: chain 'Q' and resid 3 through 7 removed outlier: 3.554A pdb=" N SER Q 25 " --> pdb=" O GLN Q 3 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER Q 7 " --> pdb=" O SER Q 21 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER Q 21 " --> pdb=" O SER Q 7 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 10 through 12 removed outlier: 3.972A pdb=" N THR Q 122 " --> pdb=" O GLU Q 10 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS Q 12 " --> pdb=" O THR Q 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'Q' and resid 46 through 50 removed outlier: 5.443A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY Q 49 " --> pdb=" O TRP Q 36 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Q' and resid 69 through 72 Processing sheet with id=AH2, first strand: chain 'Q' and resid 132 through 133 removed outlier: 3.526A pdb=" N LEU Q 150 " --> pdb=" O THR Q 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR Q 188 " --> pdb=" O GLY Q 156 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU Q 189 " --> pdb=" O ALA Q 180 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ALA Q 180 " --> pdb=" O LEU Q 189 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER Q 191 " --> pdb=" O PHE Q 178 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Q' and resid 163 through 166 Processing sheet with id=AH4, first strand: chain 'R' and resid 3 through 7 removed outlier: 3.555A pdb=" N SER R 25 " --> pdb=" O GLN R 3 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER R 7 " --> pdb=" O SER R 21 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER R 21 " --> pdb=" O SER R 7 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'R' and resid 10 through 12 removed outlier: 3.972A pdb=" N THR R 122 " --> pdb=" O GLU R 10 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS R 12 " --> pdb=" O THR R 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'R' and resid 46 through 50 removed outlier: 5.444A pdb=" N TRP R 47 " --> pdb=" O ARG R 38 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ARG R 38 " --> pdb=" O TRP R 47 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY R 49 " --> pdb=" O TRP R 36 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'R' and resid 69 through 72 Processing sheet with id=AH8, first strand: chain 'R' and resid 132 through 133 removed outlier: 3.525A pdb=" N LEU R 150 " --> pdb=" O THR R 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR R 188 " --> pdb=" O GLY R 156 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU R 189 " --> pdb=" O ALA R 180 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ALA R 180 " --> pdb=" O LEU R 189 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER R 191 " --> pdb=" O PHE R 178 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'R' and resid 163 through 166 948 hydrogen bonds defined for protein. 2520 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: 7.07 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10997 1.34 - 1.46: 7645 1.46 - 1.58: 16530 1.58 - 1.70: 6 1.70 - 1.82: 180 Bond restraints: 35358 Sorted by residual: bond pdb=" N SER F 124 " pdb=" CA SER F 124 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.23e-02 6.61e+03 8.05e+00 bond pdb=" N SER Q 124 " pdb=" CA SER Q 124 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.23e-02 6.61e+03 7.71e+00 bond pdb=" N SER D 124 " pdb=" CA SER D 124 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.23e-02 6.61e+03 7.68e+00 bond pdb=" N SER R 124 " pdb=" CA SER R 124 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.23e-02 6.61e+03 7.55e+00 bond pdb=" N SER K 124 " pdb=" CA SER K 124 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.23e-02 6.61e+03 7.42e+00 ... (remaining 35353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 46822 2.89 - 5.79: 1070 5.79 - 8.68: 228 8.68 - 11.58: 18 11.58 - 14.47: 12 Bond angle restraints: 48150 Sorted by residual: angle pdb=" CA TYR H 49 " pdb=" CB TYR H 49 " pdb=" CG TYR H 49 " ideal model delta sigma weight residual 113.90 123.67 -9.77 1.80e+00 3.09e-01 2.95e+01 angle pdb=" CA TYR O 49 " pdb=" CB TYR O 49 " pdb=" CG TYR O 49 " ideal model delta sigma weight residual 113.90 123.67 -9.77 1.80e+00 3.09e-01 2.95e+01 angle pdb=" CA TYR E 49 " pdb=" CB TYR E 49 " pdb=" CG TYR E 49 " ideal model delta sigma weight residual 113.90 123.67 -9.77 1.80e+00 3.09e-01 2.94e+01 angle pdb=" CA TYR I 49 " pdb=" CB TYR I 49 " pdb=" CG TYR I 49 " ideal model delta sigma weight residual 113.90 123.66 -9.76 1.80e+00 3.09e-01 2.94e+01 angle pdb=" CA TYR L 49 " pdb=" CB TYR L 49 " pdb=" CG TYR L 49 " ideal model delta sigma weight residual 113.90 123.65 -9.75 1.80e+00 3.09e-01 2.93e+01 ... (remaining 48145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.38: 19584 13.38 - 26.77: 1140 26.77 - 40.15: 336 40.15 - 53.53: 102 53.53 - 66.92: 12 Dihedral angle restraints: 21174 sinusoidal: 8184 harmonic: 12990 Sorted by residual: dihedral pdb=" CA PRO K 135 " pdb=" C PRO K 135 " pdb=" N LEU K 136 " pdb=" CA LEU K 136 " ideal model delta harmonic sigma weight residual 180.00 134.28 45.72 0 5.00e+00 4.00e-02 8.36e+01 dihedral pdb=" CA PRO R 135 " pdb=" C PRO R 135 " pdb=" N LEU R 136 " pdb=" CA LEU R 136 " ideal model delta harmonic sigma weight residual 180.00 134.31 45.69 0 5.00e+00 4.00e-02 8.35e+01 dihedral pdb=" CA PRO Q 135 " pdb=" C PRO Q 135 " pdb=" N LEU Q 136 " pdb=" CA LEU Q 136 " ideal model delta harmonic sigma weight residual 180.00 134.32 45.68 0 5.00e+00 4.00e-02 8.35e+01 ... (remaining 21171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3859 0.055 - 0.110: 1219 0.110 - 0.166: 306 0.166 - 0.221: 61 0.221 - 0.276: 21 Chirality restraints: 5466 Sorted by residual: chirality pdb=" CA GLU H 1 " pdb=" N GLU H 1 " pdb=" C GLU H 1 " pdb=" CB GLU H 1 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA GLU L 1 " pdb=" N GLU L 1 " pdb=" C GLU L 1 " pdb=" CB GLU L 1 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA GLU O 1 " pdb=" N GLU O 1 " pdb=" C GLU O 1 " pdb=" CB GLU O 1 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 5463 not shown) Planarity restraints: 6186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 13 " 0.075 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO D 14 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO D 14 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO D 14 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 13 " -0.075 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO F 14 " 0.197 5.00e-02 4.00e+02 pdb=" CA PRO F 14 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO F 14 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS G 13 " -0.074 5.00e-02 4.00e+02 1.14e-01 2.07e+01 pdb=" N PRO G 14 " 0.197 5.00e-02 4.00e+02 pdb=" CA PRO G 14 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO G 14 " -0.063 5.00e-02 4.00e+02 ... (remaining 6183 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1654 2.71 - 3.25: 32750 3.25 - 3.80: 58824 3.80 - 4.35: 73442 4.35 - 4.90: 121881 Nonbonded interactions: 288551 Sorted by model distance: nonbonded pdb=" OG SER L 116 " pdb=" OG1 THR K 149 " model vdw 2.157 3.040 nonbonded pdb=" OE2 GLU M 186 " pdb=" OH TYR R 104 " model vdw 2.182 3.040 nonbonded pdb=" O ALA R 101 " pdb=" OG SER R 106 " model vdw 2.207 3.040 nonbonded pdb=" O ALA Q 101 " pdb=" OG SER Q 106 " model vdw 2.207 3.040 nonbonded pdb=" O ALA K 101 " pdb=" OG SER K 106 " model vdw 2.207 3.040 ... (remaining 288546 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'M' selection = chain 'N' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'P' } 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: 4.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 29.500 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5358 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 : 0.008 0.105 35382 Z= 0.333 Angle : 1.099 14.472 48198 Z= 0.594 Chirality : 0.061 0.276 5466 Planarity : 0.010 0.114 6186 Dihedral : 10.178 66.915 12822 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.80 % Allowed : 11.36 % Favored : 87.84 % Rotamer: Outliers : 1.09 % Allowed : 4.22 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 2.08 % Twisted General : 1.04 % 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: -4.41 (0.10), residues: 4506 helix: -2.69 (0.13), residues: 828 sheet: -2.85 (0.13), residues: 1218 loop : -3.09 (0.11), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 98 TYR 0.053 0.003 TYR P 49 PHE 0.043 0.005 PHE H 98 TRP 0.043 0.004 TRP D 115 HIS 0.015 0.004 HIS E 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00763 / 0.33 (35358) covalent geometry : angle 1.09857 / 0.59 (48150) SS BOND : bond 0.00518 / 0.32 ( 24) SS BOND : angle 1.60067 / 1.09 ( 48) hydrogen bonds : bond 0.21434 / 14.95 ( 948) hydrogen bonds : angle 9.49373 / 6.69 ( 2520) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1025 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 983 time to evaluate : 1.186 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: A 21 ARG cc_start: 0.7387 (mmm-85) cc_final: 0.7184 (mtt180) REVERT: A 46 ASP cc_start: 0.5912 (t0) cc_final: 0.5562 (t0) REVERT: A 227 ILE cc_start: 0.8524 (mm) cc_final: 0.8284 (mt) REVERT: D 48 MET cc_start: 0.6907 (ptm) cc_final: 0.6072 (ttp) REVERT: D 105 ARG cc_start: 0.5153 (mtp180) cc_final: 0.4750 (ttt-90) REVERT: E 42 GLN cc_start: 0.5914 (mm-40) cc_final: 0.5651 (mt0) REVERT: E 83 PHE cc_start: 0.4375 (m-10) cc_final: 0.3834 (m-10) REVERT: E 148 TRP cc_start: 0.2182 (m100) cc_final: 0.1063 (m100) REVERT: B 32 ARG cc_start: 0.8103 (mtt180) cc_final: 0.7538 (mtt-85) REVERT: B 46 ASP cc_start: 0.6236 (t0) cc_final: 0.5861 (t0) REVERT: B 48 LYS cc_start: 0.5057 (tttt) cc_final: 0.4755 (tttm) REVERT: B 227 ILE cc_start: 0.8609 (mm) cc_final: 0.8340 (mt) REVERT: H 171 SER cc_start: 0.5114 (m) cc_final: 0.4641 (p) REVERT: I 83 PHE cc_start: 0.5632 (m-10) cc_final: 0.5164 (m-10) REVERT: I 171 SER cc_start: 0.5674 (m) cc_final: 0.5401 (p) REVERT: M 225 ARG cc_start: 0.0870 (ptt180) cc_final: 0.0646 (ptt180) REVERT: M 259 TYR cc_start: 0.3099 (t80) cc_final: 0.2639 (t80) REVERT: M 265 TYR cc_start: 0.2646 (t80) cc_final: 0.2402 (t80) REVERT: M 278 VAL cc_start: 0.2106 (t) cc_final: 0.1788 (p) REVERT: L 88 CYS cc_start: 0.1266 (p) cc_final: 0.0570 (p) REVERT: L 146 VAL cc_start: 0.2500 (t) cc_final: 0.2294 (p) REVERT: N 241 THR cc_start: 0.4236 (p) cc_final: 0.3940 (p) REVERT: N 306 LEU cc_start: 0.2201 (tt) cc_final: 0.1807 (tp) REVERT: J 24 VAL cc_start: 0.2375 (m) cc_final: 0.2165 (m) REVERT: J 122 TRP cc_start: 0.2171 (t-100) cc_final: 0.1897 (t-100) REVERT: J 165 VAL cc_start: 0.1486 (t) cc_final: 0.1120 (p) REVERT: O 124 GLN cc_start: 0.0448 (tt0) cc_final: 0.0107 (tt0) REVERT: O 138 ASN cc_start: 0.3470 (m-40) cc_final: 0.2892 (m-40) REVERT: O 139 PHE cc_start: 0.1105 (p90) cc_final: 0.0871 (p90) REVERT: P 1 GLU cc_start: 0.2585 (OUTLIER) cc_final: 0.2228 (mp0) REVERT: P 118 PHE cc_start: 0.0369 (m-80) cc_final: 0.0096 (m-80) REVERT: F 48 MET cc_start: 0.6728 (ptm) cc_final: 0.5588 (ttp) REVERT: F 65 GLN cc_start: 0.5441 (mp-120) cc_final: 0.4939 (tp40) REVERT: F 73 ASP cc_start: 0.6340 (t70) cc_final: 0.5973 (t0) REVERT: F 82 GLU cc_start: 0.6216 (mt-10) cc_final: 0.5935 (mt-10) REVERT: F 125 SER cc_start: 0.7117 (OUTLIER) cc_final: 0.6683 (p) REVERT: G 23 LYS cc_start: 0.6824 (tmtp) cc_final: 0.6299 (tttp) REVERT: G 73 ASP cc_start: 0.5990 (t70) cc_final: 0.5714 (t0) REVERT: G 153 LEU cc_start: 0.3920 (tt) cc_final: 0.3318 (mp) REVERT: K 69 THR cc_start: 0.4297 (p) cc_final: 0.3741 (m) REVERT: K 125 SER cc_start: 0.3268 (OUTLIER) cc_final: 0.2876 (p) REVERT: K 167 ASN cc_start: 0.3351 (m-40) cc_final: 0.2994 (m-40) REVERT: K 207 CYS cc_start: 0.0087 (p) cc_final: -0.0177 (p) REVERT: Q 30 THR cc_start: 0.4130 (p) cc_final: 0.3807 (m) REVERT: Q 69 THR cc_start: 0.3574 (p) cc_final: 0.3192 (m) REVERT: Q 147 MET cc_start: 0.0485 (mmm) cc_final: 0.0047 (tpp) REVERT: Q 158 PHE cc_start: 0.1319 (t80) cc_final: 0.0655 (t80) REVERT: R 36 TRP cc_start: 0.2405 (m100) cc_final: 0.1594 (m100) REVERT: R 147 MET cc_start: 0.1319 (mmm) cc_final: 0.0977 (tpp) REVERT: R 158 PHE cc_start: 0.2828 (t80) cc_final: 0.2589 (t80) outliers start: 42 outliers final: 7 residues processed: 1014 average time/residue: 0.2248 time to fit residues: 356.7512 Evaluate side-chains 521 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 511 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain P residue 1 GLU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain R residue 122 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: [432, 197, 388, 215, 20, 132, 261, 248, 207, 401, 424] chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.5980 chunk 401 optimal weight: 6.9990 chunk 424 optimal weight: 0.2980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 HIS A 126 HIS A 141 HIS D 1 GLN D 31 ASN D 59 ASN D 109 HIS D 183 GLN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS B 126 HIS B 141 HIS ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS C 115 HIS C 141 HIS H 38 GLN H 189 HIS I 38 GLN I 137 ASN I 212 ASN M 126 HIS N 126 HIS J 115 HIS J 126 HIS ** J 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 GLN O 137 ASN O 161 ASN P 137 ASN F 1 GLN F 31 ASN F 39 GLN F 59 ASN F 109 HIS ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 ASN G 59 ASN G 65 GLN G 109 HIS ** G 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 GLN K 31 ASN ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 31 ASN Q 59 ASN Q 110 ASN ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN ** R 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.197517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.164792 restraints weight = 68676.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.161427 restraints weight = 117805.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.159159 restraints weight = 100420.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.158522 restraints weight = 89815.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.156729 restraints weight = 87499.169| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5579 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 35382 Z= 0.156 Angle : 0.792 15.852 48198 Z= 0.407 Chirality : 0.049 0.204 5466 Planarity : 0.008 0.118 6186 Dihedral : 7.441 50.903 4898 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.87 % Favored : 88.84 % Rotamer: Outliers : 3.28 % Allowed : 8.75 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 2.08 % Twisted General : 0.50 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.12), residues: 4506 helix: -1.02 (0.17), residues: 792 sheet: -2.41 (0.13), residues: 1350 loop : -2.51 (0.12), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 155 TYR 0.036 0.002 TYR P 49 PHE 0.022 0.002 PHE P 98 TRP 0.032 0.002 TRP Q 36 HIS 0.009 0.002 HIS I 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (35358) covalent geometry : angle 0.79122 / 0.41 (48150) SS BOND : bond 0.00627 / 0.38 ( 24) SS BOND : angle 1.50631 / 0.99 ( 48) hydrogen bonds : bond 0.03802 / 2.60 ( 948) hydrogen bonds : angle 6.45526 / 4.57 ( 2520) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 607 time to evaluate : 1.128 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: A 46 ASP cc_start: 0.5882 (t0) cc_final: 0.5436 (t0) REVERT: D 48 MET cc_start: 0.7016 (ptm) cc_final: 0.6123 (ttp) REVERT: D 105 ARG cc_start: 0.5289 (mtp180) cc_final: 0.4725 (ttt-90) REVERT: E 11 LEU cc_start: 0.3999 (OUTLIER) cc_final: 0.3741 (tm) REVERT: E 13 LEU cc_start: 0.4454 (OUTLIER) cc_final: 0.4252 (tp) REVERT: E 42 GLN cc_start: 0.6058 (mm-40) cc_final: 0.5752 (mt0) REVERT: E 83 PHE cc_start: 0.4532 (m-10) cc_final: 0.4121 (m-80) REVERT: B 32 ARG cc_start: 0.8178 (mtt180) cc_final: 0.7622 (mtt-85) REVERT: B 46 ASP cc_start: 0.6281 (t0) cc_final: 0.5966 (t0) REVERT: B 48 LYS cc_start: 0.5347 (tttt) cc_final: 0.5010 (tttm) REVERT: C 267 THR cc_start: 0.7729 (p) cc_final: 0.7518 (p) REVERT: H 11 LEU cc_start: 0.4944 (OUTLIER) cc_final: 0.4150 (tp) REVERT: I 83 PHE cc_start: 0.6112 (m-10) cc_final: 0.5888 (m-10) REVERT: I 210 ASN cc_start: 0.3541 (t0) cc_final: 0.3154 (t0) REVERT: M 92 ARG cc_start: 0.1457 (mmt90) cc_final: 0.0739 (mmt90) REVERT: M 200 MET cc_start: 0.1945 (mmm) cc_final: 0.1531 (tpp) REVERT: M 259 TYR cc_start: 0.3420 (t80) cc_final: 0.2763 (t80) REVERT: M 316 ASP cc_start: 0.2626 (t0) cc_final: 0.2146 (t0) REVERT: L 175 MET cc_start: 0.0831 (ppp) cc_final: 0.0211 (tmm) REVERT: L 187 GLU cc_start: 0.4006 (pm20) cc_final: 0.3470 (mm-30) REVERT: N 273 LEU cc_start: 0.3488 (mp) cc_final: 0.3147 (tt) REVERT: N 304 PHE cc_start: 0.2275 (m-80) cc_final: 0.2002 (m-80) REVERT: N 306 LEU cc_start: 0.2503 (tt) cc_final: 0.2181 (tp) REVERT: J 165 VAL cc_start: 0.1701 (t) cc_final: 0.1344 (p) REVERT: O 33 LEU cc_start: 0.3341 (OUTLIER) cc_final: 0.2838 (pp) REVERT: O 58 ILE cc_start: 0.1589 (OUTLIER) cc_final: 0.1384 (tp) REVERT: O 70 ASP cc_start: 0.3463 (m-30) cc_final: 0.3054 (t0) REVERT: O 93 LEU cc_start: 0.4898 (OUTLIER) cc_final: 0.4486 (tm) REVERT: O 138 ASN cc_start: 0.3583 (m-40) cc_final: 0.3294 (m-40) REVERT: P 7 SER cc_start: 0.1466 (m) cc_final: 0.1062 (t) REVERT: F 18 VAL cc_start: 0.7108 (OUTLIER) cc_final: 0.6808 (m) REVERT: F 48 MET cc_start: 0.6957 (ptm) cc_final: 0.5747 (ttp) REVERT: F 59 ASN cc_start: 0.6998 (t0) cc_final: 0.6438 (t0) REVERT: F 65 GLN cc_start: 0.5295 (mp-120) cc_final: 0.4940 (tp40) REVERT: F 176 HIS cc_start: 0.2420 (OUTLIER) cc_final: 0.1240 (m90) REVERT: G 18 VAL cc_start: 0.7416 (OUTLIER) cc_final: 0.6806 (t) REVERT: G 59 ASN cc_start: 0.7006 (t0) cc_final: 0.6736 (t0) REVERT: G 73 ASP cc_start: 0.6008 (t70) cc_final: 0.5629 (t0) REVERT: G 76 THR cc_start: 0.5394 (p) cc_final: 0.5143 (t) REVERT: K 36 TRP cc_start: 0.2333 (m100) cc_final: 0.1749 (m100) REVERT: K 62 GLN cc_start: 0.6202 (pp30) cc_final: 0.5991 (pp30) REVERT: K 69 THR cc_start: 0.4745 (p) cc_final: 0.4401 (m) REVERT: K 167 ASN cc_start: 0.3283 (m-40) cc_final: 0.2836 (m-40) REVERT: K 182 LEU cc_start: 0.2934 (OUTLIER) cc_final: 0.2607 (tp) REVERT: K 207 CYS cc_start: -0.0071 (p) cc_final: -0.0297 (p) REVERT: Q 48 MET cc_start: 0.3670 (ptp) cc_final: 0.2526 (ptp) REVERT: Q 69 THR cc_start: 0.4149 (p) cc_final: 0.3647 (m) REVERT: Q 147 MET cc_start: 0.0723 (mmm) cc_final: 0.0404 (tpp) REVERT: Q 158 PHE cc_start: 0.1259 (t80) cc_final: 0.0922 (t80) REVERT: R 29 PHE cc_start: 0.4097 (t80) cc_final: 0.3854 (t80) REVERT: R 147 MET cc_start: 0.1277 (mmm) cc_final: 0.1059 (tpp) REVERT: R 153 LEU cc_start: 0.1381 (tt) cc_final: 0.1161 (tp) REVERT: R 158 PHE cc_start: 0.2841 (t80) cc_final: 0.2421 (t80) outliers start: 126 outliers final: 70 residues processed: 705 average time/residue: 0.2027 time to fit residues: 231.4025 Evaluate side-chains 505 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 425 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 126 THR Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 108 ILE Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain M residue 232 ASP Chi-restraints excluded: chain M residue 276 MET Chi-restraints excluded: chain M residue 290 THR Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 244 THR Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 300 THR Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 213 GLU Chi-restraints excluded: chain P residue 150 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 191 SER Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain R residue 122 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: [275, 245, 42, 199, 161, 88, 335, 215, 270, 248, 111] chunk 275 optimal weight: 20.0000 chunk 245 optimal weight: 0.0030 chunk 42 optimal weight: 3.9990 chunk 199 optimal weight: 5.9990 chunk 161 optimal weight: 0.3980 chunk 88 optimal weight: 0.9980 chunk 335 optimal weight: 9.9990 chunk 215 optimal weight: 20.0000 chunk 270 optimal weight: 0.8980 chunk 248 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 161 ASN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 101 HIS N 311 ASN ** J 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 HIS O 89 GLN ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN G 110 ASN G 167 ASN ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.197499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.162738 restraints weight = 67766.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.160486 restraints weight = 129254.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.160837 restraints weight = 113156.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.159466 restraints weight = 85605.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.159766 restraints weight = 79109.387| |-----------------------------------------------------------------------------| r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5500 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35382 Z= 0.137 Angle : 0.744 14.812 48198 Z= 0.377 Chirality : 0.048 0.236 5466 Planarity : 0.007 0.104 6186 Dihedral : 6.879 50.880 4890 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.99 % Favored : 88.86 % Rotamer: Outliers : 3.15 % Allowed : 10.89 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 2.08 % Twisted General : 0.42 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.12), residues: 4506 helix: -0.48 (0.17), residues: 792 sheet: -2.15 (0.14), residues: 1374 loop : -2.31 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 155 TYR 0.035 0.002 TYR O 49 PHE 0.043 0.002 PHE K 112 TRP 0.024 0.002 TRP R 115 HIS 0.018 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (35358) covalent geometry : angle 0.74285 / 0.38 (48150) SS BOND : bond 0.00417 / 0.27 ( 24) SS BOND : angle 1.73389 / 1.14 ( 48) hydrogen bonds : bond 0.03375 / 2.32 ( 948) hydrogen bonds : angle 5.92174 / 4.18 ( 2520) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 501 time to evaluate : 1.301 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: A 46 ASP cc_start: 0.5800 (t0) cc_final: 0.5528 (t0) REVERT: D 48 MET cc_start: 0.6956 (ptm) cc_final: 0.6030 (ttp) REVERT: E 11 LEU cc_start: 0.4042 (OUTLIER) cc_final: 0.3801 (tm) REVERT: E 42 GLN cc_start: 0.5930 (mm-40) cc_final: 0.5617 (mt0) REVERT: E 80 PRO cc_start: 0.2763 (Cg_endo) cc_final: 0.2555 (Cg_exo) REVERT: E 83 PHE cc_start: 0.4909 (m-10) cc_final: 0.4510 (m-80) REVERT: E 163 TRP cc_start: 0.4929 (m-10) cc_final: 0.4720 (m-10) REVERT: B 32 ARG cc_start: 0.8164 (mtt180) cc_final: 0.7495 (mtt-85) REVERT: B 46 ASP cc_start: 0.6236 (t0) cc_final: 0.5882 (t0) REVERT: C 267 THR cc_start: 0.7581 (p) cc_final: 0.7325 (p) REVERT: H 11 LEU cc_start: 0.5061 (OUTLIER) cc_final: 0.4185 (tp) REVERT: H 106 ILE cc_start: 0.6813 (mp) cc_final: 0.6123 (mt) REVERT: M 58 ILE cc_start: 0.1411 (OUTLIER) cc_final: 0.1156 (tp) REVERT: M 92 ARG cc_start: 0.1569 (mmt90) cc_final: 0.1224 (mmt90) REVERT: M 259 TYR cc_start: 0.3372 (t80) cc_final: 0.2798 (t80) REVERT: M 316 ASP cc_start: 0.2476 (t0) cc_final: 0.1894 (t0) REVERT: L 4 MET cc_start: 0.1275 (tpp) cc_final: 0.0799 (tpp) REVERT: L 47 LEU cc_start: 0.5541 (mt) cc_final: 0.4953 (mt) REVERT: L 48 ILE cc_start: 0.4877 (mm) cc_final: 0.4399 (mm) REVERT: L 175 MET cc_start: 0.0891 (ppp) cc_final: 0.0117 (tmm) REVERT: L 187 GLU cc_start: 0.3699 (pm20) cc_final: 0.3401 (mm-30) REVERT: N 304 PHE cc_start: 0.2333 (m-80) cc_final: 0.2072 (m-80) REVERT: N 306 LEU cc_start: 0.2753 (tt) cc_final: 0.2462 (tp) REVERT: O 4 MET cc_start: 0.2149 (tpp) cc_final: 0.1741 (mmm) REVERT: O 58 ILE cc_start: 0.1534 (OUTLIER) cc_final: 0.1130 (tp) REVERT: O 93 LEU cc_start: 0.4514 (OUTLIER) cc_final: 0.3931 (tm) REVERT: P 7 SER cc_start: 0.1340 (m) cc_final: 0.0978 (t) REVERT: P 33 LEU cc_start: 0.3072 (OUTLIER) cc_final: 0.2561 (pp) REVERT: F 18 VAL cc_start: 0.7062 (OUTLIER) cc_final: 0.6843 (m) REVERT: F 48 MET cc_start: 0.6811 (ptm) cc_final: 0.5752 (ttp) REVERT: F 59 ASN cc_start: 0.7054 (t0) cc_final: 0.6514 (t0) REVERT: F 65 GLN cc_start: 0.5063 (mp-120) cc_final: 0.4495 (tp40) REVERT: G 18 VAL cc_start: 0.7219 (OUTLIER) cc_final: 0.6962 (t) REVERT: G 28 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8136 (p) REVERT: G 76 THR cc_start: 0.5304 (p) cc_final: 0.5001 (t) REVERT: K 36 TRP cc_start: 0.2403 (m100) cc_final: 0.1972 (m100) REVERT: K 48 MET cc_start: 0.4312 (mtm) cc_final: 0.3899 (mtp) REVERT: K 69 THR cc_start: 0.4447 (p) cc_final: 0.3999 (m) REVERT: K 167 ASN cc_start: 0.3255 (m-40) cc_final: 0.2768 (m-40) REVERT: K 207 CYS cc_start: -0.0119 (p) cc_final: -0.0461 (p) REVERT: Q 28 THR cc_start: 0.2446 (OUTLIER) cc_final: 0.2204 (m) REVERT: Q 48 MET cc_start: 0.3566 (OUTLIER) cc_final: 0.2344 (ptp) REVERT: Q 69 THR cc_start: 0.3998 (p) cc_final: 0.3492 (m) REVERT: Q 147 MET cc_start: 0.0758 (mmm) cc_final: 0.0447 (tpp) REVERT: Q 158 PHE cc_start: 0.1042 (t80) cc_final: 0.0700 (t80) REVERT: R 23 LYS cc_start: 0.3556 (mttp) cc_final: 0.3194 (mtmm) REVERT: R 36 TRP cc_start: 0.2398 (m100) cc_final: 0.2105 (m100) REVERT: R 38 ARG cc_start: 0.1941 (ptm160) cc_final: 0.1731 (ptm160) REVERT: R 105 ARG cc_start: 0.4143 (ttm110) cc_final: 0.3919 (ttm110) REVERT: R 153 LEU cc_start: 0.1215 (tt) cc_final: 0.0997 (tp) REVERT: R 158 PHE cc_start: 0.2723 (t80) cc_final: 0.2406 (t80) outliers start: 121 outliers final: 72 residues processed: 601 average time/residue: 0.2025 time to fit residues: 198.5656 Evaluate side-chains 483 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 400 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 101 HIS Chi-restraints excluded: chain M residue 260 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain N residue 303 CYS Chi-restraints excluded: chain J residue 101 HIS Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 85 VAL Chi-restraints excluded: chain O residue 89 GLN Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain O residue 134 CYS Chi-restraints excluded: chain O residue 213 GLU Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 150 ILE Chi-restraints excluded: chain P residue 194 CYS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 191 SER Chi-restraints excluded: chain Q residue 22 CYS Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain Q residue 215 SER Chi-restraints excluded: chain R residue 37 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: [115, 10, 188, 42, 387, 405, 19, 165, 398, 58, 99] chunk 115 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 188 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 387 optimal weight: 7.9990 chunk 405 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 398 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 187 HIS N 311 ASN O 89 GLN O 161 ASN F 143 GLN ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 109 HIS ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 167 ASN ** R 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.196601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.162518 restraints weight = 67695.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.160600 restraints weight = 132116.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.160421 restraints weight = 110713.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.159531 restraints weight = 82630.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.159580 restraints weight = 82865.361| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5505 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35382 Z= 0.147 Angle : 0.733 13.625 48198 Z= 0.371 Chirality : 0.047 0.266 5466 Planarity : 0.006 0.099 6186 Dihedral : 6.593 54.338 4886 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.10 % Favored : 88.77 % Rotamer: Outliers : 3.44 % Allowed : 12.01 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 1.74 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.12), residues: 4506 helix: -0.31 (0.18), residues: 792 sheet: -1.92 (0.14), residues: 1362 loop : -2.25 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 155 TYR 0.028 0.002 TYR O 36 PHE 0.034 0.002 PHE P 98 TRP 0.031 0.002 TRP R 115 HIS 0.021 0.001 HIS M 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (35358) covalent geometry : angle 0.73185 / 0.37 (48150) SS BOND : bond 0.00366 / 0.23 ( 24) SS BOND : angle 1.53080 / 1.07 ( 48) hydrogen bonds : bond 0.03213 / 2.19 ( 948) hydrogen bonds : angle 5.71790 / 4.03 ( 2520) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 459 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.6004 (t0) cc_final: 0.5615 (t0) REVERT: A 89 LYS cc_start: 0.3552 (ptpt) cc_final: 0.3036 (mtmt) REVERT: A 288 GLU cc_start: 0.6465 (mt-10) cc_final: 0.5810 (mt-10) REVERT: D 48 MET cc_start: 0.7018 (ptm) cc_final: 0.5820 (ttp) REVERT: E 11 LEU cc_start: 0.4395 (OUTLIER) cc_final: 0.4097 (tm) REVERT: E 42 GLN cc_start: 0.5885 (mm-40) cc_final: 0.5595 (mt0) REVERT: E 80 PRO cc_start: 0.2820 (Cg_endo) cc_final: 0.2470 (Cg_exo) REVERT: B 46 ASP cc_start: 0.6288 (t0) cc_final: 0.5957 (t0) REVERT: H 155 ARG cc_start: 0.1179 (tpt90) cc_final: 0.0483 (tmt170) REVERT: M 200 MET cc_start: 0.1850 (mmm) cc_final: 0.1091 (mmt) REVERT: L 4 MET cc_start: 0.1452 (tpp) cc_final: 0.0999 (tpp) REVERT: L 48 ILE cc_start: 0.4667 (mm) cc_final: 0.4118 (mm) REVERT: N 40 LEU cc_start: 0.1982 (mt) cc_final: 0.1756 (tp) REVERT: N 151 GLU cc_start: 0.2050 (mp0) cc_final: 0.1182 (mt-10) REVERT: N 265 TYR cc_start: 0.1368 (t80) cc_final: 0.1105 (t80) REVERT: N 306 LEU cc_start: 0.2539 (tt) cc_final: 0.2201 (tp) REVERT: J 176 TYR cc_start: 0.1509 (m-10) cc_final: 0.1308 (m-10) REVERT: J 193 LEU cc_start: 0.1984 (OUTLIER) cc_final: 0.1690 (mm) REVERT: J 259 TYR cc_start: 0.2996 (t80) cc_final: 0.2592 (t80) REVERT: O 37 GLN cc_start: 0.4130 (tp-100) cc_final: 0.3836 (tp40) REVERT: O 58 ILE cc_start: 0.1441 (OUTLIER) cc_final: 0.1210 (tp) REVERT: O 70 ASP cc_start: 0.3327 (m-30) cc_final: 0.2995 (t0) REVERT: O 93 LEU cc_start: 0.4349 (OUTLIER) cc_final: 0.3749 (tm) REVERT: O 139 PHE cc_start: 0.0788 (p90) cc_final: 0.0143 (p90) REVERT: P 163 TRP cc_start: 0.2132 (m100) cc_final: 0.1114 (m100) REVERT: F 18 VAL cc_start: 0.7025 (OUTLIER) cc_final: 0.6686 (t) REVERT: F 48 MET cc_start: 0.6991 (ptm) cc_final: 0.5818 (ttp) REVERT: F 59 ASN cc_start: 0.7158 (t0) cc_final: 0.6696 (t0) REVERT: F 65 GLN cc_start: 0.5369 (mp-120) cc_final: 0.4778 (tp40) REVERT: F 145 ASN cc_start: 0.2576 (OUTLIER) cc_final: 0.2068 (m-40) REVERT: G 18 VAL cc_start: 0.7196 (OUTLIER) cc_final: 0.6972 (t) REVERT: G 28 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8122 (p) REVERT: G 59 ASN cc_start: 0.7373 (t0) cc_final: 0.7072 (t0) REVERT: G 76 THR cc_start: 0.5430 (p) cc_final: 0.5177 (t) REVERT: G 147 MET cc_start: 0.2621 (tpp) cc_final: 0.2234 (ppp) REVERT: G 193 VAL cc_start: 0.3404 (OUTLIER) cc_final: 0.3181 (t) REVERT: K 48 MET cc_start: 0.4439 (mtm) cc_final: 0.3944 (mtp) REVERT: K 69 THR cc_start: 0.4243 (p) cc_final: 0.3800 (m) REVERT: K 167 ASN cc_start: 0.3399 (m-40) cc_final: 0.2985 (m110) REVERT: K 207 CYS cc_start: 0.0009 (p) cc_final: -0.0399 (p) REVERT: Q 28 THR cc_start: 0.2269 (OUTLIER) cc_final: 0.2016 (m) REVERT: Q 29 PHE cc_start: 0.2842 (OUTLIER) cc_final: 0.2572 (t80) REVERT: Q 30 THR cc_start: 0.4262 (p) cc_final: 0.3777 (m) REVERT: Q 48 MET cc_start: 0.3324 (OUTLIER) cc_final: 0.2095 (ptp) REVERT: Q 158 PHE cc_start: 0.1234 (t80) cc_final: 0.0961 (t80) REVERT: R 27 TYR cc_start: 0.1127 (p90) cc_final: 0.0490 (p90) REVERT: R 36 TRP cc_start: 0.2739 (m100) cc_final: 0.2286 (m100) REVERT: R 48 MET cc_start: 0.4384 (ptt) cc_final: 0.4172 (ptm) REVERT: R 50 TRP cc_start: 0.3066 (t60) cc_final: 0.2398 (t60) REVERT: R 158 PHE cc_start: 0.2474 (t80) cc_final: 0.2197 (t80) outliers start: 132 outliers final: 82 residues processed: 557 average time/residue: 0.1973 time to fit residues: 179.6085 Evaluate side-chains 484 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 390 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 126 THR Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain N residue 290 THR Chi-restraints excluded: chain N residue 299 ILE Chi-restraints excluded: chain N residue 303 CYS Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 300 THR Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain P residue 150 ILE Chi-restraints excluded: chain P residue 194 CYS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 191 SER Chi-restraints excluded: chain Q residue 22 CYS Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 29 PHE Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain Q residue 216 THR Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 122 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: [42, 440, 221, 191, 297, 348, 78, 87, 92, 179, 17] chunk 42 optimal weight: 1.9990 chunk 440 optimal weight: 8.9990 chunk 221 optimal weight: 4.9990 chunk 191 optimal weight: 5.9990 chunk 297 optimal weight: 3.9990 chunk 348 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 179 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 HIS E 38 GLN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS C 60 ASN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS M 101 HIS L 189 HIS ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 311 ASN J 311 ASN O 89 GLN O 161 ASN F 143 GLN F 167 ASN ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 183 GLN Q 59 ASN R 6 GLN ** R 183 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 = 0.4616 r_free = 0.4616 target = 0.195856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.161249 restraints weight = 67389.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.158368 restraints weight = 133939.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.158932 restraints weight = 124300.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.158016 restraints weight = 86244.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.158091 restraints weight = 85560.296| |-----------------------------------------------------------------------------| r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5543 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 35382 Z= 0.174 Angle : 0.761 13.953 48198 Z= 0.384 Chirality : 0.048 0.192 5466 Planarity : 0.006 0.104 6186 Dihedral : 6.558 54.051 4886 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.47 % Favored : 88.35 % Rotamer: Outliers : 4.19 % Allowed : 12.89 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 1.04 % Twisted General : 0.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.12), residues: 4506 helix: -0.54 (0.17), residues: 834 sheet: -1.87 (0.14), residues: 1428 loop : -2.30 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 61 TYR 0.028 0.002 TYR O 49 PHE 0.037 0.002 PHE Q 112 TRP 0.043 0.002 TRP R 115 HIS 0.009 0.002 HIS N 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (35358) covalent geometry : angle 0.75991 / 0.38 (48150) SS BOND : bond 0.00463 / 0.30 ( 24) SS BOND : angle 1.24960 / 0.84 ( 48) hydrogen bonds : bond 0.03290 / 2.25 ( 948) hydrogen bonds : angle 5.60793 / 3.94 ( 2520) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 466 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.6036 (t0) cc_final: 0.5694 (t0) REVERT: A 89 LYS cc_start: 0.3613 (ptpt) cc_final: 0.2999 (mtmt) REVERT: A 100 ASP cc_start: 0.7688 (p0) cc_final: 0.7473 (p0) REVERT: A 288 GLU cc_start: 0.6657 (mt-10) cc_final: 0.5905 (mt-10) REVERT: E 11 LEU cc_start: 0.4820 (OUTLIER) cc_final: 0.4546 (tm) REVERT: E 38 GLN cc_start: 0.7997 (tt0) cc_final: 0.7793 (tt0) REVERT: E 42 GLN cc_start: 0.5863 (mm-40) cc_final: 0.5635 (mt0) REVERT: E 126 THR cc_start: 0.4257 (p) cc_final: 0.4035 (t) REVERT: E 139 PHE cc_start: 0.1210 (p90) cc_final: 0.0808 (p90) REVERT: B 46 ASP cc_start: 0.6259 (t0) cc_final: 0.5970 (t0) REVERT: H 106 ILE cc_start: 0.6798 (mp) cc_final: 0.6215 (mt) REVERT: I 78 LEU cc_start: 0.2256 (tm) cc_final: 0.2036 (tt) REVERT: M 36 LEU cc_start: 0.0935 (tp) cc_final: 0.0555 (mp) REVERT: M 200 MET cc_start: 0.2287 (mmm) cc_final: 0.1459 (mmt) REVERT: L 48 ILE cc_start: 0.4201 (mm) cc_final: 0.3693 (mm) REVERT: L 175 MET cc_start: 0.1016 (tmm) cc_final: 0.0532 (tmm) REVERT: N 40 LEU cc_start: 0.1857 (mt) cc_final: 0.1562 (tp) REVERT: N 265 TYR cc_start: 0.1240 (t80) cc_final: 0.0964 (t80) REVERT: N 306 LEU cc_start: 0.2315 (tt) cc_final: 0.2019 (tp) REVERT: J 42 GLU cc_start: 0.2521 (OUTLIER) cc_final: 0.1983 (mt-10) REVERT: J 193 LEU cc_start: 0.1824 (OUTLIER) cc_final: 0.1336 (mp) REVERT: J 259 TYR cc_start: 0.3068 (t80) cc_final: 0.2814 (t80) REVERT: O 6 GLN cc_start: 0.1236 (mt0) cc_final: 0.0383 (mp10) REVERT: O 70 ASP cc_start: 0.3203 (m-30) cc_final: 0.2900 (t0) REVERT: O 93 LEU cc_start: 0.3993 (OUTLIER) cc_final: 0.3356 (tm) REVERT: O 139 PHE cc_start: 0.0906 (p90) cc_final: 0.0304 (p90) REVERT: O 154 GLU cc_start: 0.1363 (tp30) cc_final: 0.1126 (tp30) REVERT: O 192 TYR cc_start: 0.1313 (m-80) cc_final: 0.0553 (m-10) REVERT: P 33 LEU cc_start: 0.3228 (OUTLIER) cc_final: 0.2454 (pp) REVERT: P 71 PHE cc_start: 0.4175 (m-10) cc_final: 0.3925 (m-10) REVERT: P 86 TYR cc_start: 0.2628 (m-10) cc_final: 0.2066 (m-10) REVERT: P 163 TRP cc_start: 0.2469 (m100) cc_final: 0.1560 (m100) REVERT: F 18 VAL cc_start: 0.6987 (OUTLIER) cc_final: 0.6681 (t) REVERT: F 29 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.6847 (t80) REVERT: F 48 MET cc_start: 0.7207 (ptm) cc_final: 0.5777 (ttp) REVERT: F 59 ASN cc_start: 0.7405 (t0) cc_final: 0.6968 (t0) REVERT: F 65 GLN cc_start: 0.5419 (mp-120) cc_final: 0.4894 (tp40) REVERT: F 147 MET cc_start: 0.2071 (tpp) cc_final: 0.0841 (tpp) REVERT: G 13 LYS cc_start: 0.6108 (OUTLIER) cc_final: 0.5758 (ptmm) REVERT: G 18 VAL cc_start: 0.7327 (OUTLIER) cc_final: 0.7118 (t) REVERT: G 28 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8201 (p) REVERT: G 29 PHE cc_start: 0.7319 (OUTLIER) cc_final: 0.6710 (t80) REVERT: G 59 ASN cc_start: 0.7540 (t0) cc_final: 0.7206 (t0) REVERT: G 76 THR cc_start: 0.6130 (p) cc_final: 0.5784 (t) REVERT: G 147 MET cc_start: 0.2839 (tpp) cc_final: 0.2301 (ppp) REVERT: K 48 MET cc_start: 0.4471 (mtm) cc_final: 0.4167 (mtp) REVERT: K 69 THR cc_start: 0.4262 (p) cc_final: 0.3707 (m) REVERT: K 94 TYR cc_start: 0.4368 (m-80) cc_final: 0.3757 (m-80) REVERT: K 167 ASN cc_start: 0.3421 (m-40) cc_final: 0.3065 (m110) REVERT: Q 48 MET cc_start: 0.3337 (OUTLIER) cc_final: 0.2446 (ptp) REVERT: Q 112 PHE cc_start: 0.2446 (OUTLIER) cc_final: 0.1852 (m-80) REVERT: Q 158 PHE cc_start: 0.1242 (t80) cc_final: 0.0745 (t80) REVERT: R 4 LEU cc_start: 0.3339 (tt) cc_final: 0.3044 (tt) REVERT: R 27 TYR cc_start: 0.0875 (p90) cc_final: 0.0225 (p90) REVERT: R 153 LEU cc_start: 0.1553 (OUTLIER) cc_final: 0.1289 (tp) REVERT: R 158 PHE cc_start: 0.2400 (t80) cc_final: 0.2189 (t80) REVERT: R 166 TRP cc_start: 0.0445 (m100) cc_final: -0.0138 (m100) outliers start: 161 outliers final: 102 residues processed: 590 average time/residue: 0.1970 time to fit residues: 190.6090 Evaluate side-chains 520 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 404 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 126 THR Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 101 HIS Chi-restraints excluded: chain N residue 244 THR Chi-restraints excluded: chain N residue 264 ILE Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain N residue 290 THR Chi-restraints excluded: chain N residue 299 ILE Chi-restraints excluded: chain N residue 303 CYS Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 101 HIS Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 248 VAL Chi-restraints excluded: chain J residue 299 ILE Chi-restraints excluded: chain J residue 300 THR Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 191 SER Chi-restraints excluded: chain Q residue 22 CYS Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 112 PHE Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain Q residue 216 THR Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 153 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: [187, 255, 285, 140, 282, 378, 83, 66, 125, 390, 216] chunk 187 optimal weight: 10.0000 chunk 255 optimal weight: 0.7980 chunk 285 optimal weight: 0.0770 chunk 140 optimal weight: 0.0970 chunk 282 optimal weight: 6.9990 chunk 378 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 390 optimal weight: 8.9990 chunk 216 optimal weight: 5.9990 overall best weight: 1.1738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 GLN A 101 HIS D 59 ASN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS ** M 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 HIS ** J 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 137 ASN P 189 HIS F 183 GLN K 43 GLN ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.196004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.160672 restraints weight = 66492.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.159707 restraints weight = 129491.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.159141 restraints weight = 113910.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.158972 restraints weight = 77652.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.159139 restraints weight = 72344.518| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5494 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35382 Z= 0.146 Angle : 0.738 12.941 48198 Z= 0.370 Chirality : 0.047 0.305 5466 Planarity : 0.006 0.127 6186 Dihedral : 6.387 49.844 4886 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.07 % Favored : 88.77 % Rotamer: Outliers : 3.85 % Allowed : 14.04 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 1.04 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.12), residues: 4506 helix: -0.31 (0.17), residues: 828 sheet: -1.77 (0.14), residues: 1416 loop : -2.24 (0.13), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 61 TYR 0.035 0.002 TYR E 186 PHE 0.027 0.002 PHE Q 112 TRP 0.051 0.002 TRP Q 115 HIS 0.012 0.001 HIS N 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (35358) covalent geometry : angle 0.73789 / 0.37 (48150) SS BOND : bond 0.00499 / 0.36 ( 24) SS BOND : angle 1.12669 / 0.79 ( 48) hydrogen bonds : bond 0.03149 / 2.17 ( 948) hydrogen bonds : angle 5.47331 / 3.83 ( 2520) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 435 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.6001 (t0) cc_final: 0.5693 (t0) REVERT: A 288 GLU cc_start: 0.6635 (mt-10) cc_final: 0.5991 (mt-10) REVERT: D 29 PHE cc_start: 0.7046 (OUTLIER) cc_final: 0.6681 (t80) REVERT: E 11 LEU cc_start: 0.4926 (OUTLIER) cc_final: 0.4698 (tm) REVERT: E 126 THR cc_start: 0.4288 (p) cc_final: 0.4072 (t) REVERT: E 139 PHE cc_start: 0.1181 (p90) cc_final: 0.0784 (p90) REVERT: B 46 ASP cc_start: 0.6192 (t0) cc_final: 0.5908 (t0) REVERT: B 273 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8146 (tt) REVERT: H 106 ILE cc_start: 0.6772 (mp) cc_final: 0.6222 (mt) REVERT: I 166 GLN cc_start: 0.3869 (tt0) cc_final: 0.3453 (tt0) REVERT: M 200 MET cc_start: 0.2239 (mmm) cc_final: 0.1498 (mmt) REVERT: L 4 MET cc_start: 0.1402 (tpp) cc_final: 0.0866 (tpp) REVERT: L 48 ILE cc_start: 0.4320 (OUTLIER) cc_final: 0.3733 (mm) REVERT: L 86 TYR cc_start: 0.3771 (m-80) cc_final: 0.3543 (m-80) REVERT: L 175 MET cc_start: 0.1364 (tmm) cc_final: 0.0772 (tmm) REVERT: N 40 LEU cc_start: 0.2054 (mt) cc_final: 0.1788 (tp) REVERT: N 265 TYR cc_start: 0.1352 (t80) cc_final: 0.0998 (t80) REVERT: N 306 LEU cc_start: 0.2157 (tt) cc_final: 0.1925 (tp) REVERT: J 193 LEU cc_start: 0.1950 (OUTLIER) cc_final: 0.1691 (mm) REVERT: O 6 GLN cc_start: 0.0593 (mt0) cc_final: -0.0133 (mp10) REVERT: O 73 LEU cc_start: 0.5445 (OUTLIER) cc_final: 0.5231 (tt) REVERT: O 93 LEU cc_start: 0.3997 (OUTLIER) cc_final: 0.3440 (tm) REVERT: O 139 PHE cc_start: 0.0984 (p90) cc_final: 0.0343 (p90) REVERT: O 154 GLU cc_start: 0.1040 (tp30) cc_final: 0.0830 (tp30) REVERT: P 4 MET cc_start: 0.1098 (tpp) cc_final: 0.0714 (tpp) REVERT: P 33 LEU cc_start: 0.3482 (OUTLIER) cc_final: 0.2692 (pp) REVERT: P 71 PHE cc_start: 0.3913 (m-10) cc_final: 0.3652 (m-10) REVERT: P 105 GLU cc_start: 0.0512 (mt-10) cc_final: 0.0306 (mt-10) REVERT: P 148 TRP cc_start: 0.0749 (m100) cc_final: 0.0405 (m100) REVERT: P 163 TRP cc_start: 0.2500 (m100) cc_final: 0.1661 (m100) REVERT: F 18 VAL cc_start: 0.6904 (OUTLIER) cc_final: 0.6586 (t) REVERT: F 29 PHE cc_start: 0.7507 (OUTLIER) cc_final: 0.6921 (t80) REVERT: F 59 ASN cc_start: 0.7570 (t0) cc_final: 0.7078 (t0) REVERT: F 65 GLN cc_start: 0.5273 (mp-120) cc_final: 0.4839 (tp40) REVERT: F 145 ASN cc_start: 0.2261 (OUTLIER) cc_final: 0.1734 (m-40) REVERT: F 147 MET cc_start: 0.2053 (tpp) cc_final: 0.1268 (tpt) REVERT: G 13 LYS cc_start: 0.6053 (OUTLIER) cc_final: 0.5729 (ptmm) REVERT: G 18 VAL cc_start: 0.7370 (OUTLIER) cc_final: 0.7131 (t) REVERT: G 28 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8146 (p) REVERT: G 59 ASN cc_start: 0.7565 (t0) cc_final: 0.7177 (t0) REVERT: G 76 THR cc_start: 0.6080 (p) cc_final: 0.5718 (t) REVERT: G 147 MET cc_start: 0.2746 (tpp) cc_final: 0.2424 (ppp) REVERT: K 48 MET cc_start: 0.4344 (mtm) cc_final: 0.2865 (ttm) REVERT: K 94 TYR cc_start: 0.4176 (m-80) cc_final: 0.3580 (m-80) REVERT: K 167 ASN cc_start: 0.3464 (m-40) cc_final: 0.3147 (m110) REVERT: Q 28 THR cc_start: 0.2100 (OUTLIER) cc_final: 0.1863 (m) REVERT: Q 30 THR cc_start: 0.4570 (p) cc_final: 0.4078 (m) REVERT: Q 48 MET cc_start: 0.3224 (OUTLIER) cc_final: 0.2233 (ptp) REVERT: Q 51 ILE cc_start: 0.3450 (OUTLIER) cc_final: 0.3205 (mm) REVERT: Q 70 MET cc_start: 0.4457 (tpt) cc_final: 0.3972 (tpt) REVERT: Q 112 PHE cc_start: 0.2826 (OUTLIER) cc_final: 0.1639 (m-80) REVERT: Q 147 MET cc_start: 0.0556 (mmm) cc_final: -0.0116 (tpp) REVERT: Q 211 HIS cc_start: 0.0849 (t-90) cc_final: 0.0423 (t-170) REVERT: R 27 TYR cc_start: 0.0903 (p90) cc_final: 0.0289 (p90) REVERT: R 48 MET cc_start: 0.4411 (ptt) cc_final: 0.4053 (mtm) REVERT: R 153 LEU cc_start: 0.1621 (OUTLIER) cc_final: 0.1385 (tp) outliers start: 148 outliers final: 105 residues processed: 545 average time/residue: 0.2025 time to fit residues: 181.5564 Evaluate side-chains 512 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 388 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 61 ARG Chi-restraints excluded: chain I residue 91 HIS Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 126 THR Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 145 ASN Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 101 HIS Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 264 ILE Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain N residue 290 THR Chi-restraints excluded: chain N residue 299 ILE Chi-restraints excluded: chain N residue 303 CYS Chi-restraints excluded: chain J residue 101 HIS Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 248 VAL Chi-restraints excluded: chain J residue 249 VAL Chi-restraints excluded: chain J residue 299 ILE Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain O residue 194 CYS Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain P residue 194 CYS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 191 SER Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 112 PHE Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 216 THR Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 153 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: [289, 108, 122, 378, 291, 254, 65, 323, 441, 259, 361] chunk 289 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 378 optimal weight: 7.9990 chunk 291 optimal weight: 10.0000 chunk 254 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 323 optimal weight: 20.0000 chunk 441 optimal weight: 5.9990 chunk 259 optimal weight: 1.9990 chunk 361 optimal weight: 4.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 HIS E 38 GLN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS I 42 GLN ** M 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 187 HIS J 187 HIS O 89 GLN K 43 GLN ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 143 GLN ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN R 167 ASN ** R 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.194770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.160566 restraints weight = 66187.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.158659 restraints weight = 136887.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.159205 restraints weight = 120730.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.158280 restraints weight = 87747.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.158501 restraints weight = 83468.541| |-----------------------------------------------------------------------------| r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5502 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 35382 Z= 0.178 Angle : 0.763 12.483 48198 Z= 0.383 Chirality : 0.049 0.340 5466 Planarity : 0.006 0.126 6186 Dihedral : 6.416 46.664 4886 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.41 % Favored : 88.44 % Rotamer: Outliers : 4.35 % Allowed : 14.38 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 0.35 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.12), residues: 4506 helix: -0.13 (0.18), residues: 792 sheet: -1.71 (0.14), residues: 1404 loop : -2.34 (0.13), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 96 TYR 0.030 0.002 TYR K 60 PHE 0.026 0.002 PHE O 71 TRP 0.071 0.002 TRP Q 115 HIS 0.012 0.002 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (35358) covalent geometry : angle 0.76194 / 0.38 (48150) SS BOND : bond 0.00372 / 0.25 ( 24) SS BOND : angle 1.36333 / 0.92 ( 48) hydrogen bonds : bond 0.03291 / 2.25 ( 948) hydrogen bonds : angle 5.55009 / 3.86 ( 2520) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 406 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.5987 (t0) cc_final: 0.5704 (t0) REVERT: A 89 LYS cc_start: 0.3806 (ptpt) cc_final: 0.3195 (mtmt) REVERT: A 288 GLU cc_start: 0.6681 (mt-10) cc_final: 0.6065 (mt-10) REVERT: D 29 PHE cc_start: 0.7222 (OUTLIER) cc_final: 0.6693 (t80) REVERT: E 11 LEU cc_start: 0.5088 (OUTLIER) cc_final: 0.4843 (tm) REVERT: E 126 THR cc_start: 0.4572 (p) cc_final: 0.4340 (t) REVERT: B 273 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8158 (tt) REVERT: H 61 ARG cc_start: 0.4326 (OUTLIER) cc_final: 0.3324 (ptt-90) REVERT: H 106 ILE cc_start: 0.6744 (mp) cc_final: 0.6124 (mt) REVERT: I 78 LEU cc_start: 0.3061 (tm) cc_final: 0.2693 (tt) REVERT: I 166 GLN cc_start: 0.3901 (tt0) cc_final: 0.3600 (tt0) REVERT: M 200 MET cc_start: 0.2209 (mmm) cc_final: 0.1685 (mmt) REVERT: M 294 ASN cc_start: 0.3668 (m-40) cc_final: 0.3238 (m-40) REVERT: L 4 MET cc_start: 0.1522 (tpp) cc_final: 0.0951 (tpp) REVERT: L 48 ILE cc_start: 0.4348 (OUTLIER) cc_final: 0.3808 (mm) REVERT: L 175 MET cc_start: 0.1417 (tmm) cc_final: 0.0924 (tmm) REVERT: N 40 LEU cc_start: 0.1895 (mt) cc_final: 0.1669 (tp) REVERT: N 151 GLU cc_start: 0.2027 (mp0) cc_final: 0.1291 (mp0) REVERT: N 265 TYR cc_start: 0.1334 (t80) cc_final: 0.0867 (t80) REVERT: J 42 GLU cc_start: 0.2710 (OUTLIER) cc_final: 0.2248 (mt-10) REVERT: J 193 LEU cc_start: 0.1955 (OUTLIER) cc_final: 0.1715 (mm) REVERT: O 6 GLN cc_start: 0.0605 (mt0) cc_final: 0.0058 (mp10) REVERT: O 93 LEU cc_start: 0.4457 (OUTLIER) cc_final: 0.3916 (tm) REVERT: P 4 MET cc_start: 0.1461 (tpp) cc_final: 0.1076 (tpp) REVERT: P 33 LEU cc_start: 0.3759 (OUTLIER) cc_final: 0.2886 (pp) REVERT: P 71 PHE cc_start: 0.3835 (m-10) cc_final: 0.3593 (m-10) REVERT: P 175 MET cc_start: 0.1983 (tpp) cc_final: 0.1487 (tpt) REVERT: F 18 VAL cc_start: 0.6933 (OUTLIER) cc_final: 0.6610 (t) REVERT: F 29 PHE cc_start: 0.7557 (OUTLIER) cc_final: 0.7095 (t80) REVERT: F 59 ASN cc_start: 0.7566 (t0) cc_final: 0.7195 (t0) REVERT: F 65 GLN cc_start: 0.5175 (mp-120) cc_final: 0.4852 (tp40) REVERT: F 145 ASN cc_start: 0.2384 (OUTLIER) cc_final: 0.1909 (m-40) REVERT: F 147 MET cc_start: 0.2000 (tpp) cc_final: 0.1210 (tpt) REVERT: G 13 LYS cc_start: 0.5943 (OUTLIER) cc_final: 0.5627 (ptmm) REVERT: G 18 VAL cc_start: 0.7399 (OUTLIER) cc_final: 0.7175 (t) REVERT: G 29 PHE cc_start: 0.7398 (OUTLIER) cc_final: 0.6186 (t80) REVERT: G 59 ASN cc_start: 0.7641 (t0) cc_final: 0.7264 (t0) REVERT: G 147 MET cc_start: 0.2833 (tpp) cc_final: 0.2530 (ppp) REVERT: K 48 MET cc_start: 0.4276 (mtm) cc_final: 0.3972 (mtp) REVERT: K 94 TYR cc_start: 0.4479 (m-80) cc_final: 0.3995 (m-80) REVERT: K 167 ASN cc_start: 0.3076 (m-40) cc_final: 0.2839 (m110) REVERT: Q 48 MET cc_start: 0.3159 (OUTLIER) cc_final: 0.1986 (ptm) REVERT: Q 70 MET cc_start: 0.4469 (tpt) cc_final: 0.4037 (tpt) REVERT: Q 112 PHE cc_start: 0.2949 (OUTLIER) cc_final: 0.1875 (m-80) REVERT: Q 147 MET cc_start: 0.0423 (mmm) cc_final: -0.0074 (tpp) REVERT: R 4 LEU cc_start: 0.3825 (OUTLIER) cc_final: 0.3406 (tt) REVERT: R 27 TYR cc_start: 0.0813 (p90) cc_final: 0.0186 (p90) REVERT: R 48 MET cc_start: 0.4638 (ptt) cc_final: 0.4338 (mtm) REVERT: R 153 LEU cc_start: 0.1758 (OUTLIER) cc_final: 0.1398 (tp) outliers start: 167 outliers final: 116 residues processed: 533 average time/residue: 0.1990 time to fit residues: 175.2671 Evaluate side-chains 500 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 365 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 61 ARG Chi-restraints excluded: chain I residue 91 HIS Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 126 THR Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 254 TYR Chi-restraints excluded: chain M residue 289 VAL Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 101 HIS Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 244 THR Chi-restraints excluded: chain N residue 264 ILE Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain N residue 290 THR Chi-restraints excluded: chain N residue 299 ILE Chi-restraints excluded: chain N residue 303 CYS Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 101 HIS Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 248 VAL Chi-restraints excluded: chain J residue 249 VAL Chi-restraints excluded: chain J residue 299 ILE Chi-restraints excluded: chain J residue 300 THR Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain O residue 194 CYS Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain P residue 194 CYS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 191 SER Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 112 PHE Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 215 SER Chi-restraints excluded: chain Q residue 216 THR Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 153 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: [4, 88, 284, 335, 136, 29, 102, 111, 288, 374, 31] chunk 4 optimal weight: 0.0170 chunk 88 optimal weight: 0.9990 chunk 284 optimal weight: 5.9990 chunk 335 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 288 optimal weight: 2.9990 chunk 374 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 overall best weight: 0.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 187 HIS J 187 HIS K 43 GLN ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 GLN ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 62 GLN ** R 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.196044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.161188 restraints weight = 66873.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.159353 restraints weight = 126414.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.158877 restraints weight = 114159.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.157611 restraints weight = 89355.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.157959 restraints weight = 80538.868| |-----------------------------------------------------------------------------| r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5527 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 35382 Z= 0.131 Angle : 0.729 13.351 48198 Z= 0.364 Chirality : 0.047 0.307 5466 Planarity : 0.006 0.133 6186 Dihedral : 6.190 44.281 4884 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.50 % Favored : 89.37 % Rotamer: Outliers : 3.57 % Allowed : 15.57 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 0.35 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.13), residues: 4506 helix: 0.20 (0.18), residues: 786 sheet: -1.56 (0.14), residues: 1386 loop : -2.21 (0.13), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 105 TYR 0.027 0.002 TYR O 49 PHE 0.023 0.002 PHE O 71 TRP 0.047 0.002 TRP R 115 HIS 0.006 0.001 HIS O 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (35358) covalent geometry : angle 0.72852 / 0.36 (48150) SS BOND : bond 0.00300 / 0.19 ( 24) SS BOND : angle 1.16449 / 0.78 ( 48) hydrogen bonds : bond 0.02972 / 2.06 ( 948) hydrogen bonds : angle 5.38118 / 3.74 ( 2520) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 396 time to evaluate : 1.337 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: A 46 ASP cc_start: 0.5997 (t0) cc_final: 0.5709 (t0) REVERT: A 288 GLU cc_start: 0.6640 (mt-10) cc_final: 0.6085 (mt-10) REVERT: D 29 PHE cc_start: 0.7275 (OUTLIER) cc_final: 0.6891 (t80) REVERT: E 11 LEU cc_start: 0.5124 (OUTLIER) cc_final: 0.4912 (tm) REVERT: E 126 THR cc_start: 0.4716 (p) cc_final: 0.4461 (t) REVERT: B 273 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8035 (tt) REVERT: H 61 ARG cc_start: 0.4543 (OUTLIER) cc_final: 0.4203 (ptt180) REVERT: H 106 ILE cc_start: 0.6931 (mp) cc_final: 0.6323 (mt) REVERT: M 118 LEU cc_start: -0.0030 (OUTLIER) cc_final: -0.0254 (mt) REVERT: M 200 MET cc_start: 0.2931 (mmm) cc_final: 0.2179 (mmt) REVERT: L 4 MET cc_start: 0.1349 (tpp) cc_final: 0.0849 (tpp) REVERT: L 48 ILE cc_start: 0.4397 (OUTLIER) cc_final: 0.3831 (mm) REVERT: L 94 LEU cc_start: 0.4909 (OUTLIER) cc_final: 0.4278 (tp) REVERT: L 175 MET cc_start: 0.1915 (tmm) cc_final: 0.1419 (tmm) REVERT: N 40 LEU cc_start: 0.1930 (OUTLIER) cc_final: 0.1703 (tp) REVERT: N 151 GLU cc_start: 0.2153 (mp0) cc_final: 0.1539 (mp0) REVERT: J 42 GLU cc_start: 0.2718 (OUTLIER) cc_final: 0.2268 (mt-10) REVERT: O 6 GLN cc_start: 0.0991 (mt0) cc_final: 0.0275 (mp10) REVERT: O 47 LEU cc_start: 0.4224 (mp) cc_final: 0.3577 (mt) REVERT: O 93 LEU cc_start: 0.4779 (OUTLIER) cc_final: 0.4296 (tm) REVERT: O 139 PHE cc_start: 0.0760 (p90) cc_final: 0.0096 (p90) REVERT: O 192 TYR cc_start: 0.1261 (m-80) cc_final: 0.0547 (m-10) REVERT: P 32 TYR cc_start: 0.3158 (m-10) cc_final: 0.2950 (m-80) REVERT: P 33 LEU cc_start: 0.3920 (OUTLIER) cc_final: 0.3026 (pp) REVERT: P 175 MET cc_start: 0.1997 (tpp) cc_final: 0.1615 (tpt) REVERT: F 18 VAL cc_start: 0.6920 (OUTLIER) cc_final: 0.6682 (m) REVERT: F 29 PHE cc_start: 0.7557 (OUTLIER) cc_final: 0.7054 (t80) REVERT: F 59 ASN cc_start: 0.7506 (t0) cc_final: 0.7147 (t0) REVERT: F 65 GLN cc_start: 0.5001 (mp-120) cc_final: 0.4737 (tp40) REVERT: F 73 ASP cc_start: 0.6617 (t0) cc_final: 0.6400 (t0) REVERT: F 145 ASN cc_start: 0.2131 (OUTLIER) cc_final: 0.1696 (m-40) REVERT: F 147 MET cc_start: 0.1905 (tpp) cc_final: 0.0596 (tpp) REVERT: G 13 LYS cc_start: 0.6041 (OUTLIER) cc_final: 0.5722 (ptmm) REVERT: G 18 VAL cc_start: 0.7500 (OUTLIER) cc_final: 0.7271 (t) REVERT: G 59 ASN cc_start: 0.7600 (t0) cc_final: 0.7210 (t0) REVERT: G 76 THR cc_start: 0.6074 (p) cc_final: 0.5708 (t) REVERT: G 147 MET cc_start: 0.2680 (tpp) cc_final: 0.2384 (ppp) REVERT: K 48 MET cc_start: 0.4166 (mtm) cc_final: 0.2745 (ttm) REVERT: K 94 TYR cc_start: 0.4603 (m-80) cc_final: 0.4042 (m-80) REVERT: K 167 ASN cc_start: 0.3092 (m-40) cc_final: 0.2863 (m110) REVERT: Q 48 MET cc_start: 0.3224 (OUTLIER) cc_final: 0.2101 (ptp) REVERT: Q 51 ILE cc_start: 0.3643 (OUTLIER) cc_final: 0.3248 (mm) REVERT: Q 70 MET cc_start: 0.4598 (tpt) cc_final: 0.3870 (tpt) REVERT: Q 112 PHE cc_start: 0.2960 (OUTLIER) cc_final: 0.1110 (m-80) REVERT: Q 147 MET cc_start: 0.0454 (mmm) cc_final: -0.0046 (tpp) REVERT: R 4 LEU cc_start: 0.3821 (OUTLIER) cc_final: 0.3329 (tt) REVERT: R 27 TYR cc_start: 0.1047 (p90) cc_final: 0.0482 (p90) REVERT: R 153 LEU cc_start: 0.1704 (OUTLIER) cc_final: 0.1454 (tp) outliers start: 137 outliers final: 94 residues processed: 503 average time/residue: 0.2046 time to fit residues: 169.7951 Evaluate side-chains 480 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 365 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 61 ARG Chi-restraints excluded: chain I residue 91 HIS Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 145 ASN Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 101 HIS Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain N residue 299 ILE Chi-restraints excluded: chain N residue 303 CYS Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 101 HIS Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 248 VAL Chi-restraints excluded: chain J residue 249 VAL Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain P residue 194 CYS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 191 SER Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 112 PHE Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 216 THR Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 153 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: [111, 421, 2, 260, 69, 287, 296, 388, 144, 357, 244] chunk 111 optimal weight: 1.9990 chunk 421 optimal weight: 6.9990 chunk 2 optimal weight: 0.3980 chunk 260 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 287 optimal weight: 9.9990 chunk 296 optimal weight: 10.0000 chunk 388 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 357 optimal weight: 8.9990 chunk 244 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 HIS E 38 GLN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS H 38 GLN I 189 HIS ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 GLN K 43 GLN ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 167 ASN ** R 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.194773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.163809 restraints weight = 65633.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.160188 restraints weight = 133682.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.160637 restraints weight = 112292.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.163052 restraints weight = 78501.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.160141 restraints weight = 60146.644| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5488 moved from start: 0.5759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 35382 Z= 0.168 Angle : 0.765 13.146 48198 Z= 0.382 Chirality : 0.048 0.281 5466 Planarity : 0.007 0.141 6186 Dihedral : 6.267 43.810 4884 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.34 % Favored : 88.50 % Rotamer: Outliers : 3.78 % Allowed : 15.68 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 0.35 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.12), residues: 4506 helix: 0.05 (0.18), residues: 786 sheet: -1.59 (0.14), residues: 1404 loop : -2.28 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 96 TYR 0.028 0.002 TYR J 254 PHE 0.021 0.002 PHE K 112 TRP 0.064 0.002 TRP Q 115 HIS 0.013 0.002 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (35358) covalent geometry : angle 0.76441 / 0.38 (48150) SS BOND : bond 0.00370 / 0.23 ( 24) SS BOND : angle 1.47593 / 1.05 ( 48) hydrogen bonds : bond 0.03254 / 2.24 ( 948) hydrogen bonds : angle 5.49431 / 3.80 ( 2520) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 386 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.6035 (t0) cc_final: 0.5740 (t0) REVERT: A 89 LYS cc_start: 0.3884 (ptpt) cc_final: 0.3286 (mtmt) REVERT: A 288 GLU cc_start: 0.6703 (mt-10) cc_final: 0.6183 (mt-10) REVERT: A 291 ARG cc_start: 0.8008 (ttm170) cc_final: 0.7642 (ttp-170) REVERT: D 18 VAL cc_start: 0.7331 (OUTLIER) cc_final: 0.6942 (t) REVERT: D 29 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.6707 (t80) REVERT: E 126 THR cc_start: 0.4682 (p) cc_final: 0.4402 (t) REVERT: E 151 ASP cc_start: 0.2788 (m-30) cc_final: 0.1513 (m-30) REVERT: B 273 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8116 (tt) REVERT: H 61 ARG cc_start: 0.4301 (OUTLIER) cc_final: 0.3358 (ptt-90) REVERT: H 106 ILE cc_start: 0.6966 (mp) cc_final: 0.5978 (mt) REVERT: I 58 ILE cc_start: 0.5173 (OUTLIER) cc_final: 0.4957 (tp) REVERT: M 200 MET cc_start: 0.2686 (mmm) cc_final: 0.2178 (mmt) REVERT: L 4 MET cc_start: 0.1281 (tpp) cc_final: 0.0972 (tpp) REVERT: L 37 GLN cc_start: 0.3750 (tp-100) cc_final: 0.3417 (tp40) REVERT: L 48 ILE cc_start: 0.4276 (OUTLIER) cc_final: 0.3784 (mm) REVERT: L 175 MET cc_start: 0.1619 (tmm) cc_final: 0.1131 (tmm) REVERT: L 187 GLU cc_start: 0.2533 (mm-30) cc_final: 0.2095 (mm-30) REVERT: N 40 LEU cc_start: 0.1845 (OUTLIER) cc_final: 0.1618 (tp) REVERT: N 151 GLU cc_start: 0.2043 (mp0) cc_final: 0.1466 (mp0) REVERT: J 42 GLU cc_start: 0.2650 (OUTLIER) cc_final: 0.2288 (mt-10) REVERT: O 6 GLN cc_start: 0.1030 (mt0) cc_final: 0.0179 (mp10) REVERT: O 47 LEU cc_start: 0.4186 (mp) cc_final: 0.3664 (mt) REVERT: O 93 LEU cc_start: 0.4529 (OUTLIER) cc_final: 0.3989 (tm) REVERT: O 139 PHE cc_start: 0.0792 (p90) cc_final: 0.0138 (p90) REVERT: O 192 TYR cc_start: 0.1151 (m-80) cc_final: 0.0486 (m-10) REVERT: P 32 TYR cc_start: 0.2948 (m-10) cc_final: 0.2698 (m-80) REVERT: P 33 LEU cc_start: 0.3818 (OUTLIER) cc_final: 0.2940 (pp) REVERT: P 36 TYR cc_start: 0.2038 (m-80) cc_final: 0.1803 (m-80) REVERT: P 123 GLU cc_start: 0.1537 (tm-30) cc_final: 0.0828 (tt0) REVERT: P 175 MET cc_start: 0.1806 (tpp) cc_final: 0.1463 (tpt) REVERT: F 18 VAL cc_start: 0.6676 (OUTLIER) cc_final: 0.6328 (t) REVERT: F 29 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.7042 (t80) REVERT: F 59 ASN cc_start: 0.7577 (t0) cc_final: 0.7190 (t0) REVERT: F 65 GLN cc_start: 0.4884 (mp-120) cc_final: 0.4658 (tp40) REVERT: F 73 ASP cc_start: 0.6710 (t0) cc_final: 0.6426 (t0) REVERT: F 145 ASN cc_start: 0.1960 (OUTLIER) cc_final: 0.1537 (m-40) REVERT: F 147 MET cc_start: 0.1814 (tpp) cc_final: 0.1162 (tpt) REVERT: G 13 LYS cc_start: 0.5954 (OUTLIER) cc_final: 0.5607 (ptmm) REVERT: G 29 PHE cc_start: 0.7192 (OUTLIER) cc_final: 0.5927 (t80) REVERT: G 59 ASN cc_start: 0.7745 (t0) cc_final: 0.7354 (t0) REVERT: G 125 SER cc_start: 0.6884 (p) cc_final: 0.6624 (p) REVERT: G 147 MET cc_start: 0.2774 (tpp) cc_final: 0.2574 (ppp) REVERT: K 48 MET cc_start: 0.4052 (mtm) cc_final: 0.2720 (ttm) REVERT: K 94 TYR cc_start: 0.4309 (m-80) cc_final: 0.3618 (m-80) REVERT: Q 70 MET cc_start: 0.4494 (tpt) cc_final: 0.3729 (tpt) REVERT: Q 112 PHE cc_start: 0.2967 (OUTLIER) cc_final: 0.0983 (m-80) REVERT: Q 147 MET cc_start: 0.0651 (mmm) cc_final: 0.0107 (tpp) REVERT: R 4 LEU cc_start: 0.3734 (OUTLIER) cc_final: 0.3220 (tt) REVERT: R 27 TYR cc_start: 0.1086 (p90) cc_final: 0.0491 (p90) REVERT: R 153 LEU cc_start: 0.1787 (OUTLIER) cc_final: 0.1468 (tp) outliers start: 145 outliers final: 104 residues processed: 501 average time/residue: 0.2025 time to fit residues: 166.3358 Evaluate side-chains 478 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 356 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 91 HIS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 61 ARG Chi-restraints excluded: chain I residue 91 HIS Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 101 HIS Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 244 THR Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain N residue 299 ILE Chi-restraints excluded: chain N residue 303 CYS Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 101 HIS Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 248 VAL Chi-restraints excluded: chain J residue 249 VAL Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain P residue 194 CYS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 191 SER Chi-restraints excluded: chain Q residue 29 PHE Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 112 PHE Chi-restraints excluded: chain Q residue 216 THR Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 153 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: [202, 199, 2, 10, 38, 113, 225, 376, 32, 265, 286] chunk 202 optimal weight: 0.9990 chunk 199 optimal weight: 3.9990 chunk 2 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 225 optimal weight: 7.9990 chunk 376 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 265 optimal weight: 4.9990 chunk 286 optimal weight: 5.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 HIS E 38 GLN E 42 GLN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS H 38 GLN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 HIS G 39 GLN G 43 GLN K 43 GLN ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 143 GLN Q 145 ASN ** R 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.195725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.162965 restraints weight = 67019.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.159534 restraints weight = 116632.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.157646 restraints weight = 92161.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.156252 restraints weight = 89222.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.154879 restraints weight = 92094.294| |-----------------------------------------------------------------------------| r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5592 moved from start: 0.5878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 35382 Z= 0.139 Angle : 0.744 13.657 48198 Z= 0.370 Chirality : 0.048 0.274 5466 Planarity : 0.006 0.143 6186 Dihedral : 6.155 43.269 4884 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.72 % Favored : 89.15 % Rotamer: Outliers : 3.31 % Allowed : 15.94 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.13), residues: 4506 helix: 0.11 (0.18), residues: 798 sheet: -1.46 (0.14), residues: 1386 loop : -2.18 (0.13), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 24 TYR 0.028 0.002 TYR P 49 PHE 0.022 0.002 PHE K 112 TRP 0.059 0.002 TRP R 50 HIS 0.007 0.001 HIS H 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (35358) covalent geometry : angle 0.74266 / 0.37 (48150) SS BOND : bond 0.00299 / 0.20 ( 24) SS BOND : angle 1.39121 / 1.02 ( 48) hydrogen bonds : bond 0.02986 / 2.06 ( 948) hydrogen bonds : angle 5.40375 / 3.73 ( 2520) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 382 time to evaluate : 1.354 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: A 46 ASP cc_start: 0.6074 (t0) cc_final: 0.5793 (t0) REVERT: A 288 GLU cc_start: 0.6715 (mt-10) cc_final: 0.6302 (mt-10) REVERT: A 291 ARG cc_start: 0.7942 (ttm170) cc_final: 0.7655 (ttp-170) REVERT: D 18 VAL cc_start: 0.7330 (OUTLIER) cc_final: 0.6958 (t) REVERT: D 29 PHE cc_start: 0.7271 (OUTLIER) cc_final: 0.6890 (t80) REVERT: E 151 ASP cc_start: 0.2631 (m-30) cc_final: 0.2240 (m-30) REVERT: B 273 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8015 (tt) REVERT: H 61 ARG cc_start: 0.4387 (OUTLIER) cc_final: 0.4090 (ptt180) REVERT: H 106 ILE cc_start: 0.6559 (mp) cc_final: 0.5781 (mt) REVERT: I 58 ILE cc_start: 0.5230 (OUTLIER) cc_final: 0.5012 (tp) REVERT: M 133 LEU cc_start: 0.2958 (mp) cc_final: 0.2390 (tt) REVERT: M 200 MET cc_start: 0.2762 (mmm) cc_final: 0.2300 (mmt) REVERT: L 4 MET cc_start: 0.1111 (tpp) cc_final: 0.0776 (tpp) REVERT: L 37 GLN cc_start: 0.3589 (tp-100) cc_final: 0.3299 (tp40) REVERT: L 48 ILE cc_start: 0.4469 (OUTLIER) cc_final: 0.3991 (mm) REVERT: L 175 MET cc_start: 0.1679 (tmm) cc_final: 0.1205 (tmm) REVERT: N 40 LEU cc_start: 0.1972 (OUTLIER) cc_final: 0.1763 (tp) REVERT: N 151 GLU cc_start: 0.2036 (mp0) cc_final: 0.1482 (mp0) REVERT: J 42 GLU cc_start: 0.2825 (OUTLIER) cc_final: 0.2386 (mt-10) REVERT: J 306 LEU cc_start: 0.1716 (tp) cc_final: 0.1459 (tt) REVERT: O 6 GLN cc_start: 0.1028 (mt0) cc_final: 0.0254 (mp10) REVERT: O 37 GLN cc_start: 0.3026 (tp-100) cc_final: 0.2725 (mm-40) REVERT: O 47 LEU cc_start: 0.3898 (mp) cc_final: 0.3351 (mt) REVERT: O 93 LEU cc_start: 0.4593 (OUTLIER) cc_final: 0.4045 (tm) REVERT: O 139 PHE cc_start: 0.0639 (p90) cc_final: 0.0021 (p90) REVERT: O 192 TYR cc_start: 0.1174 (m-80) cc_final: 0.0499 (m-10) REVERT: P 32 TYR cc_start: 0.2564 (m-10) cc_final: 0.2279 (m-80) REVERT: P 33 LEU cc_start: 0.3961 (OUTLIER) cc_final: 0.3060 (pp) REVERT: P 36 TYR cc_start: 0.2035 (m-80) cc_final: 0.1818 (m-80) REVERT: P 123 GLU cc_start: 0.1514 (tm-30) cc_final: 0.0859 (tt0) REVERT: P 175 MET cc_start: 0.1866 (tpp) cc_final: 0.1409 (tpt) REVERT: F 18 VAL cc_start: 0.6895 (OUTLIER) cc_final: 0.6552 (t) REVERT: F 29 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.7200 (t80) REVERT: F 59 ASN cc_start: 0.7564 (t0) cc_final: 0.7193 (t0) REVERT: F 65 GLN cc_start: 0.5282 (mp-120) cc_final: 0.4927 (tp40) REVERT: F 73 ASP cc_start: 0.6799 (t0) cc_final: 0.6546 (t0) REVERT: F 147 MET cc_start: 0.1885 (tpp) cc_final: 0.1250 (tpt) REVERT: G 13 LYS cc_start: 0.6023 (OUTLIER) cc_final: 0.5719 (ptmm) REVERT: G 59 ASN cc_start: 0.7769 (t0) cc_final: 0.7379 (t0) REVERT: G 76 THR cc_start: 0.6010 (p) cc_final: 0.5623 (t) REVERT: G 125 SER cc_start: 0.6941 (p) cc_final: 0.6634 (p) REVERT: G 147 MET cc_start: 0.2822 (tpp) cc_final: 0.2522 (ppp) REVERT: K 48 MET cc_start: 0.4144 (mtm) cc_final: 0.2796 (ttm) REVERT: K 94 TYR cc_start: 0.4296 (m-80) cc_final: 0.3528 (m-80) REVERT: Q 70 MET cc_start: 0.4596 (tpt) cc_final: 0.3510 (tpp) REVERT: Q 112 PHE cc_start: 0.2925 (OUTLIER) cc_final: 0.0939 (m-80) REVERT: Q 147 MET cc_start: 0.0667 (mmm) cc_final: 0.0087 (tpp) REVERT: R 27 TYR cc_start: 0.0949 (p90) cc_final: 0.0420 (p90) REVERT: R 48 MET cc_start: 0.4659 (ptm) cc_final: 0.4084 (mtm) REVERT: R 153 LEU cc_start: 0.1759 (OUTLIER) cc_final: 0.1456 (tp) outliers start: 127 outliers final: 104 residues processed: 484 average time/residue: 0.1995 time to fit residues: 158.4507 Evaluate side-chains 478 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 359 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 91 HIS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 61 ARG Chi-restraints excluded: chain I residue 91 HIS Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 101 HIS Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 244 THR Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain N residue 299 ILE Chi-restraints excluded: chain N residue 303 CYS Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 101 HIS Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 248 VAL Chi-restraints excluded: chain J residue 249 VAL Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain P residue 194 CYS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 191 SER Chi-restraints excluded: chain Q residue 29 PHE Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 112 PHE Chi-restraints excluded: chain Q residue 216 THR Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 153 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: [426, 355, 205, 28, 260, 228, 26, 98, 13, 375, 152] chunk 426 optimal weight: 10.0000 chunk 355 optimal weight: 20.0000 chunk 205 optimal weight: 0.6980 chunk 28 optimal weight: 0.0070 chunk 260 optimal weight: 1.9990 chunk 228 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 375 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 38 GLN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 143 GLN ** R 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.195532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.160812 restraints weight = 66544.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.158472 restraints weight = 125517.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.157666 restraints weight = 116094.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.157100 restraints weight = 97530.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.157080 restraints weight = 78928.759| |-----------------------------------------------------------------------------| r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5541 moved from start: 0.5920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.291 35382 Z= 0.253 Angle : 0.894 59.156 48198 Z= 0.473 Chirality : 0.051 0.681 5466 Planarity : 0.007 0.211 6186 Dihedral : 6.150 43.163 4884 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.85 % Favored : 89.01 % Rotamer: Outliers : 3.28 % Allowed : 16.07 % Favored : 80.65 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.13), residues: 4506 helix: 0.12 (0.18), residues: 798 sheet: -1.46 (0.14), residues: 1386 loop : -2.17 (0.13), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 67 TYR 0.077 0.002 TYR Q 102 PHE 0.020 0.002 PHE K 112 TRP 0.144 0.003 TRP Q 50 HIS 0.352 0.005 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.25 (35358) covalent geometry : angle 0.89260 / 0.47 (48150) SS BOND : bond 0.00643 / 0.41 ( 24) SS BOND : angle 1.67910 / 1.24 ( 48) hydrogen bonds : bond 0.02996 / 2.07 ( 948) hydrogen bonds : angle 5.40909 / 3.73 ( 2520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5522.76 seconds wall clock time: 97 minutes 12.36 seconds (5832.36 seconds total)