Starting phenix.real_space_refine on Fri Mar 6 20:09:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lf0_23296/03_2026/7lf0_23296.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lf0_23296/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7lf0_23296/03_2026/7lf0_23296.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lf0_23296/03_2026/7lf0_23296.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lf0_23296/03_2026/7lf0_23296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lf0_23296/03_2026/7lf0_23296.map" } 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-dev-5986/lib/python3.9/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: 4.59, per 1000 atoms: 0.13 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 F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.04 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 152 " - pdb=" SG CYS F 207 " distance=2.03 Simple disulfide: pdb=" SG CYS G 152 " - pdb=" SG CYS G 207 " distance=2.03 Simple disulfide: pdb=" SG CYS K 152 " - pdb=" SG CYS K 207 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 152 " - pdb=" SG CYS Q 207 " distance=2.03 Simple disulfide: pdb=" SG CYS R 152 " - pdb=" SG CYS R 207 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 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 134 " - pdb=" SG CYS I 194 " distance=2.02 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.02 Simple disulfide: pdb=" SG CYS O 134 " - pdb=" SG CYS O 194 " distance=2.02 Simple disulfide: pdb=" SG CYS P 134 " - pdb=" SG CYS P 194 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.4 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: 1.12 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: 6.62 Time building geometry restraints manager: 3.20 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: 0.11 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: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.360 Check model and map are aligned: 0.150 Set scattering table: 0.120 Process input model: 26.090 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.110 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5241 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 covalent geometry : bond 0.00763 (35358) covalent geometry : angle 1.09857 (48150) SS BOND : bond 0.00518 ( 24) SS BOND : angle 1.60067 ( 48) hydrogen bonds : bond 0.21434 ( 948) hydrogen bonds : angle 9.49373 ( 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 : 1.064 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: 0.2332 time to fit residues: 368.4448 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 : 1.265 ------------------------------------------------------------------------------- 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: 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... Flipped N/Q/H residues before XYZ refinement: 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: 0.5454 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 covalent geometry : bond 0.00349 (35358) covalent geometry : angle 0.79122 (48150) SS BOND : bond 0.00627 ( 24) SS BOND : angle 1.50631 ( 48) hydrogen bonds : bond 0.03802 ( 948) hydrogen bonds : angle 6.45526 ( 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 : 1.298 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: 0.2150 time to fit residues: 245.0112 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 : 1.201 ------------------------------------------------------------------------------- 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: 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.160485 restraints weight = 129254.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.160834 restraints weight = 113191.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.159469 restraints weight = 85524.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.159767 restraints weight = 79109.984| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5375 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 covalent geometry : bond 0.00311 (35358) covalent geometry : angle 0.74285 (48150) SS BOND : bond 0.00417 ( 24) SS BOND : angle 1.73389 ( 48) hydrogen bonds : bond 0.03375 ( 948) hydrogen bonds : angle 5.92174 ( 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 : 1.308 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: 0.5834 (t0) cc_final: 0.5557 (t0) REVERT: D 48 MET cc_start: 0.6991 (ptm) cc_final: 0.6053 (ttp) REVERT: E 11 LEU cc_start: 0.4029 (OUTLIER) cc_final: 0.3781 (tm) REVERT: E 42 GLN cc_start: 0.5966 (mm-40) cc_final: 0.5637 (mt0) REVERT: E 80 PRO cc_start: 0.2760 (Cg_endo) cc_final: 0.2551 (Cg_exo) REVERT: E 83 PHE cc_start: 0.4926 (m-10) cc_final: 0.4521 (m-80) REVERT: E 163 TRP cc_start: 0.4951 (m-10) cc_final: 0.4746 (m-10) REVERT: B 32 ARG cc_start: 0.8167 (mtt180) cc_final: 0.7505 (mtt-85) REVERT: B 46 ASP cc_start: 0.6265 (t0) cc_final: 0.5915 (t0) REVERT: C 267 THR cc_start: 0.7629 (p) cc_final: 0.7373 (p) REVERT: H 11 LEU cc_start: 0.5052 (OUTLIER) cc_final: 0.4178 (tp) REVERT: H 106 ILE cc_start: 0.6840 (mp) cc_final: 0.6150 (mt) REVERT: M 58 ILE cc_start: 0.1421 (OUTLIER) cc_final: 0.1167 (tp) REVERT: M 92 ARG cc_start: 0.1590 (mmt90) cc_final: 0.1247 (mmt90) REVERT: M 259 TYR cc_start: 0.3399 (t80) cc_final: 0.2808 (t80) REVERT: M 316 ASP cc_start: 0.2487 (t0) cc_final: 0.1904 (t0) REVERT: L 4 MET cc_start: 0.1275 (tpp) cc_final: 0.0800 (tpp) REVERT: L 47 LEU cc_start: 0.5594 (mt) cc_final: 0.4992 (mt) REVERT: L 48 ILE cc_start: 0.4926 (mm) cc_final: 0.4445 (mm) REVERT: L 175 MET cc_start: 0.0919 (ppp) cc_final: 0.0144 (tmm) REVERT: L 187 GLU cc_start: 0.3734 (pm20) cc_final: 0.3430 (mm-30) REVERT: N 304 PHE cc_start: 0.2352 (m-80) cc_final: 0.2095 (m-80) REVERT: N 306 LEU cc_start: 0.2768 (tt) cc_final: 0.2477 (tp) REVERT: O 4 MET cc_start: 0.2159 (tpp) cc_final: 0.1754 (mmm) REVERT: O 58 ILE cc_start: 0.1533 (OUTLIER) cc_final: 0.1131 (tp) REVERT: O 93 LEU cc_start: 0.4536 (OUTLIER) cc_final: 0.3954 (tm) REVERT: P 7 SER cc_start: 0.1362 (m) cc_final: 0.0999 (t) REVERT: P 33 LEU cc_start: 0.3100 (OUTLIER) cc_final: 0.2595 (pp) REVERT: F 18 VAL cc_start: 0.7083 (OUTLIER) cc_final: 0.6859 (m) REVERT: F 48 MET cc_start: 0.6856 (ptm) cc_final: 0.5781 (ttp) REVERT: F 59 ASN cc_start: 0.7078 (t0) cc_final: 0.6539 (t0) REVERT: F 65 GLN cc_start: 0.5131 (mp-120) cc_final: 0.4537 (tp40) REVERT: G 18 VAL cc_start: 0.7239 (OUTLIER) cc_final: 0.6981 (t) REVERT: G 28 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8150 (p) REVERT: G 76 THR cc_start: 0.5331 (p) cc_final: 0.5024 (t) REVERT: K 36 TRP cc_start: 0.2448 (m100) cc_final: 0.2004 (m100) REVERT: K 48 MET cc_start: 0.4384 (mtm) cc_final: 0.3962 (mtp) REVERT: K 69 THR cc_start: 0.4488 (p) cc_final: 0.4041 (m) REVERT: K 167 ASN cc_start: 0.3283 (m-40) cc_final: 0.2799 (m-40) REVERT: K 207 CYS cc_start: -0.0119 (p) cc_final: -0.0463 (p) REVERT: Q 28 THR cc_start: 0.2462 (OUTLIER) cc_final: 0.2220 (m) REVERT: Q 48 MET cc_start: 0.3632 (OUTLIER) cc_final: 0.2408 (ptp) REVERT: Q 69 THR cc_start: 0.4036 (p) cc_final: 0.3533 (m) REVERT: Q 147 MET cc_start: 0.0763 (mmm) cc_final: 0.0455 (tpp) REVERT: Q 158 PHE cc_start: 0.1075 (t80) cc_final: 0.0728 (t80) REVERT: R 23 LYS cc_start: 0.3607 (mttp) cc_final: 0.3235 (mtmm) REVERT: R 36 TRP cc_start: 0.2432 (m100) cc_final: 0.2135 (m100) REVERT: R 38 ARG cc_start: 0.1955 (ptm160) cc_final: 0.1742 (ptm160) REVERT: R 105 ARG cc_start: 0.4172 (ttm110) cc_final: 0.3949 (ttm110) REVERT: R 153 LEU cc_start: 0.1252 (tt) cc_final: 0.1030 (tp) REVERT: R 158 PHE cc_start: 0.2755 (t80) cc_final: 0.2429 (t80) outliers start: 121 outliers final: 72 residues processed: 601 average time/residue: 0.2100 time to fit residues: 205.4456 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 : 1.052 ------------------------------------------------------------------------------- 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: 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: 2.9990 chunk 398 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.196365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.165033 restraints weight = 67783.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.162952 restraints weight = 134629.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.163299 restraints weight = 131221.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.162263 restraints weight = 96367.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.162567 restraints weight = 83830.714| |-----------------------------------------------------------------------------| r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5320 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 35382 Z= 0.154 Angle : 0.743 13.545 48198 Z= 0.376 Chirality : 0.047 0.279 5466 Planarity : 0.007 0.100 6186 Dihedral : 6.616 54.552 4886 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.25 % Favored : 88.59 % Rotamer: Outliers : 3.41 % Allowed : 12.19 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 1.39 % 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: -2.73 (0.12), residues: 4506 helix: -0.34 (0.18), residues: 792 sheet: -1.93 (0.14), residues: 1362 loop : -2.27 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 98 TYR 0.029 0.002 TYR P 49 PHE 0.033 0.002 PHE P 98 TRP 0.030 0.002 TRP R 50 HIS 0.020 0.001 HIS M 101 Details of bonding type rmsd covalent geometry : bond 0.00358 (35358) covalent geometry : angle 0.74123 (48150) SS BOND : bond 0.00432 ( 24) SS BOND : angle 1.76624 ( 48) hydrogen bonds : bond 0.03262 ( 948) hydrogen bonds : angle 5.73576 ( 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 586 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 455 time to evaluate : 1.232 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: 0.5934 (t0) cc_final: 0.5515 (t0) REVERT: A 89 LYS cc_start: 0.3640 (ptpt) cc_final: 0.2982 (mtmt) REVERT: A 288 GLU cc_start: 0.6511 (mt-10) cc_final: 0.5856 (mt-10) REVERT: D 48 MET cc_start: 0.7104 (ptm) cc_final: 0.5813 (ttp) REVERT: E 11 LEU cc_start: 0.4548 (OUTLIER) cc_final: 0.4281 (tm) REVERT: E 42 GLN cc_start: 0.5822 (mm-40) cc_final: 0.5542 (mt0) REVERT: E 80 PRO cc_start: 0.2899 (Cg_endo) cc_final: 0.2570 (Cg_exo) REVERT: B 46 ASP cc_start: 0.6256 (t0) cc_final: 0.5929 (t0) REVERT: H 155 ARG cc_start: 0.1162 (tpt90) cc_final: 0.0450 (tmt170) REVERT: M 200 MET cc_start: 0.1810 (mmm) cc_final: 0.1038 (mmt) REVERT: L 4 MET cc_start: 0.1556 (tpp) cc_final: 0.1084 (tpp) REVERT: L 48 ILE cc_start: 0.4542 (mm) cc_final: 0.3992 (mm) REVERT: N 40 LEU cc_start: 0.1974 (mt) cc_final: 0.1746 (tp) REVERT: N 151 GLU cc_start: 0.2022 (mp0) cc_final: 0.1311 (mp0) REVERT: N 265 TYR cc_start: 0.1213 (t80) cc_final: 0.0942 (t80) REVERT: N 306 LEU cc_start: 0.2492 (tt) cc_final: 0.2148 (tp) REVERT: J 193 LEU cc_start: 0.1806 (OUTLIER) cc_final: 0.1281 (mp) REVERT: J 259 TYR cc_start: 0.2941 (t80) cc_final: 0.2653 (t80) REVERT: O 58 ILE cc_start: 0.1456 (OUTLIER) cc_final: 0.1221 (tp) REVERT: O 70 ASP cc_start: 0.3230 (m-30) cc_final: 0.2890 (t0) REVERT: O 93 LEU cc_start: 0.4350 (OUTLIER) cc_final: 0.3732 (tm) REVERT: O 139 PHE cc_start: 0.0840 (p90) cc_final: 0.0220 (p90) REVERT: F 18 VAL cc_start: 0.6922 (OUTLIER) cc_final: 0.6586 (t) REVERT: F 48 MET cc_start: 0.6970 (ptm) cc_final: 0.5831 (ttp) REVERT: F 59 ASN cc_start: 0.7145 (t0) cc_final: 0.6674 (t0) REVERT: F 65 GLN cc_start: 0.5245 (mp-120) cc_final: 0.4721 (tp40) REVERT: F 145 ASN cc_start: 0.2522 (OUTLIER) cc_final: 0.2048 (m-40) REVERT: G 18 VAL cc_start: 0.7082 (OUTLIER) cc_final: 0.6855 (t) REVERT: G 28 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8163 (p) REVERT: G 59 ASN cc_start: 0.7387 (t0) cc_final: 0.7087 (t0) REVERT: G 76 THR cc_start: 0.5577 (p) cc_final: 0.5266 (t) REVERT: G 147 MET cc_start: 0.2372 (tpp) cc_final: 0.1957 (ppp) REVERT: G 193 VAL cc_start: 0.3490 (OUTLIER) cc_final: 0.3260 (t) REVERT: K 48 MET cc_start: 0.4419 (mtm) cc_final: 0.3934 (mtp) REVERT: K 69 THR cc_start: 0.4211 (p) cc_final: 0.3764 (m) REVERT: K 167 ASN cc_start: 0.3443 (m-40) cc_final: 0.2998 (m110) REVERT: K 207 CYS cc_start: 0.0100 (p) cc_final: -0.0293 (p) REVERT: Q 30 THR cc_start: 0.4138 (p) cc_final: 0.3608 (m) REVERT: Q 48 MET cc_start: 0.3252 (OUTLIER) cc_final: 0.2029 (ptp) REVERT: Q 158 PHE cc_start: 0.1187 (t80) cc_final: 0.0920 (t80) REVERT: R 27 TYR cc_start: 0.1198 (p90) cc_final: 0.0548 (p90) REVERT: R 36 TRP cc_start: 0.2584 (m100) cc_final: 0.2166 (m100) REVERT: R 48 MET cc_start: 0.4292 (ptt) cc_final: 0.4083 (ptm) REVERT: R 50 TRP cc_start: 0.3034 (t60) cc_final: 0.2108 (t60) REVERT: R 158 PHE cc_start: 0.2445 (t80) cc_final: 0.2179 (t80) outliers start: 131 outliers final: 89 residues processed: 554 average time/residue: 0.2089 time to fit residues: 189.4439 Evaluate side-chains 491 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 392 time to evaluate : 1.291 ------------------------------------------------------------------------------- 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 C residue 311 ASN 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 M residue 101 HIS 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 101 HIS Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 290 THR 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 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 P residue 97 THR 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 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 37 VAL 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 122 THR Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain Q residue 153 LEU 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 Chi-restraints excluded: chain R residue 147 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 42 optimal weight: 2.9990 chunk 440 optimal weight: 6.9990 chunk 221 optimal weight: 2.9990 chunk 191 optimal weight: 7.9990 chunk 297 optimal weight: 0.0270 chunk 348 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 179 optimal weight: 0.8980 chunk 17 optimal weight: 0.0170 overall best weight: 0.9478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN ** C 79 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 GLN ** K 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN R 6 GLN ** 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 = 0.4628 r_free = 0.4628 target = 0.196947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.161306 restraints weight = 67667.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.159577 restraints weight = 136324.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.159224 restraints weight = 122630.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.157777 restraints weight = 94870.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.158142 restraints weight = 79589.023| |-----------------------------------------------------------------------------| r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5419 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35382 Z= 0.138 Angle : 0.721 13.612 48198 Z= 0.363 Chirality : 0.047 0.193 5466 Planarity : 0.006 0.098 6186 Dihedral : 6.421 56.967 4886 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.07 % Favored : 88.79 % Rotamer: Outliers : 3.62 % Allowed : 13.33 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 1.04 % Twisted General : 0.31 % 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: -0.32 (0.17), residues: 828 sheet: -1.83 (0.14), residues: 1374 loop : -2.20 (0.13), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 67 TYR 0.038 0.002 TYR E 186 PHE 0.043 0.002 PHE Q 112 TRP 0.039 0.002 TRP R 115 HIS 0.009 0.001 HIS N 187 Details of bonding type rmsd covalent geometry : bond 0.00316 (35358) covalent geometry : angle 0.72003 (48150) SS BOND : bond 0.00317 ( 24) SS BOND : angle 1.21328 ( 48) hydrogen bonds : bond 0.03038 ( 948) hydrogen bonds : angle 5.48687 ( 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 582 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 443 time to evaluate : 1.277 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: A 46 ASP cc_start: 0.5915 (t0) cc_final: 0.5558 (t0) REVERT: A 89 LYS cc_start: 0.3605 (ptpt) cc_final: 0.2954 (mtmt) REVERT: A 288 GLU cc_start: 0.6430 (mt-10) cc_final: 0.5681 (mt-10) REVERT: D 48 MET cc_start: 0.7046 (ptm) cc_final: 0.5637 (ttp) REVERT: E 11 LEU cc_start: 0.4726 (OUTLIER) cc_final: 0.4450 (tm) REVERT: E 42 GLN cc_start: 0.5882 (mm-40) cc_final: 0.5594 (mt0) REVERT: E 139 PHE cc_start: 0.1204 (p90) cc_final: 0.0707 (p90) REVERT: B 46 ASP cc_start: 0.6236 (t0) cc_final: 0.5928 (t0) REVERT: H 106 ILE cc_start: 0.6853 (mp) cc_final: 0.6249 (mt) REVERT: M 200 MET cc_start: 0.2372 (mmm) cc_final: 0.1645 (mmt) REVERT: L 4 MET cc_start: 0.1690 (tpp) cc_final: 0.1256 (tpp) REVERT: L 48 ILE cc_start: 0.4320 (mm) cc_final: 0.3828 (mm) REVERT: L 192 TYR cc_start: 0.1530 (m-80) cc_final: 0.1132 (m-80) REVERT: N 40 LEU cc_start: 0.2004 (mt) cc_final: 0.1745 (tp) REVERT: N 265 TYR cc_start: 0.1253 (t80) cc_final: 0.0940 (t80) REVERT: N 306 LEU cc_start: 0.2460 (tt) cc_final: 0.2124 (tp) REVERT: J 193 LEU cc_start: 0.1985 (OUTLIER) cc_final: 0.1709 (mm) REVERT: O 93 LEU cc_start: 0.4258 (OUTLIER) cc_final: 0.3630 (tm) REVERT: O 139 PHE cc_start: 0.0883 (p90) cc_final: 0.0244 (p90) REVERT: P 33 LEU cc_start: 0.3319 (OUTLIER) cc_final: 0.2684 (pp) REVERT: P 163 TRP cc_start: 0.2255 (m100) cc_final: 0.1169 (m100) REVERT: F 18 VAL cc_start: 0.7025 (OUTLIER) cc_final: 0.6700 (t) REVERT: F 29 PHE cc_start: 0.7542 (OUTLIER) cc_final: 0.6876 (t80) REVERT: F 48 MET cc_start: 0.7054 (ptm) cc_final: 0.5807 (ttp) REVERT: F 59 ASN cc_start: 0.7265 (t0) cc_final: 0.6788 (t0) REVERT: F 65 GLN cc_start: 0.5413 (mp-120) cc_final: 0.4826 (tp40) REVERT: F 99 GLU cc_start: 0.6548 (mt-10) cc_final: 0.6226 (mt-10) REVERT: F 147 MET cc_start: 0.2295 (tpp) cc_final: 0.1051 (tpp) REVERT: G 13 LYS cc_start: 0.6195 (OUTLIER) cc_final: 0.5782 (ptmm) REVERT: G 18 VAL cc_start: 0.7293 (OUTLIER) cc_final: 0.7090 (t) REVERT: G 28 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8153 (p) REVERT: G 29 PHE cc_start: 0.7106 (OUTLIER) cc_final: 0.6457 (t80) REVERT: G 59 ASN cc_start: 0.7451 (t0) cc_final: 0.7142 (t0) REVERT: G 76 THR cc_start: 0.5587 (p) cc_final: 0.5280 (t) REVERT: G 147 MET cc_start: 0.2714 (tpp) cc_final: 0.2199 (ppp) REVERT: K 36 TRP cc_start: 0.2458 (m100) cc_final: 0.1842 (m100) REVERT: K 48 MET cc_start: 0.4380 (mtm) cc_final: 0.4024 (mtp) REVERT: K 69 THR cc_start: 0.4263 (p) cc_final: 0.3755 (m) REVERT: K 94 TYR cc_start: 0.4269 (m-80) cc_final: 0.3667 (m-80) REVERT: K 167 ASN cc_start: 0.3517 (m-40) cc_final: 0.3174 (m110) REVERT: K 207 CYS cc_start: -0.0005 (p) cc_final: -0.0416 (p) REVERT: Q 28 THR cc_start: 0.2216 (OUTLIER) cc_final: 0.1913 (m) REVERT: Q 30 THR cc_start: 0.4835 (p) cc_final: 0.4287 (m) REVERT: Q 48 MET cc_start: 0.3428 (ptp) cc_final: 0.2484 (ptp) REVERT: Q 70 MET cc_start: 0.5570 (mmm) cc_final: 0.5298 (tpt) REVERT: Q 158 PHE cc_start: 0.1274 (t80) cc_final: 0.0763 (t80) REVERT: R 4 LEU cc_start: 0.3355 (tt) cc_final: 0.3071 (tt) REVERT: R 27 TYR cc_start: 0.1038 (p90) cc_final: 0.0415 (p90) REVERT: R 50 TRP cc_start: 0.3164 (t60) cc_final: 0.2928 (t60) REVERT: R 153 LEU cc_start: 0.1653 (OUTLIER) cc_final: 0.1380 (tp) REVERT: R 158 PHE cc_start: 0.2219 (t80) cc_final: 0.1992 (t80) REVERT: R 166 TRP cc_start: 0.0544 (m100) cc_final: -0.0072 (m100) outliers start: 139 outliers final: 88 residues processed: 548 average time/residue: 0.2104 time to fit residues: 188.1106 Evaluate side-chains 494 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 394 time to evaluate : 1.294 ------------------------------------------------------------------------------- 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 285 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain D residue 20 VAL 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 93 LEU 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 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 102 THR 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 47 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 93 LEU 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 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 102 THR Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 101 HIS Chi-restraints excluded: chain N residue 264 ILE 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 101 HIS Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 299 ILE 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 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 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 51 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 209 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 123 VAL 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 58 THR Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 122 THR 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 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: chunk 187 optimal weight: 9.9990 chunk 255 optimal weight: 6.9990 chunk 285 optimal weight: 3.9990 chunk 140 optimal weight: 0.0980 chunk 282 optimal weight: 9.9990 chunk 378 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 390 optimal weight: 8.9990 chunk 216 optimal weight: 20.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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 312 HIS O 89 GLN P 53 ASN P 137 ASN F 167 ASN K 43 GLN ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 183 GLN Q 6 GLN Q 59 ASN Q 143 GLN ** 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.194337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.160439 restraints weight = 66975.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.159013 restraints weight = 145067.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.158622 restraints weight = 128596.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.158191 restraints weight = 90889.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.158556 restraints weight = 79441.587| |-----------------------------------------------------------------------------| r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5409 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 35382 Z= 0.239 Angle : 0.830 12.540 48198 Z= 0.420 Chirality : 0.050 0.209 5466 Planarity : 0.007 0.111 6186 Dihedral : 6.745 50.941 4886 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.03 % Favored : 87.73 % Rotamer: Outliers : 4.35 % Allowed : 13.93 % Favored : 81.72 % 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: -2.90 (0.12), residues: 4506 helix: -0.71 (0.17), residues: 834 sheet: -1.90 (0.13), residues: 1434 loop : -2.40 (0.13), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 98 TYR 0.029 0.002 TYR P 49 PHE 0.037 0.003 PHE P 98 TRP 0.050 0.003 TRP Q 115 HIS 0.023 0.002 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00566 (35358) covalent geometry : angle 0.82884 (48150) SS BOND : bond 0.00454 ( 24) SS BOND : angle 1.35277 ( 48) hydrogen bonds : bond 0.03787 ( 948) hydrogen bonds : angle 5.81749 ( 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 615 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 448 time to evaluate : 1.161 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: 0.6082 (t0) cc_final: 0.5765 (t0) REVERT: A 89 LYS cc_start: 0.3750 (ptpt) cc_final: 0.3202 (mtmt) REVERT: A 291 ARG cc_start: 0.8006 (ttm170) cc_final: 0.7764 (ttp-170) REVERT: D 29 PHE cc_start: 0.7103 (OUTLIER) cc_final: 0.6537 (t80) REVERT: E 11 LEU cc_start: 0.5088 (OUTLIER) cc_final: 0.4832 (tm) REVERT: C 319 ASN cc_start: 0.5400 (m-40) cc_final: 0.4903 (p0) REVERT: H 106 ILE cc_start: 0.6835 (mp) cc_final: 0.6125 (mt) REVERT: L 48 ILE cc_start: 0.4432 (mm) cc_final: 0.3909 (mm) REVERT: L 81 GLU cc_start: 0.4427 (pm20) cc_final: 0.4159 (pm20) REVERT: N 40 LEU cc_start: 0.1865 (mt) cc_final: 0.1633 (tp) REVERT: N 151 GLU cc_start: 0.2091 (mp0) cc_final: 0.1337 (mp0) REVERT: J 42 GLU cc_start: 0.2414 (OUTLIER) cc_final: 0.2022 (mt-10) REVERT: J 193 LEU cc_start: 0.1873 (OUTLIER) cc_final: 0.1364 (mp) REVERT: O 6 GLN cc_start: 0.0973 (mt0) cc_final: 0.0346 (mp10) REVERT: O 73 LEU cc_start: 0.5446 (OUTLIER) cc_final: 0.5233 (tt) REVERT: O 93 LEU cc_start: 0.4292 (OUTLIER) cc_final: 0.3723 (tm) REVERT: P 33 LEU cc_start: 0.3554 (OUTLIER) cc_final: 0.2689 (pp) REVERT: P 71 PHE cc_start: 0.4160 (m-10) cc_final: 0.3871 (m-10) REVERT: P 86 TYR cc_start: 0.2617 (m-10) cc_final: 0.2104 (m-10) REVERT: P 163 TRP cc_start: 0.2481 (m100) cc_final: 0.1568 (m100) REVERT: F 29 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.6959 (t80) REVERT: F 59 ASN cc_start: 0.7684 (t0) cc_final: 0.7310 (t0) REVERT: F 65 GLN cc_start: 0.5419 (mp-120) cc_final: 0.4875 (tp40) REVERT: F 99 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6568 (mt-10) REVERT: F 145 ASN cc_start: 0.2658 (OUTLIER) cc_final: 0.2183 (m-40) REVERT: F 147 MET cc_start: 0.2010 (tpp) cc_final: 0.0890 (tpp) REVERT: G 18 VAL cc_start: 0.7469 (OUTLIER) cc_final: 0.7236 (t) REVERT: G 29 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.6328 (t80) REVERT: G 59 ASN cc_start: 0.7681 (t0) cc_final: 0.7323 (t0) REVERT: G 147 MET cc_start: 0.2913 (tpp) cc_final: 0.2508 (ppp) REVERT: K 48 MET cc_start: 0.4386 (mtm) cc_final: 0.4184 (mtp) REVERT: K 69 THR cc_start: 0.4604 (p) cc_final: 0.4144 (m) REVERT: K 71 THR cc_start: 0.5481 (p) cc_final: 0.5272 (m) REVERT: K 94 TYR cc_start: 0.4024 (m-80) cc_final: 0.3358 (m-80) REVERT: K 167 ASN cc_start: 0.3310 (m-40) cc_final: 0.3004 (m110) REVERT: Q 48 MET cc_start: 0.3641 (OUTLIER) cc_final: 0.2372 (ptm) REVERT: Q 70 MET cc_start: 0.5498 (mmm) cc_final: 0.5130 (tpt) REVERT: Q 147 MET cc_start: 0.0401 (mmm) cc_final: -0.0094 (tpp) REVERT: Q 211 HIS cc_start: 0.0850 (t-90) cc_final: 0.0390 (t-170) REVERT: R 4 LEU cc_start: 0.3510 (tt) cc_final: 0.3259 (tt) REVERT: R 27 TYR cc_start: 0.0878 (p90) cc_final: 0.0214 (p90) REVERT: R 48 MET cc_start: 0.4794 (ptt) cc_final: 0.4256 (mtm) REVERT: R 153 LEU cc_start: 0.1563 (OUTLIER) cc_final: 0.1285 (tp) outliers start: 167 outliers final: 119 residues processed: 578 average time/residue: 0.2067 time to fit residues: 195.6923 Evaluate side-chains 528 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 396 time to evaluate : 1.494 ------------------------------------------------------------------------------- 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 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 2 VAL 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 77 SER Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 26 GLU 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 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 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 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 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 M residue 289 VAL 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 72 THR Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 145 ASN Chi-restraints excluded: chain N residue 24 VAL 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 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 290 THR Chi-restraints excluded: chain J residue 299 ILE Chi-restraints excluded: chain J residue 300 THR 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 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 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 182 LEU 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 64 LEU Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 120 LEU 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 22 CYS 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 153 LEU Chi-restraints excluded: chain Q residue 215 SER 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 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 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: chunk 289 optimal weight: 10.0000 chunk 108 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 378 optimal weight: 8.9990 chunk 291 optimal weight: 6.9990 chunk 254 optimal weight: 20.0000 chunk 65 optimal weight: 0.8980 chunk 323 optimal weight: 8.9990 chunk 441 optimal weight: 0.7980 chunk 259 optimal weight: 1.9990 chunk 361 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN E 38 GLN ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 HIS ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.195631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.161423 restraints weight = 67645.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.159258 restraints weight = 122279.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.156699 restraints weight = 110562.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.155808 restraints weight = 101993.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.153856 restraints weight = 96580.986| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5511 moved from start: 0.5378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 35382 Z= 0.147 Angle : 0.742 12.941 48198 Z= 0.373 Chirality : 0.047 0.271 5466 Planarity : 0.006 0.129 6186 Dihedral : 6.446 50.975 4886 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.87 % Favored : 88.97 % Rotamer: Outliers : 3.62 % Allowed : 15.08 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 0.35 % Twisted General : 0.31 % 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: -2.67 (0.12), residues: 4506 helix: -0.31 (0.18), residues: 822 sheet: -1.78 (0.14), residues: 1434 loop : -2.32 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 24 TYR 0.025 0.002 TYR J 254 PHE 0.027 0.002 PHE P 98 TRP 0.078 0.002 TRP Q 115 HIS 0.010 0.001 HIS N 187 Details of bonding type rmsd covalent geometry : bond 0.00347 (35358) covalent geometry : angle 0.74192 (48150) SS BOND : bond 0.00335 ( 24) SS BOND : angle 1.17118 ( 48) hydrogen bonds : bond 0.03138 ( 948) hydrogen bonds : angle 5.56517 ( 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 553 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 414 time to evaluate : 1.017 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: 0.5986 (t0) cc_final: 0.5718 (t0) REVERT: A 288 GLU cc_start: 0.6605 (mt-10) cc_final: 0.6040 (mt-10) REVERT: D 203 GLU cc_start: 0.2297 (pm20) cc_final: 0.1345 (pm20) REVERT: E 11 LEU cc_start: 0.5075 (OUTLIER) cc_final: 0.4827 (tm) REVERT: B 46 ASP cc_start: 0.6314 (t0) cc_final: 0.6078 (t0) REVERT: B 273 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8182 (tt) REVERT: H 61 ARG cc_start: 0.4387 (OUTLIER) cc_final: 0.3350 (ptt-90) REVERT: H 81 GLU cc_start: 0.2698 (pp20) cc_final: 0.2281 (pp20) REVERT: H 106 ILE cc_start: 0.6830 (mp) cc_final: 0.6196 (mt) REVERT: I 58 ILE cc_start: 0.5323 (OUTLIER) cc_final: 0.5071 (tp) REVERT: L 4 MET cc_start: 0.1145 (tpp) cc_final: 0.0732 (tpp) REVERT: L 48 ILE cc_start: 0.4252 (OUTLIER) cc_final: 0.3746 (mm) REVERT: L 81 GLU cc_start: 0.4374 (pm20) cc_final: 0.4145 (pm20) REVERT: L 147 LYS cc_start: 0.2474 (ptmm) cc_final: 0.2176 (ttpp) REVERT: N 40 LEU cc_start: 0.1886 (mt) cc_final: 0.1676 (tp) REVERT: J 42 GLU cc_start: 0.2853 (OUTLIER) cc_final: 0.2389 (mt-10) REVERT: J 193 LEU cc_start: 0.1604 (OUTLIER) cc_final: 0.1283 (mm) REVERT: O 6 GLN cc_start: 0.0624 (mt0) cc_final: 0.0092 (mp10) REVERT: O 73 LEU cc_start: 0.5700 (OUTLIER) cc_final: 0.5494 (tt) REVERT: O 93 LEU cc_start: 0.4050 (OUTLIER) cc_final: 0.3481 (tm) REVERT: O 98 PHE cc_start: 0.2861 (OUTLIER) cc_final: 0.2418 (m-10) REVERT: O 139 PHE cc_start: 0.0739 (p90) cc_final: 0.0069 (p90) REVERT: P 4 MET cc_start: 0.1676 (tpp) cc_final: 0.1224 (tpp) REVERT: P 33 LEU cc_start: 0.3581 (OUTLIER) cc_final: 0.2737 (pp) REVERT: P 71 PHE cc_start: 0.3740 (m-10) cc_final: 0.3509 (m-10) REVERT: P 86 TYR cc_start: 0.2685 (m-10) cc_final: 0.2152 (m-10) REVERT: P 148 TRP cc_start: 0.0857 (m100) cc_final: 0.0488 (m100) REVERT: P 163 TRP cc_start: 0.2442 (m100) cc_final: 0.1564 (m100) REVERT: F 29 PHE cc_start: 0.7581 (OUTLIER) cc_final: 0.7150 (t80) REVERT: F 59 ASN cc_start: 0.7589 (t0) cc_final: 0.7216 (t0) REVERT: F 65 GLN cc_start: 0.5181 (mp-120) cc_final: 0.4802 (tp40) REVERT: F 145 ASN cc_start: 0.2248 (OUTLIER) cc_final: 0.1751 (m-40) REVERT: F 147 MET cc_start: 0.1953 (tpp) cc_final: 0.1143 (tpt) REVERT: G 13 LYS cc_start: 0.6049 (OUTLIER) cc_final: 0.5687 (ptmm) REVERT: G 18 VAL cc_start: 0.7395 (OUTLIER) cc_final: 0.7186 (t) REVERT: G 29 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.6170 (t80) REVERT: G 59 ASN cc_start: 0.7595 (t0) cc_final: 0.7182 (t0) REVERT: G 76 THR cc_start: 0.6017 (p) cc_final: 0.5729 (t) REVERT: G 99 GLU cc_start: 0.6907 (mt-10) cc_final: 0.6689 (mt-10) REVERT: G 147 MET cc_start: 0.2840 (tpp) cc_final: 0.2586 (ppp) REVERT: K 48 MET cc_start: 0.4294 (mtm) cc_final: 0.2881 (ttm) REVERT: K 94 TYR cc_start: 0.4002 (m-80) cc_final: 0.3384 (m-80) REVERT: K 167 ASN cc_start: 0.3059 (m-40) cc_final: 0.2815 (m110) REVERT: Q 48 MET cc_start: 0.3444 (OUTLIER) cc_final: 0.2200 (ptm) REVERT: Q 70 MET cc_start: 0.5545 (mmm) cc_final: 0.5007 (tpt) REVERT: Q 147 MET cc_start: 0.0431 (mmm) cc_final: -0.0077 (tpp) REVERT: Q 211 HIS cc_start: 0.0888 (t-90) cc_final: 0.0445 (t-170) REVERT: R 4 LEU cc_start: 0.3487 (tt) cc_final: 0.3228 (tt) REVERT: R 27 TYR cc_start: 0.0776 (p90) cc_final: 0.0184 (p90) REVERT: R 48 MET cc_start: 0.4373 (ptt) cc_final: 0.4103 (mtm) REVERT: R 153 LEU cc_start: 0.1558 (OUTLIER) cc_final: 0.1317 (tp) outliers start: 139 outliers final: 99 residues processed: 517 average time/residue: 0.2062 time to fit residues: 175.5608 Evaluate side-chains 490 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 373 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 118 LEU 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 28 THR 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 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 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 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 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 7 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 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 L residue 33 LEU Chi-restraints excluded: chain L residue 47 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 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 299 ILE Chi-restraints excluded: chain N residue 303 CYS Chi-restraints excluded: chain N residue 306 LEU 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 290 THR Chi-restraints excluded: chain O residue 33 LEU 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 98 PHE 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 P residue 194 CYS 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 K residue 37 VAL 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 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 93 VAL Chi-restraints excluded: chain Q residue 112 PHE Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain Q residue 215 SER 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 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: chunk 4 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 284 optimal weight: 20.0000 chunk 335 optimal weight: 0.4980 chunk 136 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 288 optimal weight: 5.9990 chunk 374 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 HIS P 189 HIS K 43 GLN ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.196056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.162136 restraints weight = 66884.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.161233 restraints weight = 127309.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.160668 restraints weight = 107081.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.160457 restraints weight = 75064.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.160548 restraints weight = 69815.483| |-----------------------------------------------------------------------------| r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5351 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 35382 Z= 0.135 Angle : 0.731 12.284 48198 Z= 0.365 Chirality : 0.047 0.352 5466 Planarity : 0.006 0.137 6186 Dihedral : 6.228 46.073 4886 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.90 % Favored : 88.95 % Rotamer: Outliers : 3.39 % Allowed : 15.49 % Favored : 81.12 % 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: -2.45 (0.12), residues: 4506 helix: -0.06 (0.18), residues: 822 sheet: -1.60 (0.14), residues: 1398 loop : -2.23 (0.13), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 24 TYR 0.029 0.002 TYR J 254 PHE 0.024 0.002 PHE P 98 TRP 0.066 0.002 TRP Q 115 HIS 0.006 0.001 HIS O 91 Details of bonding type rmsd covalent geometry : bond 0.00322 (35358) covalent geometry : angle 0.73010 (48150) SS BOND : bond 0.00317 ( 24) SS BOND : angle 1.18387 ( 48) hydrogen bonds : bond 0.03083 ( 948) hydrogen bonds : angle 5.41050 ( 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 539 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 409 time to evaluate : 1.342 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: A 46 ASP cc_start: 0.5928 (t0) cc_final: 0.5667 (t0) REVERT: A 288 GLU cc_start: 0.6615 (mt-10) cc_final: 0.6182 (mt-10) REVERT: A 291 ARG cc_start: 0.7902 (ttm170) cc_final: 0.7585 (ttp-170) REVERT: D 18 VAL cc_start: 0.7287 (OUTLIER) cc_final: 0.6942 (t) REVERT: D 203 GLU cc_start: 0.2155 (pm20) cc_final: 0.1323 (pm20) REVERT: B 46 ASP cc_start: 0.6374 (t0) cc_final: 0.6150 (t0) REVERT: B 273 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8063 (tt) REVERT: H 61 ARG cc_start: 0.4249 (OUTLIER) cc_final: 0.3163 (ptt-90) REVERT: H 81 GLU cc_start: 0.2659 (pp20) cc_final: 0.2457 (mp0) REVERT: H 106 ILE cc_start: 0.7043 (mp) cc_final: 0.6311 (mt) REVERT: I 58 ILE cc_start: 0.5295 (OUTLIER) cc_final: 0.5049 (tp) REVERT: M 200 MET cc_start: 0.1962 (mmm) cc_final: 0.1628 (mmp) REVERT: L 4 MET cc_start: 0.1364 (tpp) cc_final: 0.0797 (tpp) REVERT: L 48 ILE cc_start: 0.4308 (OUTLIER) cc_final: 0.3749 (mm) REVERT: L 81 GLU cc_start: 0.4422 (pm20) cc_final: 0.4217 (pm20) REVERT: L 147 LYS cc_start: 0.2615 (ptmm) cc_final: 0.2319 (ttpp) REVERT: L 175 MET cc_start: 0.1483 (tmm) cc_final: 0.0888 (tmm) REVERT: N 151 GLU cc_start: 0.2082 (mp0) cc_final: 0.1370 (mp0) REVERT: J 42 GLU cc_start: 0.2627 (OUTLIER) cc_final: 0.2200 (mt-10) REVERT: O 6 GLN cc_start: 0.0553 (mt0) cc_final: -0.0181 (mp10) REVERT: O 93 LEU cc_start: 0.4156 (OUTLIER) cc_final: 0.3643 (tm) REVERT: O 98 PHE cc_start: 0.3205 (OUTLIER) cc_final: 0.1800 (m-10) REVERT: O 139 PHE cc_start: 0.0628 (p90) cc_final: 0.0020 (p90) REVERT: P 4 MET cc_start: 0.1656 (tpp) cc_final: 0.1217 (tpp) REVERT: P 32 TYR cc_start: 0.3149 (m-10) cc_final: 0.2894 (m-80) REVERT: P 33 LEU cc_start: 0.3802 (OUTLIER) cc_final: 0.2957 (pp) REVERT: P 71 PHE cc_start: 0.3673 (m-10) cc_final: 0.3466 (m-10) REVERT: P 86 TYR cc_start: 0.2821 (m-10) cc_final: 0.2272 (m-10) REVERT: P 123 GLU cc_start: 0.1391 (tm-30) cc_final: 0.0714 (tt0) REVERT: P 148 TRP cc_start: 0.0842 (m100) cc_final: 0.0472 (m100) REVERT: P 175 MET cc_start: 0.2185 (tpp) cc_final: 0.1919 (tpt) REVERT: F 29 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.7031 (t80) REVERT: F 59 ASN cc_start: 0.7658 (t0) cc_final: 0.7226 (t0) REVERT: F 145 ASN cc_start: 0.2129 (OUTLIER) cc_final: 0.1680 (m-40) REVERT: F 147 MET cc_start: 0.1786 (tpp) cc_final: 0.1118 (tpt) REVERT: G 13 LYS cc_start: 0.6009 (OUTLIER) cc_final: 0.5675 (ptmm) REVERT: G 18 VAL cc_start: 0.7490 (OUTLIER) cc_final: 0.7254 (t) REVERT: G 59 ASN cc_start: 0.7592 (t0) cc_final: 0.7230 (t0) REVERT: G 76 THR cc_start: 0.5981 (p) cc_final: 0.5625 (t) REVERT: K 48 MET cc_start: 0.4308 (mtm) cc_final: 0.2864 (ttm) REVERT: K 94 TYR cc_start: 0.4198 (m-80) cc_final: 0.3625 (m-80) REVERT: K 167 ASN cc_start: 0.3051 (m-40) cc_final: 0.2819 (m110) REVERT: Q 70 MET cc_start: 0.5335 (mmm) cc_final: 0.4808 (tpt) REVERT: Q 147 MET cc_start: 0.0452 (mmm) cc_final: -0.0059 (tpp) REVERT: R 27 TYR cc_start: 0.0823 (p90) cc_final: 0.0261 (p90) REVERT: R 153 LEU cc_start: 0.1549 (OUTLIER) cc_final: 0.1334 (tp) outliers start: 130 outliers final: 96 residues processed: 510 average time/residue: 0.2017 time to fit residues: 169.6026 Evaluate side-chains 481 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 371 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 126 HIS 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 64 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 74 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 7 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 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 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 97 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 L residue 145 ASN Chi-restraints excluded: chain N residue 24 VAL 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 299 ILE Chi-restraints excluded: chain N residue 303 CYS Chi-restraints excluded: chain N residue 306 LEU 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 O residue 58 ILE Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 98 PHE 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 194 CYS 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 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 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 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 153 LEU Chi-restraints excluded: chain Q residue 215 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 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: chunk 111 optimal weight: 0.9990 chunk 421 optimal weight: 10.0000 chunk 2 optimal weight: 0.0010 chunk 260 optimal weight: 9.9990 chunk 69 optimal weight: 0.0050 chunk 287 optimal weight: 10.0000 chunk 296 optimal weight: 6.9990 chunk 388 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 357 optimal weight: 7.9990 chunk 244 optimal weight: 6.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS ** 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 156 GLN I 189 HIS ** 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 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 69 ASN J 187 HIS ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN ** 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 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 62 GLN R 109 HIS ** R 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 183 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.193598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.158869 restraints weight = 65318.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.154873 restraints weight = 118232.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.152942 restraints weight = 101867.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.151783 restraints weight = 97836.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.150184 restraints weight = 95692.724| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5559 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 35382 Z= 0.221 Angle : 0.829 11.451 48198 Z= 0.415 Chirality : 0.051 0.310 5466 Planarity : 0.007 0.147 6186 Dihedral : 6.505 46.799 4884 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.90 % Favored : 87.91 % Rotamer: Outliers : 3.62 % Allowed : 15.86 % Favored : 80.52 % 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: -2.81 (0.12), residues: 4506 helix: -0.65 (0.17), residues: 858 sheet: -1.71 (0.14), residues: 1404 loop : -2.46 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 61 TYR 0.027 0.002 TYR O 49 PHE 0.028 0.003 PHE N 304 TRP 0.049 0.003 TRP C 164 HIS 0.019 0.002 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00532 (35358) covalent geometry : angle 0.82894 (48150) SS BOND : bond 0.00402 ( 24) SS BOND : angle 1.25444 ( 48) hydrogen bonds : bond 0.03703 ( 948) hydrogen bonds : angle 5.75252 ( 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 535 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 396 time to evaluate : 1.222 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: 0.6246 (t0) cc_final: 0.5933 (t0) REVERT: A 89 LYS cc_start: 0.3828 (ptpt) cc_final: 0.3246 (mtmt) REVERT: A 291 ARG cc_start: 0.8047 (ttm170) cc_final: 0.7679 (ttp-170) REVERT: D 18 VAL cc_start: 0.7361 (OUTLIER) cc_final: 0.6994 (t) REVERT: D 29 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6718 (t80) REVERT: D 203 GLU cc_start: 0.2260 (pm20) cc_final: 0.1469 (pm20) REVERT: B 273 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8273 (tt) REVERT: H 61 ARG cc_start: 0.4262 (OUTLIER) cc_final: 0.3327 (ptt-90) REVERT: H 93 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7817 (mt) REVERT: H 106 ILE cc_start: 0.7086 (mp) cc_final: 0.6303 (mt) REVERT: I 58 ILE cc_start: 0.5193 (OUTLIER) cc_final: 0.4944 (tp) REVERT: I 78 LEU cc_start: 0.2788 (tm) cc_final: 0.2555 (tm) REVERT: M 294 ASN cc_start: 0.3650 (m-40) cc_final: 0.3305 (m-40) REVERT: L 4 MET cc_start: 0.1365 (tpp) cc_final: 0.1063 (tpp) REVERT: L 48 ILE cc_start: 0.4625 (OUTLIER) cc_final: 0.4091 (mm) REVERT: L 73 LEU cc_start: 0.4379 (tp) cc_final: 0.4045 (tt) REVERT: L 147 LYS cc_start: 0.2497 (ptmm) cc_final: 0.2182 (ttpp) REVERT: L 175 MET cc_start: 0.1917 (tmm) cc_final: 0.1397 (tmm) REVERT: N 151 GLU cc_start: 0.2135 (mp0) cc_final: 0.1392 (mp0) REVERT: J 42 GLU cc_start: 0.2815 (OUTLIER) cc_final: 0.2513 (mt-10) REVERT: O 6 GLN cc_start: 0.0715 (mt0) cc_final: 0.0023 (mp10) REVERT: O 93 LEU cc_start: 0.4694 (OUTLIER) cc_final: 0.4248 (tm) REVERT: O 98 PHE cc_start: 0.3309 (OUTLIER) cc_final: 0.2678 (m-10) REVERT: O 139 PHE cc_start: 0.0946 (p90) cc_final: 0.0230 (p90) REVERT: O 192 TYR cc_start: 0.1002 (m-80) cc_final: 0.0680 (m-10) REVERT: P 32 TYR cc_start: 0.3089 (m-10) cc_final: 0.2851 (m-80) REVERT: P 33 LEU cc_start: 0.3957 (OUTLIER) cc_final: 0.2995 (pp) REVERT: P 71 PHE cc_start: 0.3961 (m-10) cc_final: 0.3709 (m-80) REVERT: P 123 GLU cc_start: 0.1562 (tm-30) cc_final: 0.0842 (tt0) REVERT: F 29 PHE cc_start: 0.7538 (OUTLIER) cc_final: 0.7137 (t80) REVERT: F 59 ASN cc_start: 0.7791 (t0) cc_final: 0.7376 (t0) REVERT: F 145 ASN cc_start: 0.2373 (OUTLIER) cc_final: 0.1915 (m-40) REVERT: F 147 MET cc_start: 0.1913 (tpp) cc_final: 0.0625 (tpp) REVERT: G 13 LYS cc_start: 0.6168 (OUTLIER) cc_final: 0.5827 (ptmm) REVERT: G 29 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.6392 (t80) REVERT: G 59 ASN cc_start: 0.7835 (t0) cc_final: 0.7465 (t0) REVERT: G 125 SER cc_start: 0.7082 (p) cc_final: 0.6803 (p) REVERT: K 48 MET cc_start: 0.4405 (mtm) cc_final: 0.3104 (ttm) REVERT: K 94 TYR cc_start: 0.4552 (m-80) cc_final: 0.3660 (m-80) REVERT: Q 70 MET cc_start: 0.5398 (mmm) cc_final: 0.4942 (tpt) REVERT: Q 81 MET cc_start: 0.1853 (ppp) cc_final: 0.1501 (ppp) REVERT: Q 147 MET cc_start: 0.0636 (mmm) cc_final: 0.0087 (tpp) REVERT: R 4 LEU cc_start: 0.3657 (tt) cc_final: 0.3171 (tt) REVERT: R 153 LEU cc_start: 0.1746 (OUTLIER) cc_final: 0.1486 (tp) outliers start: 139 outliers final: 111 residues processed: 499 average time/residue: 0.2032 time to fit residues: 166.3486 Evaluate side-chains 492 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 365 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 87 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 78 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 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 7 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 33 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 58 ILE 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 97 LEU Chi-restraints excluded: chain M residue 254 TYR Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain L residue 47 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 145 ASN Chi-restraints excluded: chain N residue 24 VAL 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 N residue 306 LEU 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 J residue 300 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 98 PHE 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 150 ILE 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 173 SER 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 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 74 THR 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 29 PHE 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 153 LEU Chi-restraints excluded: chain Q residue 215 SER Chi-restraints excluded: chain Q residue 216 THR Chi-restraints excluded: chain R residue 20 VAL 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: chunk 202 optimal weight: 0.6980 chunk 199 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 225 optimal weight: 8.9990 chunk 376 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 265 optimal weight: 3.9990 chunk 286 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 101 HIS ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 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** L 90 GLN ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN K 43 GLN ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN ** R 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.195539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.162144 restraints weight = 66602.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.158120 restraints weight = 113764.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.155376 restraints weight = 104178.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.154695 restraints weight = 95715.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.152213 restraints weight = 91932.412| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5524 moved from start: 0.6017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 35382 Z= 0.138 Angle : 0.753 14.357 48198 Z= 0.374 Chirality : 0.048 0.307 5466 Planarity : 0.006 0.141 6186 Dihedral : 6.220 45.325 4884 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.76 % Favored : 89.10 % Rotamer: Outliers : 2.94 % Allowed : 16.85 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 0.35 % Twisted General : 0.21 % 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 (0.13), residues: 4506 helix: -0.17 (0.18), residues: 834 sheet: -1.58 (0.14), residues: 1416 loop : -2.24 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 67 TYR 0.033 0.002 TYR J 254 PHE 0.023 0.002 PHE P 98 TRP 0.050 0.002 TRP Q 111 HIS 0.010 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00328 (35358) covalent geometry : angle 0.75256 (48150) SS BOND : bond 0.00318 ( 24) SS BOND : angle 1.17983 ( 48) hydrogen bonds : bond 0.03086 ( 948) hydrogen bonds : angle 5.46233 ( 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 516 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 403 time to evaluate : 1.174 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: 0.5984 (t0) cc_final: 0.5736 (t0) REVERT: A 89 LYS cc_start: 0.3653 (ptpt) cc_final: 0.3133 (mtmt) REVERT: A 288 GLU cc_start: 0.6800 (mt-10) cc_final: 0.6359 (mt-10) REVERT: A 291 ARG cc_start: 0.7969 (ttm170) cc_final: 0.7667 (ttp-170) REVERT: D 18 VAL cc_start: 0.7292 (OUTLIER) cc_final: 0.6978 (t) REVERT: D 29 PHE cc_start: 0.7139 (OUTLIER) cc_final: 0.6706 (t80) REVERT: D 203 GLU cc_start: 0.2184 (pm20) cc_final: 0.1428 (pm20) REVERT: E 151 ASP cc_start: 0.2829 (m-30) cc_final: 0.2449 (m-30) REVERT: B 273 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8083 (tt) REVERT: H 61 ARG cc_start: 0.4311 (OUTLIER) cc_final: 0.3933 (ptt-90) REVERT: H 81 GLU cc_start: 0.2796 (pp20) cc_final: 0.2430 (pp20) REVERT: H 106 ILE cc_start: 0.6865 (mp) cc_final: 0.6301 (mp) REVERT: I 58 ILE cc_start: 0.5155 (OUTLIER) cc_final: 0.4924 (tp) REVERT: I 78 LEU cc_start: 0.2478 (tm) cc_final: 0.2187 (tt) REVERT: M 133 LEU cc_start: 0.3059 (mp) cc_final: 0.2460 (tt) REVERT: L 4 MET cc_start: 0.1110 (tpp) cc_final: 0.0793 (tpp) REVERT: L 48 ILE cc_start: 0.4599 (OUTLIER) cc_final: 0.4107 (mm) REVERT: L 73 LEU cc_start: 0.4382 (tp) cc_final: 0.4052 (tt) REVERT: L 135 PHE cc_start: 0.1724 (m-80) cc_final: 0.1480 (m-80) REVERT: L 145 ASN cc_start: 0.2121 (OUTLIER) cc_final: 0.1788 (p0) REVERT: L 147 LYS cc_start: 0.2766 (ptmm) cc_final: 0.2455 (ttpp) REVERT: L 175 MET cc_start: 0.1901 (tmm) cc_final: 0.1392 (tmm) REVERT: L 187 GLU cc_start: 0.2729 (mm-30) cc_final: 0.2081 (mm-30) REVERT: N 151 GLU cc_start: 0.2063 (mp0) cc_final: 0.1291 (mp0) REVERT: J 42 GLU cc_start: 0.2708 (OUTLIER) cc_final: 0.2372 (mt-10) REVERT: O 6 GLN cc_start: 0.0771 (mt0) cc_final: -0.0056 (mp-120) REVERT: O 93 LEU cc_start: 0.4542 (OUTLIER) cc_final: 0.4123 (tm) REVERT: O 98 PHE cc_start: 0.3228 (OUTLIER) cc_final: 0.2550 (m-10) REVERT: O 139 PHE cc_start: 0.0691 (p90) cc_final: 0.0120 (p90) REVERT: O 175 MET cc_start: 0.1351 (tmm) cc_final: 0.1057 (tmm) REVERT: O 192 TYR cc_start: 0.0979 (m-80) cc_final: 0.0678 (m-10) REVERT: P 32 TYR cc_start: 0.2534 (m-10) cc_final: 0.2230 (m-80) REVERT: P 123 GLU cc_start: 0.1422 (tm-30) cc_final: 0.0769 (tt0) REVERT: P 148 TRP cc_start: 0.0859 (m100) cc_final: 0.0561 (m100) REVERT: F 29 PHE cc_start: 0.7664 (OUTLIER) cc_final: 0.7172 (t80) REVERT: F 59 ASN cc_start: 0.7639 (t0) cc_final: 0.7240 (t0) REVERT: F 145 ASN cc_start: 0.2085 (OUTLIER) cc_final: 0.1657 (m-40) REVERT: F 147 MET cc_start: 0.1869 (tpp) cc_final: 0.1194 (tpt) REVERT: G 13 LYS cc_start: 0.6170 (OUTLIER) cc_final: 0.5818 (ptmm) REVERT: G 59 ASN cc_start: 0.7765 (t0) cc_final: 0.7316 (t0) REVERT: G 76 THR cc_start: 0.5895 (p) cc_final: 0.5601 (t) REVERT: K 48 MET cc_start: 0.4501 (mtm) cc_final: 0.3203 (ttm) REVERT: K 94 TYR cc_start: 0.4611 (m-80) cc_final: 0.4174 (m-80) REVERT: Q 70 MET cc_start: 0.5218 (mmm) cc_final: 0.4766 (tpt) REVERT: Q 147 MET cc_start: 0.0697 (mmm) cc_final: 0.0195 (tpp) REVERT: R 4 LEU cc_start: 0.3120 (tt) cc_final: 0.2517 (tt) REVERT: R 27 TYR cc_start: 0.0923 (p90) cc_final: 0.0044 (p90) REVERT: R 153 LEU cc_start: 0.1817 (OUTLIER) cc_final: 0.1502 (tp) outliers start: 113 outliers final: 89 residues processed: 487 average time/residue: 0.2102 time to fit residues: 167.1421 Evaluate side-chains 471 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 368 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 126 HIS 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 128 THR Chi-restraints excluded: chain D residue 195 VAL 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 285 THR Chi-restraints excluded: chain C residue 290 THR 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 47 LEU Chi-restraints excluded: chain I residue 58 ILE 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 97 LEU Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain L residue 47 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 145 ASN Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 101 HIS Chi-restraints excluded: chain N residue 244 THR Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain N residue 303 CYS Chi-restraints excluded: chain N residue 306 LEU 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 98 PHE Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain P residue 97 THR 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 88 SER 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 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 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 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 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 153 LEU Chi-restraints excluded: chain Q residue 215 SER Chi-restraints excluded: chain Q residue 216 THR Chi-restraints excluded: chain R residue 20 VAL 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: chunk 426 optimal weight: 0.9980 chunk 355 optimal weight: 10.0000 chunk 205 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 260 optimal weight: 6.9990 chunk 228 optimal weight: 20.0000 chunk 26 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 375 optimal weight: 20.0000 chunk 152 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 166 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** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN K 43 GLN ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 167 ASN ** 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 = 0.4615 r_free = 0.4615 target = 0.195642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.153947 restraints weight = 66634.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.151165 restraints weight = 100707.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.151436 restraints weight = 98028.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.149436 restraints weight = 79031.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.149286 restraints weight = 84334.714| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5600 moved from start: 0.6155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 35382 Z= 0.141 Angle : 0.762 13.938 48198 Z= 0.377 Chirality : 0.048 0.297 5466 Planarity : 0.007 0.151 6186 Dihedral : 6.132 44.298 4884 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.96 % Favored : 88.90 % Rotamer: Outliers : 3.05 % Allowed : 16.88 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.13), residues: 4506 helix: 0.08 (0.18), residues: 798 sheet: -1.50 (0.14), residues: 1416 loop : -2.16 (0.13), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 105 TYR 0.030 0.002 TYR P 173 PHE 0.027 0.002 PHE P 139 TRP 0.066 0.003 TRP P 163 HIS 0.010 0.001 HIS N 101 Details of bonding type rmsd covalent geometry : bond 0.00337 (35358) covalent geometry : angle 0.76188 (48150) SS BOND : bond 0.00306 ( 24) SS BOND : angle 1.05838 ( 48) hydrogen bonds : bond 0.03100 ( 948) hydrogen bonds : angle 5.39003 ( 2520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5522.12 seconds wall clock time: 97 minutes 15.61 seconds (5835.61 seconds total)