Starting phenix.real_space_refine on Sat Mar 16 00:14:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n26_9324/03_2024/6n26_9324_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n26_9324/03_2024/6n26_9324.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n26_9324/03_2024/6n26_9324.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n26_9324/03_2024/6n26_9324.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n26_9324/03_2024/6n26_9324_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n26_9324/03_2024/6n26_9324_neut.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.163 sd= 2.106 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 65 5.16 5 C 8710 2.51 5 N 2145 2.21 5 O 2270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 59": "NH1" <-> "NH2" Residue "B ARG 59": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "E ARG 59": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13190 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2638 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2638 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 2638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2638 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2638 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 2638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2638 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 6.91, per 1000 atoms: 0.52 Number of scatterers: 13190 At special positions: 0 Unit cell: (94.656, 94.656, 113.152, 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 65 16.00 O 2270 8.00 N 2145 7.00 C 8710 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 185 " distance=2.05 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 185 " distance=2.05 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 185 " distance=2.05 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 185 " distance=2.05 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 185 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 5.01 Conformation dependent library (CDL) restraints added in 2.3 seconds 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3060 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 0 sheets defined 75.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 27 through 32 removed outlier: 3.998A pdb=" N LEU A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 53 removed outlier: 3.745A pdb=" N LEU A 37 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 removed outlier: 3.501A pdb=" N PHE A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 65 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 99 removed outlier: 4.020A pdb=" N VAL A 81 " --> pdb=" O PRO A 77 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR A 97 " --> pdb=" O TRP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 114 removed outlier: 3.856A pdb=" N LEU A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N CYS A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 144 removed outlier: 3.507A pdb=" N SER A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE A 139 " --> pdb=" O CYS A 135 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 151 Processing helix chain 'A' and resid 154 through 160 Processing helix chain 'A' and resid 164 through 174 removed outlier: 3.950A pdb=" N LYS A 169 " --> pdb=" O PRO A 165 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 172 " --> pdb=" O HIS A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 182 through 197 removed outlier: 4.074A pdb=" N SER A 189 " --> pdb=" O CYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 228 removed outlier: 3.504A pdb=" N GLU A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.889A pdb=" N VAL A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 removed outlier: 3.534A pdb=" N LYS A 262 " --> pdb=" O ASP A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 285 removed outlier: 3.960A pdb=" N GLN A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 295 Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'B' and resid 27 through 32 removed outlier: 3.999A pdb=" N LEU B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 53 removed outlier: 3.746A pdb=" N LEU B 37 " --> pdb=" O TYR B 33 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 70 removed outlier: 3.500A pdb=" N PHE B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 65 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR B 68 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 99 removed outlier: 4.019A pdb=" N VAL B 81 " --> pdb=" O PRO B 77 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR B 97 " --> pdb=" O TRP B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 114 removed outlier: 3.856A pdb=" N LEU B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N CYS B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 144 removed outlier: 3.506A pdb=" N SER B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE B 139 " --> pdb=" O CYS B 135 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 151 Processing helix chain 'B' and resid 154 through 160 Processing helix chain 'B' and resid 164 through 174 removed outlier: 3.949A pdb=" N LYS B 169 " --> pdb=" O PRO B 165 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS B 170 " --> pdb=" O GLU B 166 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 172 " --> pdb=" O HIS B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 181 No H-bonds generated for 'chain 'B' and resid 179 through 181' Processing helix chain 'B' and resid 182 through 197 removed outlier: 4.074A pdb=" N SER B 189 " --> pdb=" O CYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 228 removed outlier: 3.503A pdb=" N GLU B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 removed outlier: 3.889A pdb=" N VAL B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 removed outlier: 3.534A pdb=" N LYS B 262 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 285 removed outlier: 3.960A pdb=" N GLN B 280 " --> pdb=" O PHE B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 295 Processing helix chain 'B' and resid 306 through 322 Processing helix chain 'C' and resid 27 through 32 removed outlier: 3.997A pdb=" N LEU C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 53 removed outlier: 3.745A pdb=" N LEU C 37 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 70 removed outlier: 3.500A pdb=" N PHE C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 65 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR C 68 " --> pdb=" O LYS C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 99 removed outlier: 4.019A pdb=" N VAL C 81 " --> pdb=" O PRO C 77 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR C 97 " --> pdb=" O TRP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 114 removed outlier: 3.856A pdb=" N LEU C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N CYS C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL C 114 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 144 removed outlier: 3.506A pdb=" N SER C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE C 139 " --> pdb=" O CYS C 135 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 151 Processing helix chain 'C' and resid 154 through 160 Processing helix chain 'C' and resid 164 through 174 removed outlier: 3.949A pdb=" N LYS C 169 " --> pdb=" O PRO C 165 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU C 172 " --> pdb=" O HIS C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 182 through 197 removed outlier: 4.073A pdb=" N SER C 189 " --> pdb=" O CYS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 228 removed outlier: 3.503A pdb=" N GLU C 213 " --> pdb=" O GLY C 209 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 removed outlier: 3.888A pdb=" N VAL C 240 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 removed outlier: 3.534A pdb=" N LYS C 262 " --> pdb=" O ASP C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 285 removed outlier: 3.960A pdb=" N GLN C 280 " --> pdb=" O PHE C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 295 Processing helix chain 'C' and resid 306 through 322 Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.998A pdb=" N LEU D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 53 removed outlier: 3.745A pdb=" N LEU D 37 " --> pdb=" O TYR D 33 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 70 removed outlier: 3.500A pdb=" N PHE D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU D 65 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR D 68 " --> pdb=" O LYS D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 99 removed outlier: 4.020A pdb=" N VAL D 81 " --> pdb=" O PRO D 77 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR D 97 " --> pdb=" O TRP D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 114 removed outlier: 3.856A pdb=" N LEU D 109 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N CYS D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 144 removed outlier: 3.506A pdb=" N SER D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE D 139 " --> pdb=" O CYS D 135 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 151 Processing helix chain 'D' and resid 154 through 160 Processing helix chain 'D' and resid 164 through 174 removed outlier: 3.949A pdb=" N LYS D 169 " --> pdb=" O PRO D 165 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS D 170 " --> pdb=" O GLU D 166 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU D 172 " --> pdb=" O HIS D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 181 No H-bonds generated for 'chain 'D' and resid 179 through 181' Processing helix chain 'D' and resid 182 through 197 removed outlier: 4.074A pdb=" N SER D 189 " --> pdb=" O CYS D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 228 removed outlier: 3.503A pdb=" N GLU D 213 " --> pdb=" O GLY D 209 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN D 215 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY D 226 " --> pdb=" O GLY D 222 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 removed outlier: 3.889A pdb=" N VAL D 240 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 removed outlier: 3.533A pdb=" N LYS D 262 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 285 removed outlier: 3.960A pdb=" N GLN D 280 " --> pdb=" O PHE D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 295 Processing helix chain 'D' and resid 306 through 322 Processing helix chain 'E' and resid 27 through 32 removed outlier: 3.998A pdb=" N LEU E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 53 removed outlier: 3.745A pdb=" N LEU E 37 " --> pdb=" O TYR E 33 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE E 46 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 70 removed outlier: 3.514A pdb=" N LEU E 65 " --> pdb=" O MET E 61 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR E 68 " --> pdb=" O LYS E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 99 removed outlier: 4.019A pdb=" N VAL E 81 " --> pdb=" O PRO E 77 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR E 97 " --> pdb=" O TRP E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 114 removed outlier: 3.856A pdb=" N LEU E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N CYS E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL E 114 " --> pdb=" O VAL E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 144 removed outlier: 3.506A pdb=" N SER E 136 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE E 139 " --> pdb=" O CYS E 135 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 151 Processing helix chain 'E' and resid 154 through 160 Processing helix chain 'E' and resid 164 through 174 removed outlier: 3.949A pdb=" N LYS E 169 " --> pdb=" O PRO E 165 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS E 170 " --> pdb=" O GLU E 166 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU E 172 " --> pdb=" O HIS E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 181 No H-bonds generated for 'chain 'E' and resid 179 through 181' Processing helix chain 'E' and resid 182 through 197 removed outlier: 4.073A pdb=" N SER E 189 " --> pdb=" O CYS E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 228 removed outlier: 3.504A pdb=" N GLU E 213 " --> pdb=" O GLY E 209 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN E 215 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY E 226 " --> pdb=" O GLY E 222 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP E 228 " --> pdb=" O LEU E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 removed outlier: 3.888A pdb=" N VAL E 240 " --> pdb=" O TYR E 236 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 removed outlier: 3.534A pdb=" N LYS E 262 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 285 removed outlier: 3.961A pdb=" N GLN E 280 " --> pdb=" O PHE E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 295 Processing helix chain 'E' and resid 306 through 322 752 hydrogen bonds defined for protein. 2241 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.62 Time building geometry restraints manager: 5.38 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: 4029 1.34 - 1.47: 3738 1.47 - 1.59: 5703 1.59 - 1.71: 0 1.71 - 1.84: 100 Bond restraints: 13570 Sorted by residual: bond pdb=" CB MET D 107 " pdb=" CG MET D 107 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.49e+00 bond pdb=" CB MET C 107 " pdb=" CG MET C 107 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.46e+00 bond pdb=" CB MET A 107 " pdb=" CG MET A 107 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.44e+00 bond pdb=" CB MET B 107 " pdb=" CG MET B 107 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.43e+00 bond pdb=" CB MET E 107 " pdb=" CG MET E 107 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.42e+00 ... (remaining 13565 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.68: 382 106.68 - 113.52: 7300 113.52 - 120.35: 5678 120.35 - 127.19: 4916 127.19 - 134.03: 179 Bond angle restraints: 18455 Sorted by residual: angle pdb=" CA TRP C 287 " pdb=" CB TRP C 287 " pdb=" CG TRP C 287 " ideal model delta sigma weight residual 113.60 121.18 -7.58 1.90e+00 2.77e-01 1.59e+01 angle pdb=" CA TRP B 287 " pdb=" CB TRP B 287 " pdb=" CG TRP B 287 " ideal model delta sigma weight residual 113.60 121.18 -7.58 1.90e+00 2.77e-01 1.59e+01 angle pdb=" CA TRP A 287 " pdb=" CB TRP A 287 " pdb=" CG TRP A 287 " ideal model delta sigma weight residual 113.60 121.17 -7.57 1.90e+00 2.77e-01 1.59e+01 angle pdb=" CA TRP D 287 " pdb=" CB TRP D 287 " pdb=" CG TRP D 287 " ideal model delta sigma weight residual 113.60 121.17 -7.57 1.90e+00 2.77e-01 1.59e+01 angle pdb=" CA TRP E 287 " pdb=" CB TRP E 287 " pdb=" CG TRP E 287 " ideal model delta sigma weight residual 113.60 121.15 -7.55 1.90e+00 2.77e-01 1.58e+01 ... (remaining 18450 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.16: 6882 9.16 - 18.32: 803 18.32 - 27.48: 105 27.48 - 36.63: 95 36.63 - 45.79: 35 Dihedral angle restraints: 7920 sinusoidal: 3185 harmonic: 4735 Sorted by residual: dihedral pdb=" CB CYS E 135 " pdb=" SG CYS E 135 " pdb=" SG CYS E 185 " pdb=" CB CYS E 185 " ideal model delta sinusoidal sigma weight residual -86.00 -118.55 32.55 1 1.00e+01 1.00e-02 1.51e+01 dihedral pdb=" CB CYS C 135 " pdb=" SG CYS C 135 " pdb=" SG CYS C 185 " pdb=" CB CYS C 185 " ideal model delta sinusoidal sigma weight residual -86.00 -118.52 32.52 1 1.00e+01 1.00e-02 1.50e+01 dihedral pdb=" CB CYS D 135 " pdb=" SG CYS D 135 " pdb=" SG CYS D 185 " pdb=" CB CYS D 185 " ideal model delta sinusoidal sigma weight residual -86.00 -118.51 32.51 1 1.00e+01 1.00e-02 1.50e+01 ... (remaining 7917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1022 0.038 - 0.075: 769 0.075 - 0.113: 188 0.113 - 0.150: 41 0.150 - 0.188: 10 Chirality restraints: 2030 Sorted by residual: chirality pdb=" CA ILE A 232 " pdb=" N ILE A 232 " pdb=" C ILE A 232 " pdb=" CB ILE A 232 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.81e-01 chirality pdb=" CA ILE C 232 " pdb=" N ILE C 232 " pdb=" C ILE C 232 " pdb=" CB ILE C 232 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.75e-01 chirality pdb=" CA ILE D 232 " pdb=" N ILE D 232 " pdb=" C ILE D 232 " pdb=" CB ILE D 232 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.72e-01 ... (remaining 2027 not shown) Planarity restraints: 2285 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 287 " -0.032 2.00e-02 2.50e+03 2.40e-02 1.44e+01 pdb=" CG TRP A 287 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A 287 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 287 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 287 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 287 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 287 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 287 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 287 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 287 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 287 " -0.032 2.00e-02 2.50e+03 2.40e-02 1.44e+01 pdb=" CG TRP E 287 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP E 287 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP E 287 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 287 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP E 287 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 287 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 287 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 287 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 287 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 287 " 0.031 2.00e-02 2.50e+03 2.39e-02 1.43e+01 pdb=" CG TRP C 287 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP C 287 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C 287 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 287 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP C 287 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 287 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 287 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 287 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 287 " 0.003 2.00e-02 2.50e+03 ... (remaining 2282 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3827 2.80 - 3.33: 11764 3.33 - 3.85: 21311 3.85 - 4.38: 27095 4.38 - 4.90: 44551 Nonbonded interactions: 108548 Sorted by model distance: nonbonded pdb=" OD2 ASP B 104 " pdb=" NH2 ARG C 218 " model vdw 2.277 2.520 nonbonded pdb=" O LEU C 20 " pdb=" NE2 GLN D 238 " model vdw 2.327 2.520 nonbonded pdb=" OD2 ASP D 104 " pdb=" NH2 ARG E 218 " model vdw 2.363 2.520 nonbonded pdb=" N PHE B 17 " pdb=" OE2 GLU C 292 " model vdw 2.367 2.520 nonbonded pdb=" NE ARG D 105 " pdb=" OE1 GLU D 213 " model vdw 2.387 2.520 ... (remaining 108543 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.470 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 34.710 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 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 0.061 13570 Z= 0.494 Angle : 0.830 8.585 18455 Z= 0.442 Chirality : 0.051 0.188 2030 Planarity : 0.006 0.051 2285 Dihedral : 9.204 45.792 4845 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.12 (0.12), residues: 1575 helix: -4.06 (0.07), residues: 1145 sheet: None (None), residues: 0 loop : -3.25 (0.24), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.004 TRP E 287 HIS 0.006 0.002 HIS A 168 PHE 0.021 0.003 PHE A 17 TYR 0.042 0.003 TYR A 236 ARG 0.006 0.001 ARG C 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 1.520 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8693 (tttt) cc_final: 0.8193 (tppp) REVERT: A 46 ILE cc_start: 0.8854 (mt) cc_final: 0.8598 (mm) REVERT: A 92 ARG cc_start: 0.7766 (tmt90) cc_final: 0.7327 (tpt170) REVERT: A 308 ASN cc_start: 0.7630 (m-40) cc_final: 0.7364 (m-40) REVERT: B 30 LYS cc_start: 0.8876 (tttt) cc_final: 0.8367 (tptm) REVERT: B 46 ILE cc_start: 0.9001 (mt) cc_final: 0.8758 (mm) REVERT: B 92 ARG cc_start: 0.7781 (tmt90) cc_final: 0.7529 (mmt180) REVERT: B 203 ASP cc_start: 0.7720 (m-30) cc_final: 0.7283 (m-30) REVERT: B 289 LYS cc_start: 0.8552 (mmmt) cc_final: 0.8273 (mmmt) REVERT: B 308 ASN cc_start: 0.7603 (m-40) cc_final: 0.7246 (m-40) REVERT: C 41 SER cc_start: 0.8392 (m) cc_final: 0.8049 (p) REVERT: C 46 ILE cc_start: 0.8469 (mt) cc_final: 0.8165 (mm) REVERT: C 54 LEU cc_start: 0.8157 (mt) cc_final: 0.7898 (mt) REVERT: C 88 LEU cc_start: 0.8473 (mt) cc_final: 0.8270 (mt) REVERT: C 92 ARG cc_start: 0.7723 (tmt90) cc_final: 0.7219 (tpt170) REVERT: C 259 ASP cc_start: 0.7913 (t0) cc_final: 0.7682 (t0) REVERT: C 328 ASP cc_start: 0.7186 (t70) cc_final: 0.6875 (p0) REVERT: D 30 LYS cc_start: 0.8598 (tttt) cc_final: 0.8151 (mmtm) REVERT: D 46 ILE cc_start: 0.8745 (mt) cc_final: 0.8522 (mm) REVERT: D 54 LEU cc_start: 0.8637 (mt) cc_final: 0.8424 (mt) REVERT: D 70 ASN cc_start: 0.9036 (t0) cc_final: 0.8796 (t0) REVERT: D 92 ARG cc_start: 0.7729 (tmt90) cc_final: 0.7340 (mmt90) REVERT: D 308 ASN cc_start: 0.7383 (m-40) cc_final: 0.6825 (p0) REVERT: E 30 LYS cc_start: 0.8549 (tttt) cc_final: 0.8326 (mmtp) REVERT: E 46 ILE cc_start: 0.8656 (mt) cc_final: 0.8352 (mm) REVERT: E 88 LEU cc_start: 0.8534 (mt) cc_final: 0.8325 (mt) REVERT: E 92 ARG cc_start: 0.7647 (tmt90) cc_final: 0.7214 (tpt170) REVERT: E 253 ILE cc_start: 0.8670 (mt) cc_final: 0.8450 (mt) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 1.2656 time to fit residues: 533.2201 Evaluate side-chains 200 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 chunk 121 optimal weight: 0.0050 chunk 47 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 140 optimal weight: 0.0070 overall best weight: 0.5812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN A 316 GLN A 339 ASN B 19 GLN B 96 GLN B 256 GLN B 296 ASN B 316 GLN B 339 ASN C 133 ASN C 190 ASN C 256 GLN C 293 GLN C 308 ASN C 339 ASN D 96 GLN D 256 GLN D 293 GLN D 339 ASN E 58 GLN E 133 ASN E 256 GLN E 339 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13570 Z= 0.180 Angle : 0.618 10.732 18455 Z= 0.321 Chirality : 0.040 0.183 2030 Planarity : 0.005 0.042 2285 Dihedral : 4.657 31.111 1765 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.70 % Allowed : 9.76 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.17), residues: 1575 helix: -1.60 (0.13), residues: 1160 sheet: None (None), residues: 0 loop : -2.82 (0.26), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 287 HIS 0.003 0.000 HIS C 156 PHE 0.024 0.002 PHE C 278 TYR 0.012 0.001 TYR C 29 ARG 0.005 0.001 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 244 time to evaluate : 1.653 Fit side-chains REVERT: A 30 LYS cc_start: 0.8665 (tttt) cc_final: 0.8049 (tppp) REVERT: A 46 ILE cc_start: 0.8883 (mt) cc_final: 0.8561 (mm) REVERT: A 53 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7900 (mt) REVERT: A 92 ARG cc_start: 0.7785 (tmt90) cc_final: 0.7125 (mmt90) REVERT: A 328 ASP cc_start: 0.7206 (p0) cc_final: 0.6942 (t0) REVERT: B 30 LYS cc_start: 0.8815 (tttt) cc_final: 0.8303 (tptt) REVERT: B 35 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6890 (tt0) REVERT: B 92 ARG cc_start: 0.7698 (tmt90) cc_final: 0.7354 (mmt90) REVERT: B 323 ASP cc_start: 0.7875 (t0) cc_final: 0.7637 (t0) REVERT: C 41 SER cc_start: 0.8349 (m) cc_final: 0.8029 (p) REVERT: C 46 ILE cc_start: 0.8486 (mt) cc_final: 0.8274 (mp) REVERT: C 92 ARG cc_start: 0.7496 (tmt90) cc_final: 0.7061 (mmt90) REVERT: C 107 MET cc_start: 0.8508 (ttp) cc_final: 0.8238 (ttp) REVERT: C 149 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8150 (ptpt) REVERT: C 249 LEU cc_start: 0.8642 (tp) cc_final: 0.8080 (mm) REVERT: D 30 LYS cc_start: 0.8582 (tttt) cc_final: 0.8235 (mmmm) REVERT: D 46 ILE cc_start: 0.8763 (mt) cc_final: 0.8464 (mm) REVERT: D 70 ASN cc_start: 0.8969 (t0) cc_final: 0.8765 (t0) REVERT: D 92 ARG cc_start: 0.7541 (tmt90) cc_final: 0.7121 (mmt90) REVERT: E 30 LYS cc_start: 0.8652 (tttt) cc_final: 0.8305 (tptm) REVERT: E 46 ILE cc_start: 0.8716 (mt) cc_final: 0.8395 (mm) REVERT: E 92 ARG cc_start: 0.7679 (tmt90) cc_final: 0.7224 (mmt90) REVERT: E 120 TYR cc_start: 0.8317 (t80) cc_final: 0.7912 (t80) REVERT: E 262 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6739 (mptp) REVERT: E 295 ILE cc_start: 0.8532 (tt) cc_final: 0.8274 (mt) outliers start: 39 outliers final: 13 residues processed: 269 average time/residue: 0.9522 time to fit residues: 285.5166 Evaluate side-chains 200 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 183 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 262 LYS Chi-restraints excluded: chain E residue 273 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 0.1980 chunk 43 optimal weight: 6.9990 chunk 117 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 chunk 139 optimal weight: 20.0000 chunk 48 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN B 19 GLN C 256 GLN D 256 GLN E 339 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13570 Z= 0.161 Angle : 0.528 9.642 18455 Z= 0.269 Chirality : 0.038 0.175 2030 Planarity : 0.004 0.037 2285 Dihedral : 4.167 26.351 1765 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.56 % Allowed : 13.36 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.19), residues: 1575 helix: -0.24 (0.14), residues: 1160 sheet: None (None), residues: 0 loop : -2.48 (0.27), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 287 HIS 0.003 0.001 HIS C 326 PHE 0.026 0.001 PHE A 80 TYR 0.010 0.001 TYR C 225 ARG 0.003 0.000 ARG C 59 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 200 time to evaluate : 1.504 Fit side-chains REVERT: A 30 LYS cc_start: 0.8650 (tttt) cc_final: 0.8062 (tppp) REVERT: A 46 ILE cc_start: 0.8906 (mt) cc_final: 0.8563 (mm) REVERT: A 53 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7802 (mt) REVERT: A 92 ARG cc_start: 0.7713 (tmt90) cc_final: 0.7170 (mmt90) REVERT: B 30 LYS cc_start: 0.8861 (tttt) cc_final: 0.8355 (tptt) REVERT: B 92 ARG cc_start: 0.7555 (tmt90) cc_final: 0.7255 (mmt90) REVERT: B 323 ASP cc_start: 0.7780 (t0) cc_final: 0.7564 (t0) REVERT: C 41 SER cc_start: 0.8410 (m) cc_final: 0.8108 (p) REVERT: C 46 ILE cc_start: 0.8620 (mt) cc_final: 0.8309 (tt) REVERT: C 92 ARG cc_start: 0.7475 (tmt90) cc_final: 0.7116 (mmt90) REVERT: C 149 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8164 (ptpt) REVERT: C 249 LEU cc_start: 0.8667 (tp) cc_final: 0.8096 (mm) REVERT: D 30 LYS cc_start: 0.8555 (tttt) cc_final: 0.8209 (mmtm) REVERT: D 46 ILE cc_start: 0.8757 (mt) cc_final: 0.8393 (tt) REVERT: D 92 ARG cc_start: 0.7578 (tmt90) cc_final: 0.7124 (mmt90) REVERT: E 30 LYS cc_start: 0.8675 (tttt) cc_final: 0.8342 (tptm) REVERT: E 46 ILE cc_start: 0.8742 (mt) cc_final: 0.8424 (mm) REVERT: E 92 ARG cc_start: 0.7694 (tmt90) cc_final: 0.7113 (mmt-90) REVERT: E 262 LYS cc_start: 0.7296 (OUTLIER) cc_final: 0.6896 (mptp) outliers start: 37 outliers final: 17 residues processed: 228 average time/residue: 0.9998 time to fit residues: 253.2279 Evaluate side-chains 192 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 172 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 262 LYS Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 67 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 141 optimal weight: 0.9990 chunk 149 optimal weight: 0.0470 chunk 134 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 124 optimal weight: 20.0000 overall best weight: 4.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN A 256 GLN A 326 HIS B 19 GLN B 220 GLN D 256 GLN E 326 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13570 Z= 0.251 Angle : 0.580 9.757 18455 Z= 0.294 Chirality : 0.041 0.261 2030 Planarity : 0.004 0.040 2285 Dihedral : 4.205 34.818 1765 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.60 % Allowed : 13.91 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.20), residues: 1575 helix: 0.26 (0.14), residues: 1175 sheet: None (None), residues: 0 loop : -2.14 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 229 HIS 0.005 0.001 HIS A 326 PHE 0.030 0.002 PHE C 278 TYR 0.020 0.001 TYR E 225 ARG 0.003 0.001 ARG E 130 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 178 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8671 (tttt) cc_final: 0.8052 (tppp) REVERT: A 46 ILE cc_start: 0.9005 (mt) cc_final: 0.8710 (mp) REVERT: A 92 ARG cc_start: 0.7689 (tmt90) cc_final: 0.7148 (mmt90) REVERT: B 30 LYS cc_start: 0.8899 (tttt) cc_final: 0.8410 (tptt) REVERT: B 92 ARG cc_start: 0.7580 (tmt90) cc_final: 0.7223 (mmt90) REVERT: B 323 ASP cc_start: 0.7926 (t0) cc_final: 0.7628 (t0) REVERT: C 41 SER cc_start: 0.8456 (m) cc_final: 0.8167 (p) REVERT: C 46 ILE cc_start: 0.8762 (mt) cc_final: 0.8440 (mm) REVERT: C 92 ARG cc_start: 0.7540 (tmt90) cc_final: 0.7118 (mmt90) REVERT: C 249 LEU cc_start: 0.8789 (tp) cc_final: 0.8181 (mm) REVERT: D 30 LYS cc_start: 0.8619 (tttt) cc_final: 0.8334 (mmtp) REVERT: D 46 ILE cc_start: 0.8795 (mt) cc_final: 0.8521 (mm) REVERT: D 92 ARG cc_start: 0.7581 (tmt90) cc_final: 0.7175 (mmt90) REVERT: D 325 MET cc_start: 0.8934 (mtp) cc_final: 0.8426 (mtp) REVERT: E 46 ILE cc_start: 0.8801 (mt) cc_final: 0.8504 (mm) REVERT: E 92 ARG cc_start: 0.7744 (tmt90) cc_final: 0.7219 (mmt90) REVERT: E 129 MET cc_start: 0.8853 (mmm) cc_final: 0.8475 (mmp) REVERT: E 149 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7987 (ptpt) REVERT: E 262 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.6993 (mptp) outliers start: 52 outliers final: 30 residues processed: 218 average time/residue: 0.9317 time to fit residues: 227.6887 Evaluate side-chains 202 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 170 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 262 LYS Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN B 19 GLN C 256 GLN D 256 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 13570 Z= 0.348 Angle : 0.638 9.714 18455 Z= 0.319 Chirality : 0.044 0.216 2030 Planarity : 0.004 0.042 2285 Dihedral : 4.404 34.569 1765 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.15 % Allowed : 13.98 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.20), residues: 1575 helix: 0.34 (0.14), residues: 1165 sheet: None (None), residues: 0 loop : -2.11 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 229 HIS 0.006 0.001 HIS C 326 PHE 0.033 0.002 PHE B 80 TYR 0.026 0.002 TYR E 225 ARG 0.003 0.000 ARG B 130 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 177 time to evaluate : 1.572 Fit side-chains REVERT: A 30 LYS cc_start: 0.8653 (tttt) cc_final: 0.8106 (tppp) REVERT: A 46 ILE cc_start: 0.8993 (mt) cc_final: 0.8691 (mp) REVERT: A 92 ARG cc_start: 0.7765 (tmt90) cc_final: 0.7208 (mmt90) REVERT: B 30 LYS cc_start: 0.8823 (tttt) cc_final: 0.8280 (mmtp) REVERT: B 92 ARG cc_start: 0.7508 (tmt90) cc_final: 0.7267 (mmt90) REVERT: C 41 SER cc_start: 0.8700 (m) cc_final: 0.8353 (p) REVERT: C 46 ILE cc_start: 0.8959 (mt) cc_final: 0.8608 (mm) REVERT: C 92 ARG cc_start: 0.7800 (tmt90) cc_final: 0.7172 (mmt90) REVERT: D 30 LYS cc_start: 0.8727 (tttt) cc_final: 0.8272 (tptm) REVERT: D 46 ILE cc_start: 0.8847 (mt) cc_final: 0.8639 (mm) REVERT: D 92 ARG cc_start: 0.7647 (tmt90) cc_final: 0.7120 (mmt90) REVERT: D 259 ASP cc_start: 0.8243 (t0) cc_final: 0.8034 (t0) REVERT: D 320 MET cc_start: 0.8502 (ttt) cc_final: 0.8273 (ttp) REVERT: E 30 LYS cc_start: 0.8678 (tttt) cc_final: 0.8239 (tttt) REVERT: E 46 ILE cc_start: 0.8934 (mt) cc_final: 0.8669 (mm) REVERT: E 92 ARG cc_start: 0.7663 (tmt90) cc_final: 0.7233 (mmt90) REVERT: E 129 MET cc_start: 0.8888 (mmm) cc_final: 0.8618 (mmp) REVERT: E 149 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8119 (ptpt) REVERT: E 262 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.7196 (mptp) outliers start: 60 outliers final: 39 residues processed: 226 average time/residue: 0.8998 time to fit residues: 228.8326 Evaluate side-chains 207 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 166 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 262 LYS Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 87 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 149 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 49 optimal weight: 0.0040 chunk 78 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN B 19 GLN D 256 GLN D 296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13570 Z= 0.188 Angle : 0.548 10.644 18455 Z= 0.275 Chirality : 0.040 0.251 2030 Planarity : 0.004 0.040 2285 Dihedral : 4.161 31.997 1765 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.77 % Allowed : 15.85 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.20), residues: 1575 helix: 0.68 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -1.89 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 229 HIS 0.002 0.000 HIS C 178 PHE 0.029 0.001 PHE E 278 TYR 0.013 0.001 TYR A 225 ARG 0.003 0.000 ARG D 159 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 176 time to evaluate : 1.570 Fit side-chains REVERT: A 30 LYS cc_start: 0.8595 (tttt) cc_final: 0.8095 (tppp) REVERT: A 46 ILE cc_start: 0.8980 (mt) cc_final: 0.8763 (mt) REVERT: A 92 ARG cc_start: 0.7662 (tmt90) cc_final: 0.7116 (mmt90) REVERT: B 30 LYS cc_start: 0.8799 (tttt) cc_final: 0.8261 (mmtp) REVERT: B 67 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8822 (mp) REVERT: B 92 ARG cc_start: 0.7490 (tmt90) cc_final: 0.7177 (mmt90) REVERT: C 41 SER cc_start: 0.8729 (m) cc_final: 0.8442 (p) REVERT: C 46 ILE cc_start: 0.8945 (mt) cc_final: 0.8649 (mm) REVERT: C 92 ARG cc_start: 0.7719 (tmt90) cc_final: 0.7119 (mmt90) REVERT: C 252 LEU cc_start: 0.8934 (tp) cc_final: 0.8696 (tm) REVERT: D 30 LYS cc_start: 0.8717 (tttt) cc_final: 0.8327 (mmtp) REVERT: D 46 ILE cc_start: 0.8812 (mt) cc_final: 0.8564 (mm) REVERT: D 92 ARG cc_start: 0.7585 (tmt90) cc_final: 0.7078 (mmt90) REVERT: E 30 LYS cc_start: 0.8672 (tttt) cc_final: 0.8285 (tptt) REVERT: E 41 SER cc_start: 0.8734 (m) cc_final: 0.8479 (p) REVERT: E 46 ILE cc_start: 0.8929 (mt) cc_final: 0.8666 (mm) REVERT: E 92 ARG cc_start: 0.7589 (tmt90) cc_final: 0.7285 (mmt90) REVERT: E 149 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8098 (ptpt) REVERT: E 262 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.7175 (mptp) outliers start: 40 outliers final: 27 residues processed: 207 average time/residue: 0.9436 time to fit residues: 218.5037 Evaluate side-chains 195 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 165 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 262 LYS Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN B 19 GLN C 190 ASN D 220 GLN D 296 ASN E 220 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13570 Z= 0.172 Angle : 0.536 11.282 18455 Z= 0.266 Chirality : 0.039 0.242 2030 Planarity : 0.004 0.042 2285 Dihedral : 4.049 30.264 1765 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.84 % Allowed : 15.99 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.20), residues: 1575 helix: 0.89 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -1.82 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 229 HIS 0.002 0.000 HIS C 326 PHE 0.032 0.001 PHE B 80 TYR 0.013 0.001 TYR A 97 ARG 0.002 0.000 ARG B 159 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 177 time to evaluate : 1.385 Fit side-chains REVERT: A 30 LYS cc_start: 0.8584 (tttt) cc_final: 0.8121 (tppp) REVERT: A 41 SER cc_start: 0.8732 (m) cc_final: 0.8463 (p) REVERT: A 46 ILE cc_start: 0.8980 (mt) cc_final: 0.8751 (mm) REVERT: A 92 ARG cc_start: 0.7648 (tmt90) cc_final: 0.7117 (mmt90) REVERT: B 30 LYS cc_start: 0.8741 (tttt) cc_final: 0.8219 (mmtp) REVERT: B 67 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8816 (mp) REVERT: B 92 ARG cc_start: 0.7596 (tmt90) cc_final: 0.7176 (mmt90) REVERT: B 323 ASP cc_start: 0.7934 (t0) cc_final: 0.7657 (t0) REVERT: C 41 SER cc_start: 0.8755 (m) cc_final: 0.8434 (p) REVERT: C 46 ILE cc_start: 0.8949 (mt) cc_final: 0.8666 (mm) REVERT: C 92 ARG cc_start: 0.7692 (tmt90) cc_final: 0.7086 (mmt90) REVERT: D 30 LYS cc_start: 0.8700 (tttt) cc_final: 0.8326 (mmtp) REVERT: D 46 ILE cc_start: 0.8804 (mt) cc_final: 0.8551 (mm) REVERT: D 92 ARG cc_start: 0.7568 (tmt90) cc_final: 0.7092 (mmt90) REVERT: E 30 LYS cc_start: 0.8646 (tttt) cc_final: 0.8221 (tttt) REVERT: E 41 SER cc_start: 0.8661 (m) cc_final: 0.8359 (p) REVERT: E 46 ILE cc_start: 0.8527 (mt) cc_final: 0.8266 (tt) REVERT: E 92 ARG cc_start: 0.7574 (tmt90) cc_final: 0.7156 (mmt90) REVERT: E 149 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8103 (ptpt) REVERT: E 262 LYS cc_start: 0.7398 (OUTLIER) cc_final: 0.7169 (mptp) outliers start: 41 outliers final: 26 residues processed: 211 average time/residue: 0.9047 time to fit residues: 214.2080 Evaluate side-chains 195 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 166 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 262 LYS Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 0.0670 chunk 89 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 117 optimal weight: 0.5980 chunk 135 optimal weight: 8.9990 overall best weight: 3.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN D 220 GLN D 296 ASN E 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13570 Z= 0.245 Angle : 0.591 11.308 18455 Z= 0.290 Chirality : 0.041 0.252 2030 Planarity : 0.004 0.039 2285 Dihedral : 4.100 30.485 1765 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.77 % Allowed : 16.96 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.20), residues: 1575 helix: 0.87 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -1.80 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 229 HIS 0.003 0.001 HIS C 326 PHE 0.023 0.002 PHE E 80 TYR 0.017 0.001 TYR D 225 ARG 0.010 0.000 ARG E 202 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 172 time to evaluate : 1.317 Fit side-chains REVERT: A 30 LYS cc_start: 0.8559 (tttt) cc_final: 0.8098 (tppp) REVERT: A 41 SER cc_start: 0.8743 (m) cc_final: 0.8422 (p) REVERT: A 46 ILE cc_start: 0.8792 (mt) cc_final: 0.8536 (mp) REVERT: A 92 ARG cc_start: 0.7686 (tmt90) cc_final: 0.7119 (mmt90) REVERT: B 30 LYS cc_start: 0.8715 (tttt) cc_final: 0.8162 (tttt) REVERT: B 67 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8812 (mp) REVERT: B 92 ARG cc_start: 0.7580 (tmt90) cc_final: 0.7101 (mmt90) REVERT: B 323 ASP cc_start: 0.7997 (t0) cc_final: 0.7742 (t0) REVERT: C 41 SER cc_start: 0.8733 (m) cc_final: 0.8471 (p) REVERT: C 92 ARG cc_start: 0.7754 (tmt90) cc_final: 0.7123 (mmt90) REVERT: D 30 LYS cc_start: 0.8705 (tttt) cc_final: 0.8295 (mmtp) REVERT: D 92 ARG cc_start: 0.7645 (tmt90) cc_final: 0.7124 (mmt90) REVERT: D 259 ASP cc_start: 0.8246 (t0) cc_final: 0.8023 (t0) REVERT: D 320 MET cc_start: 0.8508 (ttt) cc_final: 0.8288 (ttp) REVERT: E 30 LYS cc_start: 0.8602 (tttt) cc_final: 0.8206 (tttt) REVERT: E 41 SER cc_start: 0.8695 (m) cc_final: 0.8434 (p) REVERT: E 46 ILE cc_start: 0.8754 (mt) cc_final: 0.8421 (tt) REVERT: E 92 ARG cc_start: 0.7575 (tmt90) cc_final: 0.7215 (mmt90) REVERT: E 149 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7958 (ptpt) outliers start: 40 outliers final: 28 residues processed: 203 average time/residue: 0.8918 time to fit residues: 204.6565 Evaluate side-chains 185 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 155 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 83 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 109 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 131 optimal weight: 7.9990 chunk 138 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN C 220 GLN D 220 GLN D 296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13570 Z= 0.194 Angle : 0.569 11.498 18455 Z= 0.276 Chirality : 0.040 0.285 2030 Planarity : 0.004 0.042 2285 Dihedral : 4.020 29.273 1765 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.56 % Allowed : 17.44 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.21), residues: 1575 helix: 1.03 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -1.71 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 229 HIS 0.002 0.000 HIS C 178 PHE 0.038 0.001 PHE B 80 TYR 0.014 0.001 TYR C 97 ARG 0.010 0.000 ARG E 202 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 165 time to evaluate : 1.486 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8557 (tttt) cc_final: 0.8099 (tppp) REVERT: A 41 SER cc_start: 0.8734 (m) cc_final: 0.8412 (p) REVERT: A 46 ILE cc_start: 0.8789 (mt) cc_final: 0.8545 (mp) REVERT: A 92 ARG cc_start: 0.7659 (tmt90) cc_final: 0.7118 (mmt90) REVERT: B 30 LYS cc_start: 0.8710 (tttt) cc_final: 0.8217 (mmtp) REVERT: B 67 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8807 (mp) REVERT: B 92 ARG cc_start: 0.7508 (tmt90) cc_final: 0.6980 (mmt90) REVERT: C 30 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.7960 (ttmt) REVERT: C 41 SER cc_start: 0.8717 (m) cc_final: 0.8460 (p) REVERT: C 46 ILE cc_start: 0.8617 (mp) cc_final: 0.8155 (tt) REVERT: C 92 ARG cc_start: 0.7732 (tmt90) cc_final: 0.7110 (mmt90) REVERT: D 92 ARG cc_start: 0.7644 (tmt90) cc_final: 0.7122 (mmt90) REVERT: D 252 LEU cc_start: 0.8942 (tm) cc_final: 0.8715 (tp) REVERT: E 19 GLN cc_start: 0.7269 (pm20) cc_final: 0.7013 (pt0) REVERT: E 30 LYS cc_start: 0.8595 (tttt) cc_final: 0.8207 (tttt) REVERT: E 41 SER cc_start: 0.8740 (m) cc_final: 0.8484 (p) REVERT: E 46 ILE cc_start: 0.8739 (mt) cc_final: 0.8408 (tt) REVERT: E 92 ARG cc_start: 0.7534 (tmt90) cc_final: 0.7086 (mmt90) REVERT: E 149 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7952 (ptpt) outliers start: 37 outliers final: 27 residues processed: 194 average time/residue: 0.9382 time to fit residues: 204.2913 Evaluate side-chains 188 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 158 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 0.2980 chunk 89 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN C 220 GLN D 296 ASN E 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13570 Z= 0.201 Angle : 0.579 11.472 18455 Z= 0.280 Chirality : 0.041 0.314 2030 Planarity : 0.004 0.043 2285 Dihedral : 4.043 29.032 1765 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.15 % Allowed : 17.85 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.21), residues: 1575 helix: 1.08 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -1.67 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 229 HIS 0.002 0.001 HIS C 326 PHE 0.018 0.001 PHE E 278 TYR 0.014 0.001 TYR E 225 ARG 0.010 0.000 ARG E 202 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 165 time to evaluate : 1.532 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8550 (tttt) cc_final: 0.8022 (tppp) REVERT: A 41 SER cc_start: 0.8766 (m) cc_final: 0.8443 (p) REVERT: A 46 ILE cc_start: 0.8777 (mt) cc_final: 0.8532 (mp) REVERT: A 92 ARG cc_start: 0.7649 (tmt90) cc_final: 0.7096 (mmt90) REVERT: B 30 LYS cc_start: 0.8681 (tttt) cc_final: 0.8181 (mmtp) REVERT: B 67 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8819 (mp) REVERT: B 92 ARG cc_start: 0.7498 (tmt90) cc_final: 0.6993 (mmt90) REVERT: B 154 MET cc_start: 0.8048 (mmm) cc_final: 0.7802 (mmp) REVERT: C 30 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.7979 (ttmt) REVERT: C 41 SER cc_start: 0.8736 (m) cc_final: 0.8476 (p) REVERT: C 46 ILE cc_start: 0.8682 (mp) cc_final: 0.8215 (tt) REVERT: C 92 ARG cc_start: 0.7766 (tmt90) cc_final: 0.7138 (mmt90) REVERT: D 92 ARG cc_start: 0.7679 (tmt90) cc_final: 0.7132 (mmt90) REVERT: D 252 LEU cc_start: 0.8911 (tm) cc_final: 0.8641 (tp) REVERT: E 19 GLN cc_start: 0.7263 (pm20) cc_final: 0.6909 (pt0) REVERT: E 30 LYS cc_start: 0.8600 (tttt) cc_final: 0.8222 (tttt) REVERT: E 41 SER cc_start: 0.8753 (m) cc_final: 0.8496 (p) REVERT: E 46 ILE cc_start: 0.8782 (mt) cc_final: 0.8466 (tt) REVERT: E 92 ARG cc_start: 0.7513 (tmt90) cc_final: 0.7181 (mmt90) REVERT: E 149 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7958 (ptpt) outliers start: 31 outliers final: 25 residues processed: 190 average time/residue: 0.9477 time to fit residues: 201.6982 Evaluate side-chains 183 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 155 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 18 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 126 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN C 220 GLN D 220 GLN D 296 ASN E 220 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.118636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.094670 restraints weight = 22143.547| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.94 r_work: 0.3084 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13570 Z= 0.215 Angle : 0.581 11.453 18455 Z= 0.281 Chirality : 0.041 0.260 2030 Planarity : 0.004 0.042 2285 Dihedral : 4.039 29.080 1765 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.08 % Allowed : 18.13 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.20), residues: 1575 helix: 1.12 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -1.66 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 229 HIS 0.002 0.001 HIS C 156 PHE 0.042 0.002 PHE A 80 TYR 0.015 0.001 TYR C 97 ARG 0.010 0.000 ARG E 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4429.07 seconds wall clock time: 78 minutes 58.47 seconds (4738.47 seconds total)