Starting phenix.real_space_refine on Wed Nov 15 21:10:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n26_9324/11_2023/6n26_9324_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n26_9324/11_2023/6n26_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_9324/11_2023/6n26_9324.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n26_9324/11_2023/6n26_9324.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n26_9324/11_2023/6n26_9324_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n26_9324/11_2023/6n26_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 7.17, per 1000 atoms: 0.54 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: 4.98 Conformation dependent library (CDL) restraints added in 2.4 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: 1.26 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: 4.43 Time building geometry restraints manager: 5.42 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: 0.110 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: 1.680 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 36.980 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.970 ------------------------------------------------------------------------------- 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 *********************** 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 : 1.465 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 1.2749 time to fit residues: 537.3288 Evaluate side-chains 189 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.633 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1742 ------------------------------------------------------------------------------- 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: 5.9990 chunk 65 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 62 optimal weight: 20.0000 chunk 121 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 256 GLN C 293 GLN C 308 ASN C 339 ASN D 256 GLN D 293 GLN D 308 ASN D 339 ASN E 58 GLN E 256 GLN E 339 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 13570 Z= 0.202 Angle : 0.636 10.604 18455 Z= 0.330 Chirality : 0.041 0.178 2030 Planarity : 0.005 0.043 2285 Dihedral : 4.664 30.950 1765 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.98 % Allowed : 9.76 % Favored : 87.27 % 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: -3.17 (0.17), residues: 1575 helix: -1.72 (0.12), residues: 1170 sheet: None (None), residues: 0 loop : -2.74 (0.27), residues: 405 *********************** 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 276 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 233 time to evaluate : 1.585 Fit side-chains outliers start: 43 outliers final: 14 residues processed: 262 average time/residue: 0.9205 time to fit residues: 271.2718 Evaluate side-chains 188 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 174 time to evaluate : 1.585 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.6381 time to fit residues: 4.4651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 0.0170 chunk 43 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 141 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 139 optimal weight: 0.0170 chunk 48 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- 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 B 96 GLN C 256 GLN D 256 GLN E 96 GLN E 339 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13570 Z= 0.143 Angle : 0.515 9.540 18455 Z= 0.261 Chirality : 0.038 0.170 2030 Planarity : 0.004 0.037 2285 Dihedral : 4.174 25.543 1765 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.56 % Allowed : 13.70 % Favored : 83.74 % 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: -1.33 (0.19), residues: 1575 helix: -0.27 (0.14), residues: 1160 sheet: None (None), residues: 0 loop : -2.40 (0.27), residues: 415 *********************** 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 232 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 195 time to evaluate : 1.602 Fit side-chains outliers start: 37 outliers final: 17 residues processed: 225 average time/residue: 0.9547 time to fit residues: 240.8630 Evaluate side-chains 183 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 166 time to evaluate : 1.399 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 1 average time/residue: 1.0272 time to fit residues: 3.0043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 20.0000 chunk 106 optimal weight: 0.0030 chunk 73 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 67 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 149 optimal weight: 0.3980 chunk 134 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 124 optimal weight: 20.0000 overall best weight: 4.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13570 Z= 0.267 Angle : 0.589 9.766 18455 Z= 0.298 Chirality : 0.041 0.187 2030 Planarity : 0.004 0.041 2285 Dihedral : 4.196 34.846 1765 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.18 % Allowed : 14.60 % Favored : 82.21 % 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: -0.61 (0.20), residues: 1575 helix: 0.28 (0.14), residues: 1155 sheet: None (None), residues: 0 loop : -2.17 (0.27), residues: 420 *********************** 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 223 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 177 time to evaluate : 1.660 Fit side-chains outliers start: 46 outliers final: 28 residues processed: 213 average time/residue: 0.8386 time to fit residues: 203.2794 Evaluate side-chains 189 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 161 time to evaluate : 1.613 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 26 residues processed: 2 average time/residue: 0.7883 time to fit residues: 4.1155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 134 optimal weight: 20.0000 chunk 37 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- 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 B 19 GLN D 256 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 13570 Z= 0.290 Angle : 0.605 9.900 18455 Z= 0.302 Chirality : 0.042 0.191 2030 Planarity : 0.004 0.042 2285 Dihedral : 4.277 33.613 1765 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.53 % Allowed : 14.46 % Favored : 82.01 % 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: -0.33 (0.20), residues: 1575 helix: 0.48 (0.14), residues: 1155 sheet: None (None), residues: 0 loop : -2.05 (0.27), residues: 420 *********************** 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 225 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 174 time to evaluate : 1.708 Fit side-chains outliers start: 51 outliers final: 34 residues processed: 214 average time/residue: 0.8424 time to fit residues: 205.8962 Evaluate side-chains 191 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 157 time to evaluate : 1.589 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 31 residues processed: 3 average time/residue: 0.2332 time to fit residues: 3.1230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 chunk 124 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 78 optimal weight: 0.4980 chunk 144 optimal weight: 0.9980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 256 GLN B 19 GLN D 296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13570 Z= 0.185 Angle : 0.538 10.558 18455 Z= 0.269 Chirality : 0.040 0.230 2030 Planarity : 0.004 0.040 2285 Dihedral : 4.086 31.735 1765 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.91 % Allowed : 16.26 % Favored : 80.83 % 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: 0.08 (0.20), residues: 1575 helix: 0.71 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -1.82 (0.29), residues: 395 *********************** 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 213 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 171 time to evaluate : 1.612 Fit side-chains outliers start: 42 outliers final: 30 residues processed: 207 average time/residue: 0.8385 time to fit residues: 197.7715 Evaluate side-chains 187 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 157 time to evaluate : 1.568 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 29 residues processed: 1 average time/residue: 0.1665 time to fit residues: 2.3801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 109 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 149 optimal weight: 0.7980 chunk 93 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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: 0.8159 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13570 Z= 0.157 Angle : 0.524 10.718 18455 Z= 0.258 Chirality : 0.039 0.267 2030 Planarity : 0.003 0.041 2285 Dihedral : 3.969 29.639 1765 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.77 % Allowed : 16.68 % Favored : 80.55 % 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: 0.40 (0.21), residues: 1575 helix: 0.93 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -1.67 (0.29), residues: 395 *********************** 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 212 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 172 time to evaluate : 1.666 Fit side-chains outliers start: 40 outliers final: 31 residues processed: 208 average time/residue: 0.8883 time to fit residues: 208.7577 Evaluate side-chains 188 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 157 time to evaluate : 1.527 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 30 residues processed: 1 average time/residue: 1.1159 time to fit residues: 3.2925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 E 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13570 Z= 0.314 Angle : 0.635 10.940 18455 Z= 0.314 Chirality : 0.043 0.264 2030 Planarity : 0.004 0.040 2285 Dihedral : 4.236 31.715 1765 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.39 % Allowed : 16.33 % Favored : 80.28 % 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: 0.17 (0.20), residues: 1575 helix: 0.78 (0.15), residues: 1165 sheet: None (None), residues: 0 loop : -1.72 (0.28), residues: 410 *********************** 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 211 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 162 time to evaluate : 1.556 Fit side-chains outliers start: 49 outliers final: 31 residues processed: 203 average time/residue: 0.8273 time to fit residues: 192.5046 Evaluate side-chains 186 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 155 time to evaluate : 1.537 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 30 residues processed: 1 average time/residue: 0.1134 time to fit residues: 2.1707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 83 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 109 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 125 optimal weight: 0.1980 chunk 131 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN B 19 GLN D 220 GLN D 296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13570 Z= 0.152 Angle : 0.555 11.800 18455 Z= 0.272 Chirality : 0.040 0.297 2030 Planarity : 0.004 0.040 2285 Dihedral : 4.022 32.384 1765 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.35 % Allowed : 17.72 % Favored : 79.93 % 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: 0.63 (0.21), residues: 1575 helix: 1.10 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -1.57 (0.30), residues: 395 *********************** 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 197 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 163 time to evaluate : 1.472 Fit side-chains outliers start: 34 outliers final: 28 residues processed: 193 average time/residue: 0.8602 time to fit residues: 188.8879 Evaluate side-chains 179 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 151 time to evaluate : 1.715 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 28 residues processed: 0 time to fit residues: 2.1563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 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 D 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13570 Z= 0.222 Angle : 0.598 11.638 18455 Z= 0.291 Chirality : 0.042 0.343 2030 Planarity : 0.004 0.039 2285 Dihedral : 4.119 34.014 1765 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.15 % Allowed : 18.62 % Favored : 79.24 % 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: 0.62 (0.21), residues: 1575 helix: 1.08 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -1.55 (0.30), residues: 395 ********************** 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 192 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 161 time to evaluate : 1.653 Fit side-chains outliers start: 31 outliers final: 30 residues processed: 190 average time/residue: 0.8558 time to fit residues: 184.9756 Evaluate side-chains 179 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 149 time to evaluate : 1.557 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 29 residues processed: 1 average time/residue: 1.1087 time to fit residues: 3.2580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3591 r_free = 0.3591 target = 0.118124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.094372 restraints weight = 22397.402| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.96 r_work: 0.3085 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13570 Z= 0.237 Angle : 0.608 11.513 18455 Z= 0.295 Chirality : 0.042 0.269 2030 Planarity : 0.004 0.043 2285 Dihedral : 4.164 34.494 1765 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.42 % Allowed : 18.41 % Favored : 79.17 % 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: 0.61 (0.21), residues: 1575 helix: 1.11 (0.15), residues: 1165 sheet: None (None), residues: 0 loop : -1.57 (0.29), residues: 410 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4316.41 seconds wall clock time: 77 minutes 38.28 seconds (4658.28 seconds total)