Starting phenix.real_space_refine on Fri Mar 15 22:59:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atg_15649/03_2024/8atg_15649_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atg_15649/03_2024/8atg_15649.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atg_15649/03_2024/8atg_15649.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atg_15649/03_2024/8atg_15649.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atg_15649/03_2024/8atg_15649_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atg_15649/03_2024/8atg_15649_updated.pdb" } resolution = 2.9 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= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 25 5.49 5 S 20 5.16 5 C 8680 2.51 5 N 1960 2.21 5 O 2305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 69": "OE1" <-> "OE2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "E GLU 69": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12990 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2402 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 18, 'TRANS': 292} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 75 Chain: "B" Number of atoms: 2402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2402 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 18, 'TRANS': 292} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 2402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2402 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 18, 'TRANS': 292} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 75 Chain: "D" Number of atoms: 2402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2402 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 18, 'TRANS': 292} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 75 Chain: "E" Number of atoms: 2402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2402 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 18, 'TRANS': 292} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 75 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 196 Unusual residues: {'POV': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'POV:plan-1': 4} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 196 Unusual residues: {'POV': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'POV:plan-1': 4} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 196 Unusual residues: {'POV': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'POV:plan-1': 4} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 196 Unusual residues: {'POV': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'POV:plan-1': 4} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 196 Unusual residues: {'POV': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'POV:plan-1': 4} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 6.75, per 1000 atoms: 0.52 Number of scatterers: 12990 At special positions: 0 Unit cell: (91.84, 92.66, 118.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 25 15.00 O 2305 8.00 N 1960 7.00 C 8680 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 5.34 Conformation dependent library (CDL) restraints added in 2.2 seconds 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3050 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 35 helices and 20 sheets defined 35.0% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' 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 195 through 200 Proline residue: A 199 - end of helix No H-bonds generated for 'chain 'A' and resid 195 through 200' Processing helix chain 'A' and resid 202 through 217 removed outlier: 4.244A pdb=" N ALA A 215 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N PHE A 216 " --> pdb=" O SER A 212 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N TRP A 217 " --> pdb=" O TRP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 244 removed outlier: 3.978A pdb=" N THR A 244 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 281 removed outlier: 3.639A pdb=" N ILE A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 314 removed outlier: 3.942A pdb=" N ILE A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Proline residue: A 300 - end of helix Processing helix chain 'B' and resid 119 through 121 No H-bonds generated for 'chain 'B' and resid 119 through 121' 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 195 through 200 Proline residue: B 199 - end of helix No H-bonds generated for 'chain 'B' and resid 195 through 200' Processing helix chain 'B' and resid 202 through 217 removed outlier: 4.244A pdb=" N ALA B 215 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N PHE B 216 " --> pdb=" O SER B 212 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N TRP B 217 " --> pdb=" O TRP B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 244 removed outlier: 3.978A pdb=" N THR B 244 " --> pdb=" O ILE B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 281 removed outlier: 3.639A pdb=" N ILE B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 314 removed outlier: 3.942A pdb=" N ILE B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Proline residue: B 300 - end of helix Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' 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 195 through 200 Proline residue: C 199 - end of helix No H-bonds generated for 'chain 'C' and resid 195 through 200' Processing helix chain 'C' and resid 202 through 217 removed outlier: 4.244A pdb=" N ALA C 215 " --> pdb=" O ILE C 211 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N PHE C 216 " --> pdb=" O SER C 212 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N TRP C 217 " --> pdb=" O TRP C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 244 removed outlier: 3.978A pdb=" N THR C 244 " --> pdb=" O ILE C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 281 removed outlier: 3.639A pdb=" N ILE C 259 " --> pdb=" O THR C 255 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 314 removed outlier: 3.942A pdb=" N ILE C 297 " --> pdb=" O ARG C 293 " (cutoff:3.500A) Proline residue: C 300 - end of helix Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' 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 195 through 200 Proline residue: D 199 - end of helix No H-bonds generated for 'chain 'D' and resid 195 through 200' Processing helix chain 'D' and resid 202 through 217 removed outlier: 4.243A pdb=" N ALA D 215 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N PHE D 216 " --> pdb=" O SER D 212 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N TRP D 217 " --> pdb=" O TRP D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 244 removed outlier: 3.978A pdb=" N THR D 244 " --> pdb=" O ILE D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 281 removed outlier: 3.639A pdb=" N ILE D 259 " --> pdb=" O THR D 255 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 314 removed outlier: 3.943A pdb=" N ILE D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) Proline residue: D 300 - end of helix Processing helix chain 'E' and resid 119 through 121 No H-bonds generated for 'chain 'E' and resid 119 through 121' 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 195 through 200 Proline residue: E 199 - end of helix No H-bonds generated for 'chain 'E' and resid 195 through 200' Processing helix chain 'E' and resid 202 through 217 removed outlier: 4.244A pdb=" N ALA E 215 " --> pdb=" O ILE E 211 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N PHE E 216 " --> pdb=" O SER E 212 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N TRP E 217 " --> pdb=" O TRP E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 244 removed outlier: 3.979A pdb=" N THR E 244 " --> pdb=" O ILE E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 281 removed outlier: 3.640A pdb=" N ILE E 259 " --> pdb=" O THR E 255 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE E 260 " --> pdb=" O GLY E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 314 removed outlier: 3.942A pdb=" N ILE E 297 " --> pdb=" O ARG E 293 " (cutoff:3.500A) Proline residue: E 300 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 19 through 23 removed outlier: 6.066A pdb=" N ARG A 105 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N VAL A 89 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 37 through 39 Processing sheet with id= C, first strand: chain 'A' and resid 76 through 78 removed outlier: 4.928A pdb=" N VAL A 132 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER A 182 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS A 183 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 161 through 164 removed outlier: 6.940A pdb=" N ARG A 189 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 19 through 23 removed outlier: 6.066A pdb=" N ARG B 105 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N VAL B 89 " --> pdb=" O ARG B 105 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 37 through 39 Processing sheet with id= G, first strand: chain 'B' and resid 76 through 78 removed outlier: 4.927A pdb=" N VAL B 132 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N SER B 182 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS B 183 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 161 through 164 removed outlier: 6.940A pdb=" N ARG B 189 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 19 through 23 removed outlier: 6.066A pdb=" N ARG C 105 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N VAL C 89 " --> pdb=" O ARG C 105 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 37 through 39 Processing sheet with id= K, first strand: chain 'C' and resid 76 through 78 removed outlier: 4.928A pdb=" N VAL C 132 " --> pdb=" O SER C 182 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER C 182 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS C 183 " --> pdb=" O LYS C 170 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 161 through 164 removed outlier: 6.939A pdb=" N ARG C 189 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 19 through 23 removed outlier: 6.066A pdb=" N ARG D 105 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N VAL D 89 " --> pdb=" O ARG D 105 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 37 through 39 Processing sheet with id= O, first strand: chain 'D' and resid 76 through 78 removed outlier: 4.927A pdb=" N VAL D 132 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER D 182 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS D 183 " --> pdb=" O LYS D 170 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 161 through 164 removed outlier: 6.940A pdb=" N ARG D 189 " --> pdb=" O GLU D 163 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 19 through 23 removed outlier: 6.066A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 37 through 39 Processing sheet with id= S, first strand: chain 'E' and resid 76 through 78 removed outlier: 4.927A pdb=" N VAL E 132 " --> pdb=" O SER E 182 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER E 182 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS E 183 " --> pdb=" O LYS E 170 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 161 through 164 removed outlier: 6.939A pdb=" N ARG E 189 " --> pdb=" O GLU E 163 " (cutoff:3.500A) 525 hydrogen bonds defined for protein. 1500 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: 3.48 Time building geometry restraints manager: 5.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1981 1.32 - 1.44: 3536 1.44 - 1.57: 7698 1.57 - 1.69: 50 1.69 - 1.81: 35 Bond restraints: 13300 Sorted by residual: bond pdb=" O12 POV C 401 " pdb=" P POV C 401 " ideal model delta sigma weight residual 1.657 1.605 0.052 2.00e-02 2.50e+03 6.85e+00 bond pdb=" O12 POV D 401 " pdb=" P POV D 401 " ideal model delta sigma weight residual 1.657 1.605 0.052 2.00e-02 2.50e+03 6.84e+00 bond pdb=" O12 POV E 404 " pdb=" P POV E 404 " ideal model delta sigma weight residual 1.657 1.605 0.052 2.00e-02 2.50e+03 6.81e+00 bond pdb=" O12 POV A 401 " pdb=" P POV A 401 " ideal model delta sigma weight residual 1.657 1.605 0.052 2.00e-02 2.50e+03 6.80e+00 bond pdb=" O12 POV B 404 " pdb=" P POV B 404 " ideal model delta sigma weight residual 1.657 1.605 0.052 2.00e-02 2.50e+03 6.71e+00 ... (remaining 13295 not shown) Histogram of bond angle deviations from ideal: 100.53 - 107.22: 491 107.22 - 113.91: 7688 113.91 - 120.60: 5079 120.60 - 127.29: 4693 127.29 - 133.99: 144 Bond angle restraints: 18095 Sorted by residual: angle pdb=" N VAL C 141 " pdb=" CA VAL C 141 " pdb=" C VAL C 141 " ideal model delta sigma weight residual 112.29 108.57 3.72 9.40e-01 1.13e+00 1.57e+01 angle pdb=" N VAL A 141 " pdb=" CA VAL A 141 " pdb=" C VAL A 141 " ideal model delta sigma weight residual 112.29 108.58 3.71 9.40e-01 1.13e+00 1.56e+01 angle pdb=" N VAL D 141 " pdb=" CA VAL D 141 " pdb=" C VAL D 141 " ideal model delta sigma weight residual 112.29 108.59 3.70 9.40e-01 1.13e+00 1.55e+01 angle pdb=" N VAL E 141 " pdb=" CA VAL E 141 " pdb=" C VAL E 141 " ideal model delta sigma weight residual 112.29 108.60 3.69 9.40e-01 1.13e+00 1.54e+01 angle pdb=" N VAL B 141 " pdb=" CA VAL B 141 " pdb=" C VAL B 141 " ideal model delta sigma weight residual 112.29 108.63 3.66 9.40e-01 1.13e+00 1.52e+01 ... (remaining 18090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.06: 7528 26.06 - 52.13: 362 52.13 - 78.19: 85 78.19 - 104.26: 25 104.26 - 130.32: 25 Dihedral angle restraints: 8025 sinusoidal: 3350 harmonic: 4675 Sorted by residual: dihedral pdb=" C3 POV B 403 " pdb=" C31 POV B 403 " pdb=" O31 POV B 403 " pdb=" C32 POV B 403 " ideal model delta sinusoidal sigma weight residual 172.61 -57.07 -130.32 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" C3 POV A 403 " pdb=" C31 POV A 403 " pdb=" O31 POV A 403 " pdb=" C32 POV A 403 " ideal model delta sinusoidal sigma weight residual 172.61 -57.07 -130.32 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" C3 POV C 403 " pdb=" C31 POV C 403 " pdb=" O31 POV C 403 " pdb=" C32 POV C 403 " ideal model delta sinusoidal sigma weight residual 172.61 -57.09 -130.30 1 3.00e+01 1.11e-03 1.76e+01 ... (remaining 8022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1111 0.026 - 0.053: 566 0.053 - 0.079: 181 0.079 - 0.105: 116 0.105 - 0.131: 66 Chirality restraints: 2040 Sorted by residual: chirality pdb=" CA PRO D 204 " pdb=" N PRO D 204 " pdb=" C PRO D 204 " pdb=" CB PRO D 204 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA PRO B 204 " pdb=" N PRO B 204 " pdb=" C PRO B 204 " pdb=" CB PRO B 204 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA PRO A 204 " pdb=" N PRO A 204 " pdb=" C PRO A 204 " pdb=" CB PRO A 204 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 2037 not shown) Planarity restraints: 2175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV E 404 " 0.043 2.00e-02 2.50e+03 4.27e-02 1.82e+01 pdb=" C29 POV E 404 " -0.042 2.00e-02 2.50e+03 pdb="C210 POV E 404 " -0.043 2.00e-02 2.50e+03 pdb="C211 POV E 404 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV B 404 " -0.042 2.00e-02 2.50e+03 4.25e-02 1.81e+01 pdb=" C29 POV B 404 " 0.042 2.00e-02 2.50e+03 pdb="C210 POV B 404 " 0.043 2.00e-02 2.50e+03 pdb="C211 POV B 404 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A 404 " -0.042 2.00e-02 2.50e+03 4.25e-02 1.81e+01 pdb=" C29 POV A 404 " 0.042 2.00e-02 2.50e+03 pdb="C210 POV A 404 " 0.043 2.00e-02 2.50e+03 pdb="C211 POV A 404 " -0.043 2.00e-02 2.50e+03 ... (remaining 2172 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2740 2.79 - 3.31: 12291 3.31 - 3.84: 20973 3.84 - 4.37: 24087 4.37 - 4.90: 41332 Nonbonded interactions: 101423 Sorted by model distance: nonbonded pdb=" O ILE E 25 " pdb=" ND2 ASN E 152 " model vdw 2.256 2.520 nonbonded pdb=" O ILE D 25 " pdb=" ND2 ASN D 152 " model vdw 2.256 2.520 nonbonded pdb=" O ILE A 25 " pdb=" ND2 ASN A 152 " model vdw 2.257 2.520 nonbonded pdb=" O ILE B 25 " pdb=" ND2 ASN B 152 " model vdw 2.257 2.520 nonbonded pdb=" O ILE C 25 " pdb=" ND2 ASN C 152 " model vdw 2.257 2.520 ... (remaining 101418 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: 0.750 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: 4.290 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 36.600 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.080 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:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5998 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 : 0.007 0.052 13300 Z= 0.398 Angle : 0.709 6.979 18095 Z= 0.336 Chirality : 0.043 0.131 2040 Planarity : 0.005 0.044 2175 Dihedral : 18.850 130.322 4975 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: -1.00 (0.22), residues: 1545 helix: 1.34 (0.22), residues: 535 sheet: -1.41 (0.33), residues: 275 loop : -1.94 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 160 HIS 0.002 0.001 HIS B 127 PHE 0.027 0.002 PHE E 195 TYR 0.012 0.001 TYR B 194 ARG 0.004 0.000 ARG D 189 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 PHE cc_start: 0.7501 (p90) cc_final: 0.7247 (p90) REVERT: C 174 PHE cc_start: 0.7631 (p90) cc_final: 0.7380 (p90) REVERT: D 174 PHE cc_start: 0.7689 (p90) cc_final: 0.7436 (p90) REVERT: D 187 GLN cc_start: 0.8909 (mt0) cc_final: 0.8660 (mm110) REVERT: E 248 LYS cc_start: 0.8579 (mtmt) cc_final: 0.8317 (tppt) outliers start: 0 outliers final: 1 residues processed: 244 average time/residue: 1.0501 time to fit residues: 282.7848 Evaluate side-chains 131 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 291 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 20.0000 chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 79 optimal weight: 0.0170 chunk 62 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 47 optimal weight: 20.0000 chunk 73 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 overall best weight: 2.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6154 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13300 Z= 0.239 Angle : 0.655 6.698 18095 Z= 0.329 Chirality : 0.043 0.133 2040 Planarity : 0.004 0.032 2175 Dihedral : 20.455 138.596 2477 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.34 % Favored : 93.33 % Rotamer: Outliers : 2.22 % Allowed : 14.16 % Favored : 83.62 % 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: -0.82 (0.22), residues: 1545 helix: 1.79 (0.22), residues: 515 sheet: -1.76 (0.28), residues: 325 loop : -1.75 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.005 0.001 HIS A 235 PHE 0.019 0.001 PHE D 37 TYR 0.015 0.002 TYR A 266 ARG 0.004 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 174 PHE cc_start: 0.7770 (p90) cc_final: 0.7459 (p90) REVERT: B 187 GLN cc_start: 0.8963 (mt0) cc_final: 0.8679 (mt0) REVERT: D 248 LYS cc_start: 0.8708 (mtmt) cc_final: 0.8361 (mttp) REVERT: E 187 GLN cc_start: 0.8988 (mt0) cc_final: 0.8693 (mt0) REVERT: E 248 LYS cc_start: 0.8695 (mtmt) cc_final: 0.8388 (mtmm) outliers start: 27 outliers final: 13 residues processed: 175 average time/residue: 1.2212 time to fit residues: 234.0377 Evaluate side-chains 144 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 131 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 255 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 117 optimal weight: 0.7980 chunk 95 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 125 optimal weight: 20.0000 chunk 139 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 200 ASN E 19 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6288 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13300 Z= 0.326 Angle : 0.646 7.314 18095 Z= 0.327 Chirality : 0.044 0.162 2040 Planarity : 0.004 0.035 2175 Dihedral : 19.723 146.477 2475 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.31 % Favored : 92.36 % Rotamer: Outliers : 3.87 % Allowed : 15.47 % Favored : 80.66 % 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: -0.52 (0.22), residues: 1545 helix: 2.15 (0.22), residues: 515 sheet: -1.57 (0.28), residues: 325 loop : -1.68 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 213 HIS 0.005 0.002 HIS A 235 PHE 0.012 0.002 PHE D 303 TYR 0.025 0.002 TYR B 266 ARG 0.006 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 139 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLN cc_start: 0.9078 (mt0) cc_final: 0.8744 (mt0) REVERT: B 35 GLU cc_start: 0.8341 (pm20) cc_final: 0.8049 (pm20) REVERT: B 187 GLN cc_start: 0.9060 (mt0) cc_final: 0.8724 (mt0) REVERT: B 212 SER cc_start: 0.9455 (OUTLIER) cc_final: 0.9241 (p) REVERT: B 282 GLU cc_start: 0.8359 (tt0) cc_final: 0.7724 (tm-30) REVERT: C 35 GLU cc_start: 0.8647 (pm20) cc_final: 0.8446 (pm20) REVERT: C 187 GLN cc_start: 0.9048 (mt0) cc_final: 0.8711 (mt0) REVERT: D 163 GLU cc_start: 0.7808 (mp0) cc_final: 0.7603 (mp0) REVERT: D 174 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7532 (p90) REVERT: D 187 GLN cc_start: 0.9082 (mt0) cc_final: 0.8715 (mt0) REVERT: D 248 LYS cc_start: 0.8782 (mtmt) cc_final: 0.8469 (mttp) REVERT: E 187 GLN cc_start: 0.9050 (mt0) cc_final: 0.8641 (mt0) outliers start: 47 outliers final: 29 residues processed: 171 average time/residue: 1.0956 time to fit residues: 206.2079 Evaluate side-chains 159 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 128 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 174 PHE Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 270 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 9.9990 chunk 106 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 67 optimal weight: 0.3980 chunk 94 optimal weight: 9.9990 chunk 141 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6319 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13300 Z= 0.327 Angle : 0.629 6.218 18095 Z= 0.316 Chirality : 0.043 0.150 2040 Planarity : 0.003 0.023 2175 Dihedral : 19.452 136.920 2475 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.93 % Favored : 92.82 % Rotamer: Outliers : 3.46 % Allowed : 17.37 % Favored : 79.18 % 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: -0.37 (0.22), residues: 1545 helix: 2.27 (0.22), residues: 515 sheet: -1.42 (0.27), residues: 325 loop : -1.62 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP E 213 HIS 0.005 0.002 HIS D 235 PHE 0.009 0.001 PHE E 238 TYR 0.012 0.001 TYR E 102 ARG 0.003 0.000 ARG B 189 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 136 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLN cc_start: 0.9095 (mt0) cc_final: 0.8768 (mt0) REVERT: B 187 GLN cc_start: 0.9073 (mt0) cc_final: 0.8761 (mt0) REVERT: B 212 SER cc_start: 0.9508 (OUTLIER) cc_final: 0.9305 (p) REVERT: B 282 GLU cc_start: 0.8414 (tt0) cc_final: 0.7756 (tm-30) REVERT: C 187 GLN cc_start: 0.9082 (mt0) cc_final: 0.8712 (mt0) REVERT: C 248 LYS cc_start: 0.8953 (tppt) cc_final: 0.8613 (tmtt) REVERT: D 163 GLU cc_start: 0.7810 (mp0) cc_final: 0.7577 (mp0) REVERT: D 187 GLN cc_start: 0.9073 (mt0) cc_final: 0.8676 (mt0) REVERT: D 248 LYS cc_start: 0.8833 (mtmt) cc_final: 0.8518 (mttp) REVERT: E 187 GLN cc_start: 0.9056 (mt0) cc_final: 0.8679 (mt0) REVERT: E 248 LYS cc_start: 0.9039 (mttt) cc_final: 0.8834 (mttp) outliers start: 42 outliers final: 22 residues processed: 159 average time/residue: 1.2214 time to fit residues: 212.6789 Evaluate side-chains 152 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 255 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 37 optimal weight: 20.0000 chunk 50 optimal weight: 0.0870 overall best weight: 3.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13300 Z= 0.299 Angle : 0.621 7.011 18095 Z= 0.308 Chirality : 0.042 0.148 2040 Planarity : 0.003 0.023 2175 Dihedral : 19.166 125.946 2475 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.06 % Favored : 92.75 % Rotamer: Outliers : 3.62 % Allowed : 18.77 % Favored : 77.61 % 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: -0.29 (0.22), residues: 1545 helix: 2.36 (0.22), residues: 515 sheet: -1.42 (0.27), residues: 325 loop : -1.57 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 213 HIS 0.005 0.002 HIS D 235 PHE 0.016 0.001 PHE D 37 TYR 0.011 0.001 TYR E 102 ARG 0.001 0.000 ARG C 189 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 135 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLN cc_start: 0.9083 (mt0) cc_final: 0.8752 (mt0) REVERT: B 187 GLN cc_start: 0.9046 (mt0) cc_final: 0.8725 (mt0) REVERT: B 248 LYS cc_start: 0.8951 (tppt) cc_final: 0.8653 (mmtt) REVERT: D 187 GLN cc_start: 0.9076 (mt0) cc_final: 0.8812 (mt0) REVERT: D 248 LYS cc_start: 0.8883 (mtmt) cc_final: 0.8577 (mttp) REVERT: E 187 GLN cc_start: 0.9078 (mt0) cc_final: 0.8691 (mt0) outliers start: 44 outliers final: 26 residues processed: 160 average time/residue: 1.1918 time to fit residues: 208.8997 Evaluate side-chains 153 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 127 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 174 PHE Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 255 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 124 optimal weight: 11.9990 chunk 69 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 78 optimal weight: 0.0470 chunk 144 optimal weight: 0.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 ASN E 19 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13300 Z= 0.239 Angle : 0.623 10.640 18095 Z= 0.308 Chirality : 0.042 0.176 2040 Planarity : 0.003 0.028 2175 Dihedral : 18.746 114.712 2475 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.54 % Favored : 93.27 % Rotamer: Outliers : 3.95 % Allowed : 19.34 % Favored : 76.71 % 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: -0.19 (0.22), residues: 1545 helix: 2.42 (0.22), residues: 515 sheet: -1.40 (0.27), residues: 325 loop : -1.47 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 213 HIS 0.005 0.002 HIS D 235 PHE 0.008 0.001 PHE D 265 TYR 0.010 0.001 TYR E 102 ARG 0.002 0.000 ARG E 189 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 137 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLN cc_start: 0.9066 (mt0) cc_final: 0.8639 (mm110) REVERT: B 187 GLN cc_start: 0.9022 (mt0) cc_final: 0.8703 (mt0) REVERT: B 214 THR cc_start: 0.9330 (OUTLIER) cc_final: 0.9018 (m) REVERT: C 248 LYS cc_start: 0.9037 (tppt) cc_final: 0.8527 (tmtt) REVERT: D 187 GLN cc_start: 0.9047 (mt0) cc_final: 0.8639 (mt0) REVERT: D 248 LYS cc_start: 0.8918 (mtmt) cc_final: 0.8626 (mttp) REVERT: E 187 GLN cc_start: 0.9060 (mt0) cc_final: 0.8656 (mt0) outliers start: 48 outliers final: 29 residues processed: 168 average time/residue: 1.1701 time to fit residues: 215.7641 Evaluate side-chains 154 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 124 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 305 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 109 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 chunk 126 optimal weight: 0.0370 chunk 83 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 overall best weight: 1.1660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 ASN D 19 ASN D 200 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13300 Z= 0.197 Angle : 0.617 8.846 18095 Z= 0.307 Chirality : 0.042 0.168 2040 Planarity : 0.003 0.024 2175 Dihedral : 18.340 98.569 2475 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.28 % Favored : 93.53 % Rotamer: Outliers : 3.05 % Allowed : 21.15 % Favored : 75.80 % 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: -0.10 (0.22), residues: 1545 helix: 2.42 (0.22), residues: 515 sheet: -1.23 (0.27), residues: 325 loop : -1.41 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 213 HIS 0.005 0.002 HIS D 235 PHE 0.017 0.001 PHE D 37 TYR 0.015 0.001 TYR B 28 ARG 0.002 0.000 ARG E 109 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 134 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 187 GLN cc_start: 0.8977 (mt0) cc_final: 0.8664 (mt0) REVERT: B 205 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8544 (mtp) REVERT: B 214 THR cc_start: 0.9297 (OUTLIER) cc_final: 0.8977 (m) REVERT: B 248 LYS cc_start: 0.9023 (tppt) cc_final: 0.8495 (tmtt) REVERT: B 282 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8223 (tm-30) REVERT: D 187 GLN cc_start: 0.8994 (mt0) cc_final: 0.8593 (mt0) REVERT: D 248 LYS cc_start: 0.8936 (mtmt) cc_final: 0.8645 (mttp) REVERT: E 35 GLU cc_start: 0.8406 (pm20) cc_final: 0.7708 (pm20) REVERT: E 187 GLN cc_start: 0.9036 (mt0) cc_final: 0.8667 (mt0) outliers start: 37 outliers final: 23 residues processed: 157 average time/residue: 1.2421 time to fit residues: 212.8540 Evaluate side-chains 152 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 127 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 305 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 29 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 101 optimal weight: 20.0000 chunk 73 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 117 optimal weight: 0.0170 chunk 135 optimal weight: 0.4980 overall best weight: 1.4820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN B 19 ASN B 200 ASN C 19 ASN D 19 ASN D 200 ASN E 19 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13300 Z= 0.208 Angle : 0.627 10.564 18095 Z= 0.313 Chirality : 0.042 0.182 2040 Planarity : 0.003 0.024 2175 Dihedral : 18.005 88.176 2475 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.63 % Favored : 94.17 % Rotamer: Outliers : 3.13 % Allowed : 21.15 % Favored : 75.72 % 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: -0.01 (0.23), residues: 1545 helix: 2.46 (0.22), residues: 515 sheet: -1.10 (0.28), residues: 325 loop : -1.38 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 213 HIS 0.005 0.001 HIS D 235 PHE 0.015 0.001 PHE E 37 TYR 0.016 0.001 TYR E 28 ARG 0.002 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 132 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 187 GLN cc_start: 0.8970 (mt0) cc_final: 0.8647 (mt0) REVERT: B 205 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8518 (mtp) REVERT: B 214 THR cc_start: 0.9301 (OUTLIER) cc_final: 0.8978 (m) REVERT: B 248 LYS cc_start: 0.8952 (tppt) cc_final: 0.8566 (mmmt) REVERT: C 248 LYS cc_start: 0.8899 (tppt) cc_final: 0.8615 (mmtt) REVERT: D 124 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7199 (mm110) REVERT: D 187 GLN cc_start: 0.8968 (mt0) cc_final: 0.8565 (mt0) REVERT: D 248 LYS cc_start: 0.8949 (mtmt) cc_final: 0.8657 (mttp) REVERT: E 124 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7454 (mm110) REVERT: E 187 GLN cc_start: 0.8985 (mt0) cc_final: 0.8673 (mt0) outliers start: 38 outliers final: 29 residues processed: 157 average time/residue: 1.2017 time to fit residues: 206.5596 Evaluate side-chains 156 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 125 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 174 PHE Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 305 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 109 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 138 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN B 19 ASN B 200 ASN C 19 ASN D 19 ASN D 200 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6375 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13300 Z= 0.326 Angle : 0.657 7.783 18095 Z= 0.328 Chirality : 0.043 0.233 2040 Planarity : 0.003 0.021 2175 Dihedral : 17.984 89.784 2475 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.67 % Favored : 93.14 % Rotamer: Outliers : 2.96 % Allowed : 21.81 % Favored : 75.23 % 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: -0.04 (0.22), residues: 1545 helix: 2.42 (0.22), residues: 515 sheet: -1.06 (0.28), residues: 325 loop : -1.42 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 213 HIS 0.005 0.002 HIS D 235 PHE 0.016 0.001 PHE B 37 TYR 0.010 0.001 TYR E 102 ARG 0.001 0.000 ARG B 189 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 120 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 187 GLN cc_start: 0.9038 (mt0) cc_final: 0.8691 (mt0) REVERT: B 205 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8562 (mtp) REVERT: D 187 GLN cc_start: 0.9028 (mt0) cc_final: 0.8601 (mt0) REVERT: D 212 SER cc_start: 0.9431 (t) cc_final: 0.9222 (p) REVERT: D 248 LYS cc_start: 0.8968 (mtmt) cc_final: 0.8637 (mttp) REVERT: E 187 GLN cc_start: 0.9065 (mt0) cc_final: 0.8642 (mt0) REVERT: E 248 LYS cc_start: 0.9095 (mmmt) cc_final: 0.8572 (mtmt) outliers start: 36 outliers final: 31 residues processed: 147 average time/residue: 1.1951 time to fit residues: 192.8467 Evaluate side-chains 145 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 113 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 174 PHE Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 305 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 0.9980 chunk 89 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 154 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN B 19 ASN B 200 ASN C 19 ASN D 19 ASN D 200 ASN E 19 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6362 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13300 Z= 0.277 Angle : 0.642 7.110 18095 Z= 0.321 Chirality : 0.043 0.183 2040 Planarity : 0.003 0.022 2175 Dihedral : 17.887 89.852 2475 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.76 % Favored : 94.05 % Rotamer: Outliers : 2.80 % Allowed : 21.73 % Favored : 75.47 % 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: -0.03 (0.23), residues: 1545 helix: 2.42 (0.22), residues: 515 sheet: -1.11 (0.28), residues: 325 loop : -1.37 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 213 HIS 0.005 0.002 HIS D 235 PHE 0.015 0.001 PHE B 37 TYR 0.014 0.001 TYR D 263 ARG 0.001 0.000 ARG E 109 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 120 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLN cc_start: 0.7767 (mm-40) cc_final: 0.7436 (mm110) REVERT: B 124 GLN cc_start: 0.7704 (mm-40) cc_final: 0.7464 (mm110) REVERT: B 187 GLN cc_start: 0.9061 (mt0) cc_final: 0.8719 (mt0) REVERT: B 205 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8569 (mtp) REVERT: B 248 LYS cc_start: 0.8976 (tppt) cc_final: 0.8672 (tmtt) REVERT: C 124 GLN cc_start: 0.7756 (mm-40) cc_final: 0.7471 (mm110) REVERT: D 124 GLN cc_start: 0.7639 (mm-40) cc_final: 0.7199 (mm110) REVERT: D 187 GLN cc_start: 0.9043 (mt0) cc_final: 0.8619 (mt0) REVERT: D 243 GLU cc_start: 0.8672 (tp30) cc_final: 0.8451 (tp30) REVERT: D 248 LYS cc_start: 0.8986 (mtmt) cc_final: 0.8677 (mttp) REVERT: E 187 GLN cc_start: 0.9073 (mt0) cc_final: 0.8609 (mt0) REVERT: E 248 LYS cc_start: 0.9116 (mmmt) cc_final: 0.8599 (mtmt) outliers start: 34 outliers final: 31 residues processed: 146 average time/residue: 1.2487 time to fit residues: 198.9118 Evaluate side-chains 150 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 118 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 174 PHE Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 305 LEU 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: 9.9990 chunk 113 optimal weight: 0.6980 chunk 18 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 126 optimal weight: 0.0670 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 overall best weight: 1.1120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 ASN ** B 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 ASN D 19 ASN D 200 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.087164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.062677 restraints weight = 39533.137| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.62 r_work: 0.3071 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13300 Z= 0.201 Angle : 0.630 7.864 18095 Z= 0.314 Chirality : 0.043 0.187 2040 Planarity : 0.003 0.022 2175 Dihedral : 17.653 89.893 2475 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.76 % Favored : 94.05 % Rotamer: Outliers : 2.55 % Allowed : 21.89 % Favored : 75.56 % 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: -0.07 (0.23), residues: 1545 helix: 2.45 (0.22), residues: 515 sheet: -1.29 (0.28), residues: 350 loop : -1.34 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 213 HIS 0.005 0.002 HIS D 235 PHE 0.016 0.001 PHE D 37 TYR 0.016 0.001 TYR D 263 ARG 0.003 0.000 ARG D 189 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4051.79 seconds wall clock time: 72 minutes 24.85 seconds (4344.85 seconds total)